OLIGONUCLEOTIDES COMPLEMENTARY TO MYCOBACTERIAL NUCLEIC ACIDS

Abstract: Disclosed are nucleic acid oligonucleotides which are substantially complementary to nucleic acids from Mycobacteria, and subgeneric classes thereof. More specifically, the oligonucleotides are complementary to ribosomal RNA (rRNA) and the DNA encoding rRNA (rDNA). Uses for such oligonucleotides include detection of Mycobacteria by hybridization and amplification of Mycobacterial nucleic acid by polymerase chain reaction.

Description: QI <?0 yςLEpτipES ςpMP EMENTAPY TO MYgQPACTERIAL NVCLEIC ACIPg DESCRIPTION gacKqrpunfl pf th? Invention Organisms of the genus Mycobacteria are responsible for infection of a variety of animals, including man. An important difference between Mycobacteria and other bacteria is that the former have a thick, lipid-rich envelope. This envelope gives the cells their distinctive characteristics, which include: hydrophobicity, resistance to chemical injury by acids, alkalis and many of the disinfectants used to kill other bacteria, resistance to attack by macrophages in which Mycobacteria are then able to multiply to cause disease, ability to survive long periods of starvation or aridity without dehydration and allergic and immunogenic properties. The envelope thus provides a means to identify and classify.the numerous species of Mycobacteria. Traditionally, there have been two primary diagnostic methods applicable to the detection of Mycobacteria. These are: (i) the direct observation of the etiological agent (e.g., by microscopic techniques) and (ii) its culture. Direct observation is generally reliable for some Mycobacterial species, but requires expensive equipment and highly trained personnel. Culturing of Mycobacteria, although reliable, is time consuming and inconvenient. Depending on the species, specimens must be incubated from 2-8 weeks before visible colonies appear. A need exists for an improved method for the detection of Mycobacteria. . ς uτnn^rγ of the Invention The subject invention relates to oligonucleotides which are complementary to members of the genus Mycobacteria. Such oligonucleotides are useful, for example, in hybridization based assays (e.g., detection assays) or amplification-based methodologies (e.g., polymerase chain reaction) . These oligonucleotides are grouped, based on their hybridization characteristics under defined conditions, into one of four distinct categories which are described in detail below. The invention also relates to the identification of bacteria belonging to subgeneric groups of the genus Mycobacteria by hybridization assay. Use of the oligonucleotides of this invention in an assay offers important advantages over currently employed microbiological methods for the detection of Mycobacteria in test samples (e.g., water or biological fluids). Important among these advantages is the fact that rRNAs constitute a relatively large percentage of total cellular mass as compared to that of most other potential cellular target molecules, such as genes (DNA) or RNA transcripts. Furthermore, the rRNAS (and the genes encoding them, referred to as rDNA) appear not to be subject to lateral transfer between contemporary organisms. Thus, the rRNA primary structure provides an organism-specific molecular target, rather than a gene-specific target, as would likely be the case, for example, of a plasmid-borne gene or product thereof which may be subject to lateral transmission between contemporary organisms. Other advantages of the use of the subject oligonucleotides include: a) increased sensitivity (i.e., the ability to detect fewer Mycobacteria in a given sample) ; b) potentially significant reduction in assay cost due to the use of inexpensive reagents and reduced labor; c) accurate identification of even biochemically unusual strains of Mycobacteria; and d) faster results because it is not necessary to isolate the target bacterium from the sample prior to testing. Detailed Description The present invention relates to oligonucleotides, or homologues thereof, which are substantially complementary to ribosomal RNA (rRNA) and ribosomal DNA (rDNA) from members of the genus Mycobacteria and members of subgeneric classes. It also relates to a method of detecting Mycobacteria in a sample thought to contain the organism. The oligonucleotides of the present invention can be ribose containing oligonucleotides (RNA) or deoxyribose containing oligonucleotides (DNA) . In RNA, the nitrogenous base uracil is substituted for thymidine, which is a DNA component. A homologue of an oligonucleotide is an oligonucleotide which has a nucleotide monomer sequence substantially similar to that of the oligonucleotide and, as a result, hybridizes to the same Mycobacterial nucleic acid sequence recognized (hybridized to) by the oligonculeotide under similar hybridization conditions. The sequences of two homologons oligonucleotides need not be the same and, for example, can differ from with respect to nucleotide monomer number and the presence of modified nucleotides or nucleotide analogues. Oligonucleotides of the present invention are substantially complementary to the rRNA (and to the DNA which encodes the rRNA) of the Mycobacterial genus. In particular, the oligonucleotides of this invention are substantially complementary to the 16S or 23S rRNAs, to which they hybridize under the appropriate conditions. In preferred embodiments, the oligonucleotides of this invention are deoxyribonucleotides. Substantially complementary oligonucleotides are oligonucleotides which are sufficiently complementary to hybridize in a stable manner to a rRNA (and rDNA) of Mycobacteria under defined conditions. As used herein, the term members of the genus Mycobacteria refers to bacteria classified as such in Bergey's Manual of Systematic Bacteriology (Volume 2 (1986), pp. 1435-1457, Sneath ≤fc al. editors, Williams and Wilkins, Baltimore, MD) . The genus includes a group of intracellular bacterial parasites ranging from the obligate intracellular pathogen Mycobacterium leprae and the faculative intracellular parasites tuberculosis. Mycpbac erjuff bovis and Mvcobacterium avium to such environmental species as Mycobacterium smeσmatis which seldom cause disease. Between these two extremes lie a large number of opportunistic pathogens including Mvcobacterium intracellulare and Mvcobacterium scrofulaceum. The oligonucleotides of the invention can be used, for example, to detect members of the Mycobacterial genus in a sample by hybridization. The sample is treated to render nucleic acids present available for hybridization. In one embodiment, or more oligonucleotides of this invention are then contacted with the treated sample under conditions appropriate for hybridization of substantially complementary nucleic acid sequences. If a Mycobacterial nucleic acid detectable by the oligonucleotide(s) is present, hybridization occurs. Hybridization is detected by any appropriate method. Such methods are well known to those skilled in the art. In a second embodiment, Mycobacterial oligonucleotides are first amplified through use of the oligonucleotides of this invention in an amplification based technique, such as the polymerase chain reaction (PCR) . In this technique, oligonucleotides complementary to antiparallel strands of rDNA are used to prime DNA synthesis by a DNA directed DNA polymerase, to amplify Mycobacterial sequences present in the sample. The amplified sequences are detected by conventional methods. As described in detail below, the oligonucleotides of this invention are classified into 4 categories based on the hybridization results observed when the oligonucleotides were contacted with a panel of Mycobacteria, and a panel of bacteria which are not Mycobacteria. The members of the latter group were selected by identifying bacteria which are closely related to Mycobacteria and which might be found in a mixture of bacteria containing Mycobacteria. o g onucieotitie Definitions The four categories of oligonucleotides are: 1) substantially inclusive oligonucleotides; 2) partially inclusive oligonucleotides; 3) substantially inclusive non¬ exclusive oligonucleotides and 4) partially inclusive non¬ exclusive oligonucleotides. The four categories, as used herein, are ' defined in the following paragraphs. The categorization is based on the hybridization conditions described in Example 2. One skilled in the art will recognize that if the hybridization conditions described in Example 2 are varied within defined limits, some of the oligonucleotides described herein may fall within one of the four categories which differs from the category in which it falls under the conditions described. Substantially inclusive oligonucleotides are defined as oligonucleotides which hybridize, under the assay conditions used, to rRNA (and rDNA) from substantially all (i.e., about 90% or more) of the Mycobacterial species listed in Table 3, but which do not hybridize to the rRNA of bacterial species listed in Table 4. Partially inclusive oligonucleotides are defined as oligonucleotides which hybridize, under the assay conditions used, to rRNA (and rDNA) from a subset of the Mycobacterial species listed in Table 3, but which do not hybridize to the species listed in Table 4. Substantially inclusive, non-exclusive oligonucleotides are oligonucleotides which hybridize, under the assay conditions used, to rRNA from substantially all of the Mycobacterial species listed in Table 3, and also to rRNA of at least about 10% of the other bacteria listed in Table 4. Partially inclusive, non-exclusive oligonucleotides are oligonucleotides which hybridize, under the assay conditions used, to rRNA from a subset of the Mycobacterial species listed in Table 3, and also to rRNA of at least about 10% of the other bacteria listed in Table 4. These two categories are referred to as non¬ exclusive because they hybridize not only to Mycobacteria, but also to about 10% of the other bacteria listed in Table 4. Thus, exclusivity refers to the ability of a particular oligonucleotide to discriminate between Mycobacterial nucleic acids and the nucleic acids of non-Mycobacteria (e.g. those listed in Table 4). As discussed in detail below, the subject invention also relates to the identification of subgeneric classes of Mycobacteria. Thus, oligonucleotides which are partially inclusive for the Mycobacterial genus may, for example, be substantially inclusive for the subgeneric class. The subgeneric classes include, for example, the Mycobacterium tuberculosis complex and the slow growing class of Mycobacteria. In some cases an oligonucleotide may show weak, or barely detectable, hybridization to a limited number of species in Table 4. For purposes of categorization, oligonucleotides which at a maximum hybridize weakly to less than 5% of the bacteria listed in Table 4 are considered to be oligonucleotides which do not hybridize to the species listed in the table. Oligonucleotides which at a minimum hybridize strongly to less than 5% of the bacteria listed in Table 4 are considered to be oligonucleotides which do hybridize to the species listed in the table. Strong hybridization, as used herein refers to +++ or ++++ as represented in Tables 3 or 4. Weak hybridization refers to + or ++ as represented in Tables 3 or 4. More specifically, as discussed in Example 2, ++++ designated a hybridization signal equivalent to that of with control Mycobacterial DNA for which a perfect match between probe and target sequences was determined by sequence analysis, and + designates a signal which is barely detectable even after long exposure to x-ray film. The designator ND in Table 3 is not considered as a positive or negative indicator for purposes of categorization. To provide a frame of reference which defines the relative location of the oligonucleotides of this invention, the corresponding nucleotide sequence numbers for the £. coli region, as determined by a database sequence comparison, are provided in Table 1. The £. coli nucleotides rRNA sequences have been determined and each nucleotide has been assigned an integer value for reference purposes. Table 1 shows the oligonucleotides of the invention aligned with the corresponding £. coli sequences. Dashes in Table 1 indicate that £. coli does not share sequences which are substantially complementary within the corresponding region shown. The oligonucleotides of this invention are complementary to either the 16S rRNA or the 23S rRNA of Mycobacteria. Hybridization and Amplification-Based Assays The oligonucleotides of this invention are useful in any of the known hybridization assays which rely on the formation and detection of hybrids between two or more complementary nucleic acid sequences, such as between a rRNA target nucleic acid (the presence of which in a sample is to be determined) and one or more sufficiently complementary nucleic acid sequences. Such hybridization assays include, for example, solution hybridization assays in which the complementary sequences are free in solution, or assays in which one of the complementary nucleic acid sequences is fixed to a solid support. The latter group of assays includes dot blot analysis which involves immobilizing a nucleic acid or a population of nucleic acids on a solid support such as nitrocellulose, nylon, or other derivatized membranes, many of which are available commercially. Either DNA or RNA can be immobilized on such a solid support and subsequently can be probed or tested for hybridization under any of a variety of conditions with the oligonucleotides of the present invention. Another type of assay in which a nucleic acid is fixed to a solid support is the dual probe, sandwich-type hybridization assay format (for example the homopolymer capture, dual probe liquid hybridization format described in U.S. patent application serial numbers 277,579 and 169,646, the techniques of which are incorporated herein by reference) . Such assays involve the use of a capture oligonucleotide and a detection oligonucleotide for the identification of a target nucleic acid sequence of interest. The capture oligonucleotide, which is substantially complementary to a target nucleic acid sequence, is generally derivatized by adding a member of a specific binding pair to facilitate subsequent isolation. Many useful examples of specific binding pairs are known in the art. A particularly convenient specific binding pair for use in connection with this assay is deoxyadenosine (dA)/deoxythymidine (dT) . For example, a capture oligonucleotide can be derivitized by adding a polymeric sequence of dA residues at its 3' terminus. The capture oligonucleotide is then incubated with a solution to be tested for the target nucleic acid, under conditions appropriate for hybridization of sufficiently complementary nucleic acid sequences. If target nucleic acid sequences are present in the sample, hybridization occurs and a capture oligonucleotide-target nucleic acid complex is formed. The capture oligonucleotide-target nucleic acid complexes are isolated from the mixture by means of the derivatized capture oligonucleotide. For example, if the capture oligonucleotide has been derivatized by the addition of a polymeric sequence of dA residues, the mixture containing the capture oligonucleotide-target nucleic acid complex is brought into contact with a solid support which has been derivatized to include a dT polymeric sequence which will hybridize with the dA polymeric sequence. Many types of solid supports which can be derivatized as described are well known to those skilled in the art. In a preferred embodiment, the solid support is a plastic plate having wells. The mixture containing the capture oligonucleotide-target nucleic acid complexes is placed in the derivatized well of the plastic plate for a period of time sufficient for the dA and dT polymeric sequences to hybridize. The mixture is then removed from the well and the wells are washed to remove any non- specifically bound components. The capture oligonucleotide-target nucleic acid complexes will be retained in the wells of the plate while other components of the mixture will not be retained. A detection oligonucleotide is then introduced into the wells of the plate under conditions appropriate for hybridization. The detection oligonucleotide is complementary to the target nucleic acid in a region distinct from the region of complementarity between the capture oligonucleotide and the target nucleic acid. Hybridization is then detected by an appropriate means, many of which are well known in the art. -lo¬ in preferred embodiments, the detection oligonucleotide is labeled with a detectable reporter group (such as a radioisotope) or a member of a specific binding pair (e.g., biotin/avidin) . Alternatively, a replicatable RNA sequence can be attached to the detection oligonucleotide which can be autocatalytically replicated to generate a detectable signal (see, e.g., U.S. Patent No. 4,786,600) . o gonu i ptidg Vse Substantially inclusive oligonucleotides, which are defined above, are useful, for example, for the identification of members of the genus Mycobacteria in any hybridization assay which relies on the formation and detection of a hybrid between two or more substantially complementary nucleic acid sequences: e.g. a rRNA target nucleic acid (the presence of which in a sample is to be determined) and one or more detectable nucleic acid sequences. Such oligonucleotides hybridize to rRNA (and rDNA) from substantially all of the Mycobacterial species tested. In addition, they do not hybridize to nucleic acids from other types of bacteria (non-Mycobacteria) which might be present in a sample. Thus, in addition to being substantially inclusive, these probes are exclusive, as defined above. Partially inclusive oligonucleotides, which are defined above, are also broadly useful for the detection of members of the genus Mycobacteria. These oligonucleotides detect substantially all Mycobacteria, but not all and, thus, to be useful for the identification of Mycobacteria, such oligonucleotides generally are used as a mixture with other partially inclusive oligonucleotides. Like the previous category of probes, they can also be used in a mixture with substantially inclusive oligonucleotides in order, for example, to amplify the signal from a subset of Mycobacteria which may hybridize only weakly to the substantially inclusive oligonucleotides. Such oligonucleotides are also useful as primers for PCR amplification of Mycobacterial nucleic acids to which they are substantially complementary. Substantially inclusive non-exclusive oligonucleotides, which are defined above, are useful for example as detection oligonucleotides in a capture/detection dual oligonucleotides assay system. A preferred embodiment of this assay system is described above. It is not a necessary property of the non-exclusive oligonucleotides that they do not bind to non-Mycobacteria1 nucleic acid which may be present in the sample because nucleic acids from non-Mycobacteria1 species are removed from the mixture by virtue of the properties of the capture oligonucleotide. Such oligonucleotides are also useful as primers for PCR amplification of Mycobacterial nucleic acids to which they are substantially complementary. Partially inclusive non-exclusive oligonucleotides are useful as members of sets of detection oligonucleotides in a capture/detection dual probe assay. As with the substantially inclusive non-exclusive oligonucleotides described above, exclusivity is not an important characteristic for a detection probe in a dual probe assay. The reason that these oligonucleotides must generally be used as members of probe sets is that individually, they do not detect the full spectrum of Mycobacterial species. Thus, it is possible that if a partially inclusive detection probe were used independently (rather than in a set of two or more such detection oligonucleotides) in a dual probe assay, a false negative determination could be made due to the fact that partially inclusive detection oligonucleotides, by definition, do not recognize all members of the Mycobacterial genus. Such oligonucleotides are also useful as primers for PCR amplification of Mycobacterial nucleic acids to which they are substantially complementary. Subgenerjg Specificity Partially inclusive oligonucleotides can be substantially inclusive for a subgeneric group (i.e., they are substantially complementary to about 90% or more of the bacteria in the subgenus) . For example, the Mycobacterial subgenus known as the Mycobacterium tuberculosis complex includes the species M, tuberculosis, JL. boyjg (beg) , JL. africanum. and JL. microti. As shown in Example 2, oligonucleotides 2366 and 2371 are substantially inclusive for this subgenus. In addition, they are fully exclusive in that they do not hybridize to the bacteria listed in Table 4. Another recognized Mycobacterial subgenus is the slow- growing subgenus. This subgenus is defined, for example, by Wayne and Kubica (in Berσey's Manual of Systemic Bacteriology. Volume 2 (1986), pp. 1436-1457, Sneath ≤£ al editors, Williams and Wilkins, Baltimore, MD) . This subgenus includes the following Mycobacterial species: Mvcobacterium tuberculosis. Mvcobacterium microti. Mycobacterium karisasjj, Mycpbacterjum ffiarjnuffl, Mvcobacterium σastri. Mycpbacterjum, nonchromoαenicu . Mycobacterium terrae. Mvcobacterium triviale. Mvcobacterium malmoense. Mvcobacterium shimoidei. Mvcobacterium αordonae. Mvcobacterium asjatjqum, Mycpbacterjum. szulαai. Mvcobacterium simiae. MycQbacterjun scrofulaceum. Mvcobacterium avjum, Mycobactgrju . intracellulare. Mvcobacterium xenopj, MygpbacterJUB u±gέ∑ans., Mvcobacterium haemophilum. Mygpbaςterjun farcjnoqenes, Mvcobacterium lepraemurium. Mycobacterium oaratuberculosis and Mycobacterium leprae. As shown in Example 2, oligonucleotides 2369 and 2362 are substantially inclusive for this subgeneric group (i.e. they are substantially complementary to about 90% or more of the bacteria in the subgenus) . Oligonucleotide Construction and Hybridization Conditions The oligonucleotides of this invention are prepared by conventional methods. The conditions under which the oligonucleotides are hybridized to the Mycobacterial rRNA (the hybridization criteria) are variable. Those skilled in the art recognize that hybridization criteria are governed by such reaction parameters as the concentration and type of ionic species present in the hybridization solution, the types and concentrations of denaturing agents present and/or the temperature of hybridization. Generally, as hybridization conditions become more stringent, longer.oligonucleotides are preferred if stable hybrids are to be formed. As a corollary, the stringency of the conditions under which hybridization occurs (e.g., based on the type of assay to be performed) will dictate certain characteristics of the preferred oligonucleotides to be employed. Such relationships are well understood and can be readily manipulated by those skilled in the art. In Example 2 below, hybridization was carried out at 60°C for 3 or more hours in 1.08M NaCl, 0.06M NaH 2 P0 4 (pH7.7), 6mM EDTA, 0.01% DIS, 10X Denhardt's and 100 ug/ml denatured salmon sperm DNA, followed by subsequent washes in 0.3MNaCl, 0.04M TrisHCl (pH7.8) and 2mM EDTA. Under these conditions, the oligonucleotides used are as described. If the conditions were altered, however, characteristics of the probes (e.g., length, extent of complementarity) will also be altered. EXAHPLEg Example 1: Oligonucleotide Design The first step taken in the development of the oligonucleotides of the present invention involved identification of regions of 16S and 23S rRNA which potentially could serve as target sites for Mycobacterium specific nucleic acid oligonucleotides. As a practical matter, it is difficult to predict, a priori, which non- Mycobacterial organisms might be present in any test sample. Because of the large number of such potential non- Mycobacterial bacteria, demonstrating exclusivity for any given oligonucleotide sequence is not only unpredictable, but also extremely difficult and laborious. A more rigorous criterion was adopted to obviate the need to know what non-Mycobacterial bacteria might be present in all test samples that ultimately will be screened using the oligonucleotides. This entailed knowledge of the phylogenetic relationships among different Mycobacterial species and between Mycobacteria and other groups of bacteria. Specifically, an operating but previously unproven hypothesis was adopted that the exclusivity criterion could be satisfied by determining that if a particular target region in Mycobacterium rRNA could be identified which was sufficiently different from evolutionary relatives of Mycobacteria, then an oligonucleotide complementary to such a sequence could be used to distinguish between Mycobacterium and the relatives by hybridization assay. Based on phylogenetic observations, it then was extrapolated that rRNA sequences of more distantly related organisms, even though their actual identity may not necessarily be known, should be predictably different in a particular region of sequence than the aforementioned close evolutionary relative Mycobacteria. However, it could not be predicted, a priori r whether such regions exist, or if they do, where within the rRNA such regions will be located. As the first step in identifying regions of Mycobacterial rRNA which could potentially serve as useful target sites for complementary oligonucleotides, complete nucleotide sequences of the 16S and nearly complete sequence of 23S rRNAs from a few Mycobacterial species were determined. Coding regions of 23S rRNA genes of Mycobacterium were amplified by polymerase chain reaction (see U.S. Patent No. 4,683,202) from about 0.5 to 2.0 micrograms of genomic DNA of Mycobacterium using primers 940 (forward primer) and 987 (reverse primer) as a set. Primers 940 and 1021 are designed to hybridize to the 23S rRNA. Primer 987 hybridizes to the rRNA-like strand of the 23S ribosomal RNA gene. Primer 2205 hybridizes to the rRNA-like strand of the 5S ribosomal RNA gene of Mycobacterium genus only. Oligonucleotides 940 and 987 are designed for.use in the assays employing amplification of nearly the entire 23S rRNA gene (rDNA) of nearly all bacteria including Mycobacterium. The amplified 23S rRNA genes were cloned and sequenced by standard laboratory protocols. The Mycobacterium rRNA nucleotide sequences were compared to each other and to other available rRNA nucleotide sequences, in particular to Rhodococcus equi (16S) . Comparison of the sequences of several Mycobacterial species and their close relatives Rhodococcus proved especially valuable. Several regions of sequence were identified which appeared to be different between species of Mycobacteria and between Mycobacteria and non- Mycobacterial bacteria. The locations of these regions within the 16S and 23S rRNA sequences are shown in Tables 1 and 2, respectively. Oligonucleotides, 28-52 nucleotides in length, were designed which would hybridize preferentially to Mycobacterium tuberculosis complex, Mycobacterium avium complex, Mvcobacterium kanasii. Mvcobacterium fprtuitjm or all Mycobacteria. These were designed in light of the following goals: 1) to maximally utilize the nucleotide sequence differences useful for distinguishing one Mycobacterial species from another or groups of Mycobacteria from each other or Mycobacteria from other bacteria (indicated as upper case letters in the region of Core Variation in Tables 1 and 2) ; and 2) to minimize the effect of self-complementarity both locally within the target rRNA and between probe molecules. Table 3 exemplifies the inclusivity behavior of the preferred oligonucleotides toward a representative sampling of Mycobacteria and a few non- Mycobacteria in a dot-blot hybridization assay. Table 4 exemplifies the exclusivity behavior of the preferred oligonucleotides toward a representative sampling of non-Mycobacterial bacteria in a dot-blot hybridization assay. The foregoing oligonucleotide selection strategy yielded a number of oligonucleotide probes useful for identifying Mycobacteria in samples. Oligonucleotide probes 2213, 2214, 2215, 2233, 2234, 2235, 2236, 2240, 2247, 2248, 2155, 2156, and 2257 are designed from 16S rRNA sequences. Oligonucleotides 2362, 2364, 2365, 2366, 2368, 2369, 2371, 2372, 2373, 2374, 2375, 2376, 2377, 2378, 2379, 2380, 2382, 2383, 2384, 2385, 2388, 2389, 2390, 2392, 2393, 2425, 2426 and 2428 are designed from 23S rRNA sequences. The sequences of the preferred oligonucleotides are set forth below: 16S rRNA oligonucleotides SEQ ID NO: 17: 5'-ATTTCACGAACAACGCGACAAACCACCTACGAG3' SEQ ID NO: 26: 5•-CAGGAATTCCAGTCTCCCCTGCAGTACTCTAGT-3• SEQ ID NO: 10: 5•CTTCTCCACCTACCGTCAATCCGAGAGAACCCGGACCTTCGTCG-3' SEQ ID NO: 33: 5'GGCCACAAGGGAACGCCTATCTCTAGACGCGTCCTGTGCATAT-3• SEQ ID NO: 9: 5'-CAATCCGAGAGAACCCGGACCTTCGTCGATGGTGAAAG-3 ■ SEQ ID NO: 2: 5•-AGTTTCCCAGGCTTATCCCGAAGTGCAGGGCAG-3• SEQ ID NO: 40: 5'-CGAGTCCCCACCATTACGTGCTGGCAAC-3• SEQ ID NO: 19: 5•-ATCGCCCGCACGCTCACAGTTAAGCCGTGAGATTTC-3• SEQ ID NO: 11: 5»-GCTTCTTCTCCACCTACCGTCAATCCGAGACAAC-3' SEQ ID NO: 3: 5*-TAGACCCAGTTTCCCAGGCTTATCCCGGA-3• SEQ ID NO: 41: 5'-CGAGTCCCCGGCATTACCCGCTGGCAAC-3• SEQ ID NO: 32: 5•-CTGCACACAGGCCACAAGGGAACGCCTATCTCT-3 • SEQ ID NO: 18: 5 • CTCACAGTTAAGCCGTGAGATTTCACGAACAACGCGAC-3 » 23S rRNA Oligonucleotides SEQ ID NO: 99: 5•-CTGACTGCCTCTCAGCCGGGTAGCGCTGAGACATATCCTCCC-3• SEQ ID NO: 91: 5'-GGTTACCCATGCGTGCGGTTTAGCCTGTTCCGCGTTC-3• SEQ ID NO: 67: 5 ■ -CTCTACCTCCAACAAGAAACATGTGACGCTGCACC-3 ■ SEQ ID NO: 107: 5•-CCATCACCACCCTCCTCCGGAGAGGAAAAGGAGGCTCTG-3' SEQ ID NO: 75: 5•-CTACCCACACCCACCACAAGGTGGATGTGCCGCGG-3• SEQ ID NO: 47: 5'-GGGCTTAAATTCTCCGCTTCACCTTGCGGGTTAC-3 » SEQ ID NO: 115: 5'-GAACACGCCACTATTCACACGCGCGTATGCGTGTGGGTCGCCCTATTCAG-3 ■ SEQ ID NO: 56: 5 » -CTCCGCCCCAACTGGCGTCGAGGTTTCACAGTCTC-3• SEQ ID NO: 96: 5•-GGTATCACATGCATACGGTTTAGCCATCCCTTCTTTC-3• SEQ ID NO: 60: 5•-CTCCACAACCACTGGCGTGGCTGCTTCACAGTCTC-3 ■ SEQ ID NO: 72: 5•-CGTCΓCΛ ΓGCCACACTCTTGGACTTGTCGGCATT-3• SEQ ID NO: 112: 5'-GGCACGCCATCACCCCACGACAAAGTCGAAGGCTCTG-3• SEQ ID NO: 51: 5•-GGG ITAAATTCTCTGCTTCACCCCGAAGGTTAAC-3• SEQ ID NO: 79: 5•-GCTCCCCTACCCAACGATAAATCGTTGCCGCGG-3• SEQ ID NO: 120: 5'-CCAGAACACACCACTACACCACACACTACTGTGCGGATACCCCTATTCAG-3• SEQ ID NO: 104: 5'-CTGACTACCCTCCAGCCAGGTAGAACTGGAAAAACAGGTCCC-3• SEQ ID NO: 94: 5'-GGTTACCCATGCGTGCGGTTTAGCCATGTTCCGGTTC-3' SEQ ID NO: 77: 5'-GCTCCCCTACCCAACCTTGCGGTTGTCGCGG-3• SEQ ID NO: 110: 5•-GGCACGCCATCACCCCACGAAAGGGCTCTG-3• SEQ ID NO: 102: 5 • -CTGACTGCCCCTCAGCCGGGTAGAGCTGAGACGKATCGTACCC-3' SEQ ID NO: 49: 5•-GGGCTTAAATTCTCCGCTTCACCCTTGCGGGTTAAC-3 » SEQ ID NO: 122: 5•-CCAGAACACGCAACTACACCCCRAAGGGATGCGCCCTATTCAG3• SEQ ID NO: 58: 5•-CTCCACCCCAACTGGCGTTGAGGTTTCACAGTCTC-3• SEQ ID NO: 62: 5'-CTCCΛCΛCAAACTGGGCGTCTGTGCTTCAAAGTCTC-3• SEQ ID NO: 53: 5 » -GGGCTTAAACTTCCTGCTTCACTTACGGGTTAAC-3' SEQ ID NO: 81: 5•-GCTCCCCTACCCACATCCACCGTAAAGATGAATGTGCCGCGG-3• Spacer Region Oligonucleotides (5' to 23S rRNA gene) SEQ ID NO: 84: 5'-CAACAAAAACCAAAGAATATTGCACAAAGAACACGCC-3• SEQ ID NO: 86: 5'-CAAAAACCAAAGAATAAAATTGCACAAAAGAACACGC-3' SEQ ID NO: 88: 5'-CAAAAACCAAAAATGAGTTTAAAAGAAATTGCACATC-3• The oligonucleotides and their target sequences in the 16S and 23S rRNAs of Mycobacterium tuberculosis virulent strain, Mygpbagterjum avjum, MyPPfraPterjum kansasii and Mvcobacterium fortuitum are shown in Tables 1 and 2. The corresponding nucleotide positions of the Ej_ co^i 16S and 23S rRNAs are also shown. Since the £. coli sequences were among the first full 16S and 23S sequences obtained, the assigned position numbers are a convenient standard for explicitly identifying the homologous regions in the Mycobacterial rRNAs under consideration. In addition, 9 oligonucleotide primers (1637, 1638, 1260, 940, 622, 986, 993, 987 and 2205) were designed for the PCR amplification of parts of Mycobacterium 16S and 23S rRNA genes in order to facilitate the analysis of these genes in these slow growing organisms. The sequences of these primers are given below. -20- 16S Probe Primers Primer 1637: 5•-AAGGAGGTGATCCAGCC-3 ■ (SEQ ID NO: 124) Primer 1638: 5•-AGAGTTTGATCCTGGCTC-3• (SEQ ID NO: 125) Primer 1260: 5•-TGYACACACCGCCCGT-3' (SEQ ID NO: 126) 2?g robe Pr mers Primer 622: 5 » -ATTGGCCTTTCACCCC-3' (SEQ ID NO: 127) Primer 940: 5•-GAACTGAAACATCTWAGT-3' (SEQ ID NO: 128) Primer 986: 5 » -TTAGCMTTTCACCCC-3• (SEQ ID NO: 129) Primer 987: 5 « -CTTAGATGCYTTCAGC-3• (SEQ ID NO: 130) Primer 993: 5'-TTGGCMTTTCACCCC-3 ■ (SEQ ID NO: 131) Primer 1021: 5•-AGGGRAACARCCCAGA-3• (SEQ ID NO: 132) 5s rRNA Prpbe Primer Primer 2203:5'-ccgaattcgtcgacaacCAGGCTTAGCTTCCGGGTTCGG-3' (SEQ ID NO: 133) Lower case letters used in the above listing designate sequence designed to add useful restriction endonuclease recognition cloning sites to the amplified products. Letters other than A, T, G or C designate the following: N - A, T, G or C M = A or C R = A or G W = A or T S = C or G Y ■ C or T K = G or T B = C, G or T D = A, G or T H = A, C or T V ■ A, C or G More than one oligonucleotide probe has been designed to a number of the target regions shown in Table 2 corresponding variously to complements of the sequences of M PPbac erirø tyberculpg g, or Mvcobacterium ayjum or MygpfragteriwB Kansasii or Myco agterjum fprtuitw or ail four. The particular sequence upon which each oligonucleotide is based (i.e., is complementary to) is provided in Tables 1 and 2 by inspection of the aligned oligonucleotide and target sequences. Thus, for example, it can be seen in Table 2 that probe 2371 is perfectly complementary to the Mvcobacterium kansasii sequence. Base pairing rules dictate that A pairs with T and G pairs with C, although various non-canonical base pairs to a first approximation [i.e. G:U, G:T or A:G] can be introduced into the probe for specific purposes. However, it is expected (and desirable) that some cross-hybridization between species by one or both oligonucleotide probes will take place. Likewise, oligonucleotide probes 2235 and 2248 are based on Mvcobacterium tuberculosis. Mvcobacterium avium. Mvcobacterium Kan a jj and Mvcobacterium fortuitum 16S rRNA sequences. The specific hybridization behavior of the oligonucleotide probes described above are dependent to a significant extent on the assay format in which they are employed. Conversely, the assay format will dictate certain of the optimal design features of particular oligonucleotides. The scope of this invention is not to be construed as restricted to the specific sequence of nucleotides in the list of oligonucleotides above. For example, the length of these particular oligonucleotides was optimized for use in the dot blot assay (and certain other anticipated assays) described herein. It is well known to one skilled in the art that optimal oligonucleotides length will be a function of the stringency of the hybridization conditions chosen and hence the length of the instant oligonucleotides may be altered in accordance therewith. Also, in considering sets comprised of more than one oligonucleotide, it is desirable that all oligonucleotides behave in a compatible manner in any particular format in which they are both employed. Thus, the exact length of a particular oligonucleotide will to a certain extent reflect its specific intended use. The sequence data in Tables 1 and 2 suggest that the oligonucleotides of the present invention should exhibit a variety of useful hybridization properties with respect to the specific detection of Mvcobacterium tuberculosis. Mycobacterium aviu . and Mycobacterium fortuitum or all Mycobacteria to the exclusion of other bacteria. However, relatively few Mycobacterial sequences were inspected. It is possible that sequence variation might exist in other Mycobacterial strains not inspected by sequence analysis. Such variation might reduce or eliminate hybridization by the prospective oligonucleotides to some or many untested Mycobacteria. Equally as important as the inclusivity behavior of the oligonucleotides, is their exclusivity behavior. The number and types of non-Mycobacterial strains which might be encountered in a sample are extremely large. Therefore, the behavior of the oligonucleotides toward representative Mycobacteria and non-Mycobacterial species was determined by hybridization analysis using a dot blot procedure. While hybridization data for each of the individual oligonucleotides of the present invention are provided, it should be noted that useful combinations (sets) of oligonucleotides which exhibit hybridization behaviors that are the sum of the individual oligonucleotides also is explicitly predicted by the data. EXAMPLE 2 ; Dot Blot Analysis of Oligonucleotide Hybrjfljzatjpn Behavjor Dot blot analysis, in accordance with well known procedures, involves immobilizing a nucleic acid or a population of nucleic acids on a solid support, such as nitrocellulose, nylon, or other derivatized membranes. Either DNA or RNA can be easily immobilized on such a support and subsequently can be probed or tested for hybridization under any of a variety of conditions (i.e., stringencies) with oligonucleotides of interest. Under stringent conditions, oligonucleotides whose nucleotide sequences have greater complementarity to the target sequence will exhibit a higher level of hybridization than oligonucleotides having a lesser degree of less complementarity. For the experiment shown in Tables 3 and 4, rRNA was extracted by CsTFA method and DNA was extracted from Mycobacteria by standard methods. 16S and 23S rRNA genes of Mycobacterium from about 0.5 to 1.0 micrograms of total DNA were amplified using 16S rRNA-specific primers 1638 (forward primer) and 1637 (reverse primer) , or 23S primers 940 (forward primer) and 987 (reverse primer) by polymerase chain reaction. One tenth of a microgram of purified RNA (Lane et al., Proc. Natl. Acad. Sci. USA ££:6955-6959 (1985)), or PCR amplified ribosomal DNA from each of the indicated organisms was spotted on Nytran or nitrocellulose filters. The oligonucleotides were end labeled with radioactive phosphorous 32, using standard procedures. For the oligonucleotides described herein, prehybridization was done at 60 degrees C for 3 or more hours (in a solution containing 1.08M NaCl, 0.06M NaH 2 P0 4 (pH 7.7), 6mM EDTA, 0.01% SDS, 10X Denhardt's and 100 micrograms/milliliter denatured salmon sperm DNA) . Hybridization to rDNA targets was done at 60 degrees C for 14-16 hours (in a hybridization solution containing 1.08M NaCl, 0.06M NaH 2 P04 (pH 7.7), 6mM EDTA and 0.01% SDS), followed by three 15 minute post-hybridization washes at 60 degrees C (in 0.3M NaCl, 0.04M Tris-HCl (pH 7.8), 2mM EDTA) to remove unbound oligonucleotide probes. Following hybridization and washing as described above, the hybridization filters were exposed to X-ray film and the intensity of the signal was scored visually with respect to control lanes having a known quantity of target material (DNA) . A scale of hybridization intensity ranging from ++++ (hybridization signal equivalent to that of control Mycobacterial DNA for which a perfect match between oligonucleotide probe and target sequences was explicitly determined by sequence analysis) to + (barely detectable even after long exposure of X-ray film) and - (no detectable hybridization) has been used to conveniently compare hybridization signals between different organisms and the oligonucleotides. This reporting format is preferred to raw numerical representation of the extent of hybridization as it permits ready visual scanning of the summary data. As is evident in Table 3, oligonucleotide probe 2235 hybridizes to the amplified 16S ribosomal RNA genes and RNA of all the Mycobacterium isolates except JL. ulcerans. The rest of the oligonucleotide probes hybridize to different Mycobacterial species in varying potentially useful patterns to either the amplified 16S or 23S rDNA. The above example also demonstrates that primer set 1637 and 1638 can be used to amplify Mycobacterial 16S rRNA genes and primer set 940 and 987 can be used to amplify 23S rRNA genes from #189 to #2759, and primer set 940 and 2203 can be used to amplify 23S rRNA gene from #189 into 5S rRNA gene from genomic DNA and that the amplified material can be further tested with specific oligonucleotides targeted to the 16S and 23S rRNA. Equi alentg Those skilled in the art will know, or be able to ascertain, using no more than routine experimentation, many equivalents to the speci ic embodiments of the invention described herein. These and all other equivalents are intended to be encompassed by the following claims. TABLE I: 16S rRNA-TARCETED PROBES AND TARGET SEQUENCES 6 132 143 164 171 I I I I GUCUGGG-AAACUGCCUCAUGGAGGCGCAUAACUACUGGAAACGCUAGCUAAUACC E. coli 3'-GΛCGGGACCTCAAGCCCTATTCGGACCCTTTCA-5' P2233 3* -AGGCCCΓATTCGGACCCTTTGACCCAGAT-5' P2240 ACGUGCCUCAUCUgCCCUGCACUUCGGGAUAAGCCUGGGAAACUGGGUCUAAUACC M. tbRv37 ACGUGGGCAΛUCUGcCCUGCACUUCGGGAUAAGCCUGGGAΛACUGGGUCUAAUACC M. a iuβ ACGUCGGCAAUCUCCCCUGCACACCGGGAUAAGCCUGGGAAACUGGGUCUAAUACC M. kanεa ACGUGGGUAAUCUGCCCUGCACUIUGGGAUAAGCCUGGGAAACUGGGUCUAAUACC M. fortu E. coli «E 436 446 459 4B1 497 501 I I I I I I 8- E. coli CGGGUUGUAAAGUACUUUCACCGGGGACGAAGG-GAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAACAAGCACCGGCUAAC E. co i 9- P2215 3' -GAAAGTGGTAGCTGCTTCCAGGCCCAA GAGAGCCTAAC-5' P2215 10- P2213 3' -GCTGCTTCCAGGCCCAA GAGAGCCTAACTGCCATCCACCTCTTC-5' P2213 II- P2236 3' -CAA GAGAC^CTAACTGCCATCCACCTCTTC-5' P2236 12- M. tbR3 CGCGUnGUAAACCUCUUUCACCAUCGΛCGAACGUCCGGGUυ CUCUCGGAUUGACGGUAGGUGGAGAAGAAGCACCGGCCAAC M. tb 3 O 13- M. aviuβ CGGGUnGUAAACCUCUUUCACCAUCGACGAΛCGUCCGCGUυ UUCUCGGAUUGACGGUAGGUGGACAAGAAGCACCGGCCAAC M. aviun 14- M. kaπεa CGGGUUGUAAACCUCUUUCACCAUCGACGAAGGUCCGGGUU CUCUCGGAUUGACGGUAGGUGGAGAAGAAGCACCGGCCAAC M. kanea 15- M. fortu CGCGUnGUAAACCGUUUUCAAUAGGGACGAACCC CAAGUGACGGUACCUAUΛGAAGAAGGACCGGCCAΛC M. fortu n E. coli ffs 57B 592 606 610 629 641 645 649 o I I I I I I I I GGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAGCUUGAGUCUCGUAGAG 3'-GAGCATCCACCAAACAGCGCAACAAGCACTTTA-5' 3* -CAGCGCAACAΛCCΛCTTTAGΛGTGCCGAATTGΛCACTC-5' 3* -CrπTAGACTrcCCGAATTGACACTCGCACGCCCGCTA-5' 3' -TGATCTCATGACGTCC GGCCCUAAAGAGCUCGUAGGUnGUUUGUCGCGUnGUUCGUGAAAUCUCACGGCUUAACUGUGAGCGUGCGGGCGAUnCGGCCAGACUAGAGUACUGCGCG CGGCGUAAAGAGCUCGUAGGUnCUUUGUCGCCUnnUUCGUGAAAUCUCACGGCUUAACUGUGAGCGUGCGGGCGAUACGGGCACACUAGAGUACUGCAGG GGGCGUAAAGAGCUCGUAGGUGGUUUGUCGCGUUGUUCGUGAAAUCUCACGGCUUAACUGUGAGCGUGCGNGCGAUACGGGCAGACUAGAGUACUGCAGG GCXK:GUAAACU-GCUCGUAGGUnGUUUGUCGCGUnnUUCCUGAAAACUCACAGCUUnACUGUGGGCGUGCGGGCGAUACGGGCAGACUAGAGUACUGCnGG E. coli fts 6B0 I 25- E. coli CGGGGUAGAAUUCCAGGUGUAGCGGU E. coli 26- P2156 CCTCTGACCTTAAGGAC-5' P2156 27- H. tbR37 GGAGGCUGGAAUUCCUGGUGUAGCGG M .tbR37 28- M. aviua GGAGACUGGAAUUCCUGGUGUAGCGG M. avium 29- M. kanεa GGAGACUGGAAUUCCUGGUGUAGCGG M. kanεa 30- N. fortu GGAGACUGGAAUUCCUGGUGUAGCGG M. fortu TABLE 1 ( cont ' d ) : 16S rRNA-TARGETED PROBES AND TARGET SEQUENCES 993 1010 1024 1036 1045 1052 I I I I I I ACCUGGUCUUGACAUCC— ACGGAAGUUUUCAGAGAUGAGAAUGUGCCUU-CGGGAACC-GUGAGACAGGUGCUGCAUGGCUGU E. col i 3 ' -TCTCTATCCG CAΛGGGAA-CACCGG-ACACACGTC-5 ' P224B 3 ' -TATACCrr -TCCTGCGCAGATCTCTATCCG CAAGGGAA-CACCGG-5 ' P2214 3 * - AAGGGAA-CACCGG- ACACACGTCCACCACG- 5 ' PROBE ACCUGGGUUUGACAUGCACAGGUCGCGUCUAGAGAUAGGC GUUCCCUU-GUGGCC-UGUGUGCAGGUGGUGCAUGGCUGUC M . tbR 37 ACCUGGGUUUGACAUGCACAGGACGCGUCUAGAGAGAGGC GUUCCCUU-GUAGCCAUGUGUGCAGGUGGUGCAUGGCUGUC M . av i ua ACCUGGGUUUGACAUGCACAGGACGCGUCUAGAGAUAGGC CUUCCCUU-CUGGCC-UGUGUCCAGGUGGUGCAUGGCUGUC M. kaπea ACCUGGGUUUGACAUGCACAGGACGCCAGUAGAGAUAUUG GUUCCCUU-GUnGCC-UGUGUGCAGGUGGUGCAUGGCUGUC M. fortu E. coli #ε 1121 1147 I I 39- E. coli AACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUC CGGCCGGGAACUCAAAGGAGACUGCCAGUGAU E. col i O 40- P2234 3 ' -CAACGGTCGTGCA--TTACCACCCCTGAGC-5 ' P2234 41 - P224 3' -CAACGGTCGCCCA— TTACGGCCCCTGAGC-5 ' P2247 O O. 42- M. tbR37 CGAGCGCAACCCUUGUCUCAUGUUGCCAGCACGU— AAUGGUGGGGACUCGUGAGAGACUGCCGGGGUUAA M. tbR37 43- M. aviua CGAGCGCAACCCUUGUCUCAUGUUGCCAGCGGGU-- nAUGCCGGGGACUCGUnAGAGACUGCCGGGGUCAA M. aviua 44- N. kansa CGAGCGCAACCCUUGUCUCAUGUUGCCAGCGGGU--AAUGCCGGGGACUCGUGAGAGACUGCCGGGGUCAA M. kanεa 45- H. fortu CGAGCGCAACCCUUGUCUCAUGUUGCCAGCACGU— UAUGGUGGGGACUCGUGAGAGACUGCCGGGGUCAA N. fortu O =35 TABLE 2 (cont'd): 23S rRNA-TARGETED PROBES AND TARGET SEQUENCES E. coli#B 1B63 1894 E. coli#u I I I UUAAUUGAUGGGGUUA-GC--GCAA GC-GAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGC E. coli 3' -CAAT-TG-GGCGTT-CCA-C TCGCCTCTTAAATTCGGG-5' P2369 UUAAGAGGACCCGUUA-AC-CCGCAA-GGU-GAAGCGGAGAAUUUAAGCCCCAGUAAACGGCGGU M. tb 3' -CAAT-TG-GGCGTTCCCA-CT CGCCTCITAAATTCGGG-5* P2390 GUUAAGAGGACCCGUUA-AC-CCGCAAGGGU-GAAGCGGAGAAUUUAAGCCCCAGUAAACGGCGG M. kan 3' -CAAT-TG-GAAGC-CCCA-CTTCGTCTCTTAAATTCGGG-5' P2377 GUUAAGAGGACCUGUUA-AC-CUUCG-GGGU-GAAGCAGAGAAUUUAAGCCCCAGUAAACGGCGG M. for 3' -CAAT-TG-GGCATT--CA-CTPrcGTCCTTCAAATTCGGG-5* P2426 GUUAAGAGGACCCGUUA-AC-CCGUAA--GU-GAAGCAGGAAGUUUAAGCCCCAGUAAACGGCGG M. avium 2125 2159 E. coli#E I I GUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGU-CUGCAUGGAGCCGACCUUGAAAU E. coli I 3'-CTCTGACACTTTGGAGCTGCGGTCA-ACCCCGCCTC-5' P2372 00 GUAGGAUAGGUGGGAGACUGUGAAACCUCGACGCCAGU-UGGGGCGGAGUCGUUGUUGAAAC M. tb 3'-CTCTGACACTΓTTGGAGT GCGGTCA-ACCCCACCTC-5' P2393 GUAGGAUAGGUGGGAGACUGUGAAACCUCAACGCCAGU-UGGGGUGGAGUCGUUGUUGAAAU M. kan 3'-CTCTGACACTTCGTCGGTGCGGTCA-CCAACACCTC-5' P2374 GUAGGAUAGGUGGGAGACUGUGAAGCAGCCACGCCAGU-GGUUGUGGAGUCGUUGUUGAAAU M. for 3'-CTCTGAAAC1 CGTGTCTGCGGGTCAAACACACCTC-5' P2425 GUAGGAUMGGYSGGAGACUUUGAAGCACAGACGCCCAGUUUGUGUGGAGUCGUUGUUGAAAU M.avium TABLE 2 ( cont ' d ) : 23S rRNA-TARGETED PROBES AND TARGET SEQUENCES B30 864 E.coli#s I I I GAAAGCUAUUU-AGG-UAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGC-ACUGUUUCGGCA E. coli GAAAUGCAUUU-AGG-UGCAGCGUUGCGUGGUUCACCGCGGAGGUAGAGCUACUGGAUGCCGA M. tb GAAAUGCAUUU-AGG-UGCAGCGUUGCGUGUUUCACCACGGAGGUAGAGCUACUGGAUGCCGA M. kan 3' -CC-ACGTCGCAGTGTACAAAGAACAACCTCCATCTC-5' P2365 GAAAUGCAUUU-AGG-UGCAGCGUCACAUGUUUCUUGUUGGAGGUAGAGCUACUGGAUGCCGA M. for O 921 944 E.coli#ε O O. I I I CAAACUGCGAAUACCGGAGAAUGUUA--UCACGGGAGACACACGGCGGGUGCU E. coli CAAACUCCGAAUGCCGUGGUGUAAAG CGUGGCAGUGAGACGGCGGGGGAU M. tb CAAACUCCGAAUGCCGUGGUGUAUAG CGUGGCAGUGAGACGGCGGGGKAU M. kan 3'-TTACGGCTGTTCAGGTTCTCACACCGTCACTCTGC-5' P2375 O CAAACUCCGAAUGCCGACAAGUCCAAGAGUGUGGCAGUGAGACGGCGGGGGAU M. for X5 115B 1190 1196 E. coli#ε I I I I AAGCUGCGGCAGCGA CGCUUAUGCGUUGUUGGGUAGGGGAGC-GUUCUGUAA-GCC E. coli 3' -GGCGCCGTGTAG-GTGGAACACCACCCACACCCATC-5' P2368 AAGCCGCGGCACAUC-CACCUUGUGGUGGGUGUGGGUAGGGGAGC-GUCC--CUCAUUC M. tb 3' -GGCGCTGTTGG CGTTCCAACCCATCCCCTCG-5' P2383 AAGCCGCGACAACC GCAAGGUUGGGUAGGGGAGC-GUCC—CUCAUUC M. kan 3'-GGCGCCGT TGCTAAATAGCAACCCATCCCCTCG-5' P2378 AAGCCGCGGCA ACGAUUUAUCGUUGGGUAGGGGAGC-GUCC--UGCAUCC M. for 3'-GGCGCCGTGTAAGTAGAAATGCCACCTACACCCATCCCCTCG-5' P242B AAGCCGCGGCACAUUCAUCUUUACGGUGGAUGUGGGUAGGGGAGC-GUCC--CCCAUUC M. avium TABLE 2 : 23S rRNA-TARGETED PROBES AND TARGET SEQUENCES 3' - CUGCCGGCUAGCGGUGGCGUGUUCUUUGUGCAAUAUUCUUUGGUUUUUGUUGUGUUUGUAAGUG M. tb 3'-CGCACAAGAAAACACGTTAAAATAAGAAACCAAAAAC-5' P2367 GCGUUGCUACGGGUAGCGUGUUCUUUUGUGCAAUUUUAUUCUUUGGUUUUUGUGUUUGUAAGUG M. kan 3' -CTACACGTTAAAGAAAATTTGAGTAAAAACCAAAAAC-5' P2381 UGGUUUUGUGUGUUGAUGUGCAAUUUCUUUUAAACUCAUUUUUGGUUUUUGUG-UUGUAAGUG M. for 254 281 E. coli#ε I I I O AGCGGCGA-GCGAAC-GGGGAGCAGCCCAGAGCCUGAAUC E. coli 1 O 3' -(ZTTGCGCCTTGTCCGATTTGG-CGTGCGTACCCATTGG-5' P2364 AGUGGCGA-GCGAAC-SG-AACAGGCUAAACC-GCACGCAUGGGUAACCGGGUAGGGGUUGC M. tb AGUGGCGA-GCGAACGCGGAACAGGCUAAACC-GCACGCAUGgGUAACCGGGUAGGGGUUGU M. tb(av) n 3'-CTTG-GCCTTGTACCGATTTGGCGTGCGTACCCATTGG-5' P2382 AGUGGCGA-GCGAAC-CGGAACAUGGCUAAACCGCACGCAUGGGUAACCGGGUAGGGGUUGU M. kan O 3= 3' -CTTTCrrTCCC. ACCGATTTGG-CATACGTACACTATGG-5' P2373 im AGUGGCGA-GCGAAAGAAGGGAUGGCUAAACC-GUAUGCAUGUGAUACCGGGUAGGGGUUGU M. for 281 284 E. co I I I AGU GUGUGUGUUA E. col 3' -CCCTC-CTATACAGAGTCGCGATGGGCCGACTCTCCGTCAGTC-5' P2362 UGUGUGCGGGGUUGUGGGAG-GAUAUGUCUCAGCGCUACCGGCUGAGAGGCAGUCAGAAAGUGUCGUGGUUA M. tb GUGUGCGGGGUUGUGGGAG—AUAUGUCUCAGUGCUACCCGGCUGAGAGGCAGUCAGAAAGUGUCGUGGUUA M. tb( 3'-CCCATGCTAKGCAGAGTCGAGATGGGCCGACTCCCCGTCAGTC-5' P23B8 GUGUGCGGGGUUGUGGGAUCGAUMCGUCUCAGCUCUACCCGGCUGAGGGNCAGUCAGAAAGUGUCGUGGUUA M. kan 3'-CCCTG-GACAAAAAGGTCAAGATGGACCGACCTCCCATCAGTC-5' P2380 GUGUGCGGGGUUGUGGGAC-CUGUUUUUCCAGUUCUACCUGGCUGGAGGGUAGUCAGAAAA-UGUCGUGGUUA M. for TABLE 2 ( cont ' d ) : 23S rRNA-TARGETED PROBES AND TARGET SEQUENCES E. coliffB 535 559 E. colifε I I I 106- E. coli UACAAGCAGUGGGAGCAC-GCUU AGGCGUGUGACUGCGUACCUUUUGUAUAAUGG E. coli 107- P2366 3'-CrcTCGGAGGAAAAGCAGAGGCCT crC--CCACCACTACC-5' P2366 108- M. tb UACAAUCCGUCAGAGCCUCCUUUUCCUCUCCGGAG;AG--GGUY-GUGAUGGCGUGCCUUUUGAAGAAUGA M. tb 109- M. tb(av) UACAAUCCGUCAGAGCCUCCOIΠJUCCUCUCCGGAGGAG—GGUGGUGAUGGCGUGCCUIIUUGAAGAAUGA M. tb(av) 1 10- P23B4 3*-GTCTCGGGAAAGC ACCCCACTACCGCACGG-5' P23B4 l l l- M. kan UACAAUCCGUCAGAGCCCUUUCG UGGGGUGAUGGCGUGCCUUUUGAAGAAUGA M. kan 1 12- P2376 3'-GTfTCGGAAGCTGAAACAGC ACCCCACTACCGCACGG-5* P2376 M. for UACAAϋCCGUCAGAGCCUUCGACUUUGUCG UGGGGUGAUGGCGUGCCUUUUGAAGAAUGA M. for . 1 1 3- E. coliffε 640 666 E.cσli#B I I I 114- E. coli GGGAAACCGAGUCUUAACUGGGCG UUAAGUUGCAGGGUAUAGACCCGAAACCCGGU E. coli O 115- P2371 3'-GACTTATCCCGCKMXTWITGCGTATGCGCGCACACTTATCACCGCACAAG-5' P2371 116- M. tb GCGAAAGCGAGUCUGAAUAGGGCGACCCACACGCAUACGCGCGUGUGAAUAGUGGCGUGUUCUGGACCCGAAGCGGAGU N. tb 117- M. tb(av) GCGAAAGCGAGUCUGAAUAGKCGACCCACAS-CAUACGCGCGUGUGAAUAGUGGCGUGUUCUGGACCCGAAGCGGAGU Mtb(av) 118- PK23 3'-GACTTATCCCGCATAGCGCGCGCTCGCACAC ATCACCCACAAGACC-5' PK23 119- M. kan GCGAAAGCGAGUCUGAAUAGGGCGUAUCGCGCGCGAGCGUGUG UAGUGGCGUGUUCUGGACCCGAAGCGGAGU M.kan 120- P2379 3'-GACTTATCCCCATAGGCGTGTCATCACACACCACA TCACCACACAAGACC-5' P2379 121- M. for GCGAAAGCGAGUCUGAAUAGGGGUAUCCGCACAGUAGUGUGUGGUGU AGUGGUGUGUUCUGGACCCGAAGCGGAGU M.fσr 122- P2392 3' -GACTTATCCCG CGTAGGGAAJRCCCCA-CATCAACGCACAAGACC-5' P2392 123- M. avium GCGAAAGCGAGUCUGAAUAGGGC GCAUCCCUUnGGGGU-GUAGUUGCNUGUUCUGGACCCGAAGCGGAGU M. aviu Table 3*: DOT BLOT HYBRIDIZATION of 16S rRNA-TARGETED PROBES PROBE HYBRIDIZATION Genus strain strain 2233 2240 2215 2213 2236 Mycobactcriua tuberculosis 8v37 ATCC2561B ++++ +♦ ++++ ++++ +♦++ Mycobactcriua tuberculosis H37Ra 2487 Mycobactcriua tuberculosis coaplcz 3526 ■*+++ +++ +t- + ■ *+++ *♦ ■ ►-« • Mycobactcriua tuberculosis complex 352S ++♦+ ++ ♦+++ ++++ ++++- Mycobactcriua tuberculosis complex 3531 ♦+++ ++ ++++ ++++ ++++ Mycobactcriua tuberculosis complex 3533 ++f-+ + ++++ ♦++♦ ++++ Mycobactcriua tuberculosis complex 3535 ++++ ■ -r ++++ +++♦ ++++ Mycobactcriua tuberculosis coaplcz 3536 ++++ ++ ++++ ♦+*+ ++++ Mycobacterium tuberculosis coaplcz 3538 ++++ ++ ++++ ++♦+ ++-H- Mycob ctcriua tuberculosis coaplcz 3539 ++■» ■ + ++♦ ++++ •++++ « ■ +++ Mycob ctcriua tuberculosis coaplcz •3544 ++++ + ++++ ++++ ++++ Mycobactcriua tuberculosis complex 3545 ++++ ■ + ++++ *+++ ■ ++++ Mycobactcriua tuberculosis complex 3547 ++++ + ++++ ++++ ++++ Mycobactcriua tuberculosis complex 3548 ++++ + ++++ +« • *+ ++++ Mycobacterium tuberculosis coaplcz 3549 ++++ • ++ ■ *+++ +♦++ ++++ Mycobactcriua tuberculosis coaplcz 3552 ++++ "►+ ++++ ++++ ++++ Mycobactcriua tuberculosis coaplcz 3553 ++++ t* +++♦ ++++ ++++ Mycobactcriua tuberculosis coaplcz 3554 ++++ ++ ++++ ++++ +•*•*+ Mycobactcriua africanuB 3468 ++♦•+ • +♦♦+ *♦♦+ "t→++ +++♦ Mycobactcriua 3057 ++++ - +++♦ +♦♦+ ++++ Mycobactcriua 3246 ++++ - *♦++ ++++ ++++ Mycobactcriua 3532 *+++ - ++++ ++++ ++++ Mycobactcriua 3542 ++♦+ - ♦•++ ++++ ++++ Mycobactcriua 3555 ++++ - ♦♦♦+ ++++ ++++ Mycobactcriua 3559 ++++ - ' ++++ ++++ ++++ Mycobactcriua 3561 +++♦ - ♦++♦ ++++ ■*+++ Mycobactcriua 3562 ++++ - ■*+♦+ ++++ ++++ Mycobactcriua ++++ - +**+ ++++ •*+++ Mycobacterium ND ND ++++ ++++ +++ Mycobactcriua ND ND ++++ ++++ ++* Mycobactcriua ND ND ♦+ ++++ ++ Mycobactcriua ND ND ++ ++++ ++ Mycobactcriua ND ND ++ ++*+ ♦«► Mycobacterium ND ND * ■ * ++++ +++ Mycobacterium ND ND +++ ++++ +++ Mycobacterium ND ND +++ ++♦ +++ Mycobactcriua ND ND ♦+ « ■ + ++ Mycobactcriua ND ND ++ +♦ ++ Mycobacterium ND ND ++++ ++ ++ Mycobactcriua ND ND +++ ++ ♦+ Mycobacterium 3562 ++++ - ++♦«■ ++++ +++ Mycobacterium 3510 ++++ ++++ ++++ - ++f+ Mycobacterium ++++ + ++++ ++++ +♦■ + Mycobacterium 3260 ++++ ++ ++++ ++++ +-T-++ Mycobacterium 3422 ++++ - +++♦ ++++ -r-r-rt Mycobacterium 3425 t++ - ++++ ++++ ++♦+ Mycobacterium 3436 ++++ - ++++ ++++ ++++ Mycobacterium 3706 ++++ + ++++ ++++ -t-r-tt Table 3a (cont'd) DOT BLOT HYBRIDIZATION of 16S rRNA-TARGETED PROBES PROBE HYBRIDIZATION Table 3a ( cont 'd ) DOT BLOT HYBRIDIZATION of 16S rRNA-TARGETED PROBES TO PCR AMPLIFIED 16S rDNA GENES PROBE HYBRIDIZATION Genus strain strain 2233 2240 2215 2213 2236 Mycobacterium acapulcnεiε 3415 +++ +++ +++ Mycobacterium aviua 7 ++++ ++++ ++++ Mycobacteriua aviua 11 ++++ ++++ ++++ Mycobacterium avium 14 ++++ ++++ ++++ Mycobacteriua farcinogeneε 3704 + Mycobacteriua gastri 3702 +++ + ++ Mycobacterium paratuberculos ε ++++ +++ +++ Mycobacteriua haemophiluπ +4 +++ +++ Mycobacterium intracelluraire +++ ++ ++ Mycobacterium lepraeπurium + - + Mycobacterium nalmoenεe 3579 ++++ ++ ++ Mycobacterium microti ++ +++ +++ Mycobacterium novύm 3775 + ++ Mycobacterium simiae 3776 + Mycobacterium tuberculosis complex ++++ ++++ ++ Mycobacterium xenopi (26) ++ ++ + pending (17) ++++ ++++ ++ pending (19) ++ ++ + Table 3a ( cont 'd) : DOT BLOT HYBRIDIZATION of 16S rRNA-TARGETED PROBES PROBE HYBRIDIZATION Genus species strain 2155 2156 2235 2257 224B Mycobactcriua tuberculosis ++++ ++++ ++++ ++++ Mycobactcriua tuberculosis ++++ ++++ ++++ ++++ Mycobactcriua tuberculosis complex ++++ ++++ ++++ ++++ Mycobactcriua tuberculosis complex ++++ ++++ ++++ ++++ Mycobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Mycobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Myeobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Mycobactαriua tuberculosis coaplex ++++ ++++ ++++ ++++ Mycobaeteriua tuberculosis complex ++++ ++++ ++++ ++++ Myeobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Mycobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Mycobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Myeobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Myeobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Myeobactcr um tuberculosis coaplex ++++ ++++ ++++ ++++ Mycobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Mycobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Myeobactcriua tuberculosis coaplex ++++ ++++ ++++ ++++ Myeobactcriua africanua ++++ ++++ ++++ ++++ Myeobactcriua asiaticua ++++ ++++ ++++ ++++ Myeobactcr ua aviua ++++ ++++ ++++ ++++ Mycobactcriua aviua ++++ ++++ ++++ ++++ Myeobactcr ιιm aviua ++++ ++++ ++++ ++++ Mycobaeteriua aviua ++++ ++++ ++++ ++++ Myeobactcr um avium ++++ ++++ ++++ ++++ Myeobactcr um aviua ++++ ++++ ++++ ++++ Mycobae ■ teriua aviua ++++ ++++ ++++ ++++ Mycobactcriua aviua type 4 ++++ ++++ ++++ ++++ Mycobaeterlum aviua 1 ND ++++ +++ +++ Mycobaeter urn aviua 2 ND ++++ +++ +++ Mycobaeterium aviua 3 ND ++++ ++++ +++ Myeobactcriua aviua 4 ND +++ ++++ +++ Myeobactcr ua avium 5 ND ++++ ++++ +++ Mycobacterium aviua 6 ND ++++ +++ +++ Mycobaeter ua avium B ND ++++ +++ +++ Mycobaeter urn avium 9 ND ++++ +++ +++ Mycobaeter ua avium 10 ND ++++ +++ ++ Mycobae :teriua avium 12 ND ++++ +++ ++ Mycobaeter ua aviua 13 ND ++++ +++ ++ Myeobactcriua aviua 15 ND ++++ +++ ++ Mycobaeterium aviua ++++ ++++ ++++ ++++ Mycobaeter urn bovis ++++ ++++ ++++ ++++ Mycobaeterium bovis BCG ++++ ++++ ++++ ++++ Mycobaeter urn gordonae ++++ ++++ ++++ +-r++ Mycobaeterium intracellularae ++++ ++++ ++++ ++++ Mycobaeteriua intracellularae ++++ ++++ ++++ ++++ Mycobaeter ua intracellularae +++ ++++ ++++ ++++ Mycobaeter urn kansasii ++++ ++++ ++++ ++++ Table 3a (cont'd): DOT BLOT HYBRIDIZATION of 16S rRNA-TARGETED PROBES PROBE HYBRIDIZATION Genus species strain 2155 2156 2235 2257 2248 Mycobacteriua narinua ++++ ++++ ++++ Mycobactcriua acrofulaceua ++++ ++++ ++++ Mycobacteriua species ++++ - + Mycobactcriua species ++++ + + Mycobacteriua szulgai ++++ +++ ++ Mycobacteriua terrae ++++ - ++++ Mycobacteriua triviale ++++ Mycobacteriua ulcerans Mycobacteriua valentiae ++++ + Mycobacteriua agri ++++ ++++ Mycobacteriua aichienεe ++++ ++++ Mycobacteriua aurua ++++ ++++ Mycobactcriua austroafricanuπ ++++ ++++ Mycobacteriua chelonei ++++ + ++++ Mycobacteriua chelonei ++++ ++ ++++ Mycobacteriua chitae ++++ ++++ Mycobacteriua chubuenεe ++++ ++ ++++ Mycobacteriua diernhoferi ++++ ++ ++++ Mycobacteriua duvalii ++++ ++ ++++ Mycobacteriua fallax ++++ ++++ Mycobactcriua flavescens ++++ ++++ Mycobacteriua fortuitum ++++ ++ ++++ Mycobacteriua fortuitum ++++ ++ ++++ Mycobacteriua ga ium ++++ ++++ ++++ Mycobacteriua gilvua ++++ ++ ++++ Mycobacteriua koaossense ++++ ++++ Mycobacteriua neoaurua ++++ ++ ++++ Mycobacteriua obuense ++++ ++++ Mycobacteriua parafortuitum ++++ ++ ++++ Mycobacteriua phlei ++++ ++ ++++ Mycobacteriua porcinum ++++ ++ ++++ Mycobacteriua pulveriε ++++ ++ ++++ Mycobacterium rhodeεiae ++++ ++++ Mycobacteriua senegalenεe ++++ ++ ++++ Mycobacterium smegmatis ++++ ++ ++++ Mycobacterium sphagni ++++ + ++++ Mycobacterium theraoreεiεtable ++++ ++++ Mycobacterium takainεe ++++ ++ ++++ Mycobacteriua vaccae ++++ +++ Mycobacterium acapulenεiε ++++ ++++ Mycobacterium gallinarum ++++ ++++ Mycobacteriua engbaekii ++++ ++++ Mycobacterium lactis ++++ ++++ Mycobacterium aoriokaenεe ++++ ++ ++++ Mycobacterium petroleophilurr. ++++ + ++++ Mycobacteriua porferae ++++ + ++++ (pending) ++++ ++ ++++ (pending) ++++ + ++++ RhodococcuE + + TABLE 3a (cont'd): DOT BLOT HYBRIDIZATION of 16S rRNA-TARGETED PROBES of PCR AMPLIFIED 16S rDNA GENES TABLE 3a (cont'd) : DOT BLOT HYBRIDIZATION of 16S rRNA-TARGETED PROBES Genuε species Mycobacteriu Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium TABLE 3a (cont'd): DOT BLOT HYBRIDIZATION of 16S rRNA-TARGETED PROBES -..0- Table 3a (cont'd): DOT BLOT HYBRIDIZATION of 16S rRNA-TARGETED PROBES TO PCR AMPLIFIED 16S rDNA GENES PROBE HYBRIDIZATION Genus species strain 2214 2234 2247 Myeobactcr ua acapulcnsis 3415 4+ ++++ Mycobactcriua avium ++++ +++ ++ Mycobactcriua avium 7 ND ND ND Mycobacterium avium 11 ND ND ND Mycobacterium avium 14 ND ND ND Mycobacteriua farcinogeneε 3704 ND ND ND Mycobacteriua gastri 3702 ND ND ND Myeobaeterium paratuberculos s ++++ + + Mycobacteriua haemoph lum .++++ Mycobacterium intracellularae ++++ +++ + Mycobacteriua lcpraemurium ++++ Mycobacterium malaoenεe 3579 ND ND ND Mycobacterium microti ++++ +++ Mycobacterium novum 3775 ND ND ND Mycobacterium simiae 3776 ND ND ND Mycobacterium tuberculosis complex +♦++ +*+ Mycobacterium xenopi (26) ++++ +++ pending (17) ++++ +++ ++ pending (19) ++++ +++ + Inclusivity data was determined after four hours exposure and exclusivity was determined after overnight exposures. ** Each organism is represented by either lOOng of CβTFA purified RNA or 200ng of PCR amplified DNA. *** ++++ * positive ievel of hybridization, + * barely detectable and - = sero. TABLE 3b: DOT BLOT HYBRIDIZATION of 23S rRNA-TARGETED MYCOBACTERIUM TUBERCULOSIS COMPLEX PROBES PROBE HYBRIDIZATION CO c 00 21 H c m ω I m TABLE 3b (cont'd): DOT BLOT HYBRIDIZATION of 23S rRNA-TARGETED MYCOBACTERIUM TUBERCULOSIS COMPLEX PROBES PROBE HYBRIDIZATION o o NJ I o TABLE 3b(cont'd): DOT BLOT HYBRIDIZATION of 23S rRNA-TARGETED MYCOBACTERIUM TUBERCULOSIS COMPLEX PROBES PROBE HYBRIDIZATION Genus species strain 2364 2362 2366 2371 236B 2369 2372 Mycobacterium duvalli 3500 ++++ ++++ Mycobacterium diernhoferi 3504 ++++ Mycobacterium fallax 365B ++++ Mycobacterium flavescens 3506 +++ ++++ Mycobacterium fortuitum 3413 ++++ Mycobacterium fortuitum ++++ Mycobacterium gadium 3420 ++ ++++ Mycobacterium gilvum 3419 ++++ Mycobacterium ko ossense 3661 ++++ Mycobacterium neoaurum 3642 +++ ++++ Mycobacterium obuense 3416 ++++ - ++++ a Mycobacterium parafortuitum 3639 ++ ++++ I Mycobacterium phlei 3414 +++ ++++ I Mycobacterium porcinum 3641 ++++ =3 Mycobacterium pulvaris 3644 ++ ++++ Mycobacterium rhodensiae 3412 ++++ - ++++ Mycobacterium rhodenεiae 3412 ++++ - ++++ O Mycobacterium senegalense 3640 ++++ π Mycobacterium smegmatiε 306 +++ ++++ Mycobacterium sphagni 3659 +++ ++++ Mycobacterium thermoreεiεtible 3645 ++ ++ ++++ Mycobacterium takainse 363B ++++ - ++++ Mycobacterium vaccae 3637 ++++ - ++++ Mycobacterium acapulensis 3415 +++ ++++ Mycobacterium engbaekii 3509 ++++ Mycobacterium gallinarum 3498 ++++ - ++++ Mycobacterium lactiε 3703 ++++ Mycobacterium moriokaenεe 3656 ++ ++++ Mycobacterium petroleophilu 3655 +++ + ++++ Mycobacterium porferae 3657 ++ ++++ (pending) 3534 ++++ (pending) 355B ++++ Rhodococcus 3563 ++++ TABLE 3c: DOT BLOT HYBRIDIZATION OF 23S TARGETED MYCOBACTERIUM AVIUM COMPLEX PROBES PROBE HYBRIDIZATION Genus species strain 2392 2425 2428 Mycobacterium tuberculosis Rv37 ATCC25618 Mycobacterium tuberculosis Rh37 2487 Mycobacterium tuberculosis complex 3526 Mycobacterium tuberculosis complex 3528 Mycobacterium tuberculosis complex 3531 Mycobacterium tuberculosis complex 3533 Mycobacterium tuberculosis complex 3535 Mycobacterium tuberculosis complex 3536 Mycobacterium tuberculosis complex 3538 Mycobacterium tuberculosis complex 3539 Mycobacterium tuberculosis complex 3540 Mycobacterium tuberculosis complex 3544 Mycobacterium tuberculosis complex 3545 Mycobacterium tuberculosis complex 3547 Mycobacterium tuberculosis complex 3548 Mycobacterium tuberculosis complex 3549 Mycobacterium tuberculosis complex 3552 Mycobacterium tuberculosis complex 3553 Mycobacterium tuberculosis complex 3554 Mycobacterium africanum 3468 Mycobacterium aεianticum 3507 Mycobacterium avium 3246 Mycobacterium avium 3532 Mycobacterium avium 3542 Mycobacterium avium 3555 Mycobacterium avium 3559 Mycobacterium avium 3561 Mycobacterium avium 3562 Mycobacterium avium type 4 Mycobacterium avium 1 Mycobacterium avium 2 Mycobacterium avium 3 Mycobacterium avium 4 Mycobacterium avium 5 Mycobacterium avium 6 Mycobacterium avium B Mycobacterium avium 9 Mycobacterium aviua 10 Mycobacterium aviua 12 Mycobacterium avium 13 Mycobacterium avium 15 Mycobacterium bovis 3510 Mycobacterium BCG Mycobacterium gordσnae 3260 Mycobacterium intracellurarae 3422 Mycobacterium intracellurarae 3425 Mycobacterium intracellurarae 3436 TABLE 3c (cont'd): DOT BLOT HYBRIDIZATION OF 23S TARGETED MYCOBACTERIUM AVIUM COMPLEX PROBES PROBE HYBRIDIZATION Genus species strain 2392 2425 2428 Mycobacteriua Mycobacteriua Mycobacteriua Mycobacterium + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + + Mycobacterium Mycobacterium + Mycobacterium + Mycobacterium + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua +++ + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacterium + Mycobacteriua + Mycobacteriua + Mycobacteriua + Mycobacteriua ++ Mycobacteriua + Mycobacteriua ++ Mycobacteriua Mycobacteriua + Mycobacteriua ++ Mycobacteriua + Mycobacteriua + Mycobacteriua + TABLE 3c(cont'd): DOT BLOT HYBRIDIZATION OF 23S TARGETED MYCOBACTERIUM AVIUM COMPLEX PROBES PROBE HYBRIDIZATION Genus species strain 2392 2425 242B Mycobacteriua pβtroleophilum 3655 * Mycobactcriua porfirae 3657 - - 4 (pending) 3534 - - (pending) 3558 - - R odococcus 3563 - - * Inclusivity data was deterαined after four hours exposure and exclusivity was determined after overnight exposures. ** Each organism is represented by either lOOng of CsTFA purified RNA or 200ng of PCR amplified DNA. *** -T4+ * positive level of hybridization, » barely detectable and - * zerz, . TABLE 3d: DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM KANSASII PROBES PROBE HYBRIDIZATION Genus εpecieε εtrain 23B2 238B 23B4 2383 2390 2393 Mycobacterium Mycobacterium Mycobacterium Mycobaeterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium O Mycobacterium Mycobacterium 3 Mycobacterium Mycobacterium I Mycobacterium I Mycobacterium oo Mycobacterium EX: Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium TABLE 3d (cont'd): DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM KANSASII PROBES PROBE HYBRIDIZATION Genus species strain 23B2 23BB 2384 23B3 2390 2393 Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium I E Mycobacterium I Mycobacterium Mycobacterium : Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacteriu o I o t o i Inclusivity data was determined after four hours exposure and exclusivity was determined after overnight exposures. AA Each organism is represented by either lOOng of CsTFA purified RNA or 200πg of PCR amplified DNA. AAA 4444 = positive level of hybridization, 4 = barely detectable and - = zero. TABLE 3e: DOT BLOT HYBRIDIZATION to 23S rRNA-TARGETED MYCOBACTERIUM FORTUITUM PROBES PROBE HYBRIDIZATION Genus species strain 2373 23B0 2376 2379 2365 2375 2378 2377 2374 1660 Mycobacterium tuberculosis Rv37 ATCC2561B 4444 Mycobacterium tuberculosis 4444 Mycobacterium tuberculosis 444 Mycobacterium tuberculosis 444 Mycobacterium tuberculosis 444 Mycobacteriua tuberculosis 4444 Mycobacterium tuberculosis 444 Mycobacterium tuberculosis 444 Mycobacterium tuberculosis 44 Mycobacterium tuberculosis 444 Mycobacterium tuberculosis 444 o Mycobacterium tuberculosis 4444 Mycobacterium tuberculosis 4444 O Mycobacterium tuberculosis 44+4 O Mycobacterium tuberculosis 4444 Mycobacterium tuberculosis 444 Mycobacterium tuberculosis 444 I l_π Mycobacterium tuberculosis 444 O Mycobacterium a ricanum 444 I Mycobacterium asiaticum 444 4444 O Mycobacterium avium 4444 Ξ rt Mycobacterium avium 444 Mycobacterium avium 4444 Mycobacterium a ium 444 Mycobacterium avium 444 Mycobacterium avium 444 Mycobacterium avium 444 Mycobacterium avium type 44 Mycobacterium avium 1 4444 Mycobacterium avium 2 4444 Mycobacterium avium 3 4444 Mycobacterium avium 4 4444 TABLE 3e (cont'd): DOT BLOT HYBRIDIZATION to 23S rRNA-TARGETED MYCOBACTERIUM FORTUITUM PROBES PROBE HYBRIDIZATION Genus species 2380 2376 2379 2365 2375 2378 2377 2374 1660 Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium I UI Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobacterium Mycobac erium Mycobacterium Mycobacterium Mycobacterium TABLE 3e (cont'd): DOT BLOT HYBRIDIZATION to 23S rRNA-TARGETED MYCOBACTERIUM FORTUITUM PROBES PROBE HYBRIDIZATION Genus species strain 2373 23B0 2376 2379 2365 2375 237B 2377 2374 1660 Mycobacteriua chubuense 3497 444 ++++ ++ +++ Mycobacter ua diernhoferi 3504 44 ++++ +t+ +++ Mycoba teriua duvalii 3500 444 +++ ++++ ++++ Mycobacteriua fallax 365B +4 + ++ + ++++ Mycobacteriua flavescens 3506 44 +++ + ++ ++++ + + + +++ Mycobacteriua fortuitum 3413 444 + ++++ + ++++ ++++ + +++ ++++ +++ Mycobacteriua fortuitum 444 ++ +++ ++++ + ++++ ++++ ++++ + +++ Mycobacteriua gadium 3420 44 ++ + ++++ +++ ++++ Mycobaeteriua gilvua 3419 4+ ++++ ++ ++++ Mycobacteriua komossense 3661 + +++ Mycobacte iua neoaurua 3642 +44 +++ ++++ +++ +++ Mycobacteriua obuense 3416 ++++ +1++ ++ ++++ Mycobacteriua parafor uitua 3639 + +++ + t +++ +++ Mycobacteriua phlei 3414 +++ ++ + +++ Mycobacte iua porcinua 3641 +++ ++++ ++++ t+++ +++ +++ +++ Mycobacteriua pulveris 3644 ++ + t+ +++ + ++++ +++ . Mycobacteriua rhodeεiae 3412 ++++ ++ +++ Mycobacter ua senegalense 3640 +++ +t+ t+ +++ I +++ Ui Mycobacteriua saegaa is 306 +++ ++ +t++ + +++ ++++ I Mycobacteriua sphagni 3659 +++ + +- +++ Mycobacteriua theraoresista le 3645 + ++ +- +++ Mycobacteriua takaiense 3638 +++ 4+++ ++++ Mycobacteriua vaccae 3637 +++ ++++ ++++ ++++ o Mycobacteriua acapulensis 3415 ++++ ++ +++ ++++ C Mycobacterium gallinarum 349B +t+ +++ Mycobacterium engbaekii 3509 +++ ++++ ++++ +++ Mycobacterium lactis 3703 ++++ +++ Mycobacterium aoriokaense 3656 +++ +++ +++ +++ +++ Mycobacteriua petroleophiIum 3655 ++++ ++++ ++ +++ Mycobacterium porferae 3657 +++ + + +++ ++++ (pending) 3534 ++++ ++++ +++ ++ ++++ ++ + ++++ ++++ (pending) 355B ++++ ++++ ++++ ++++ ++++ ++++ ++++ ++ ++++ Inclusivity data was determined after four hours exposure and exclusivity was determined after overnight exposures. AA Each organism is represented by either lOOng of CsTFA purified RNA or 200ng of PCR amplified DNA. AAA ++44 = positive level of hybridization, 4 = barely detectable and - = zero. TABLE 4a (cont'd) i DOT BLOT HYBRIDIZATION OF 163 rRNA-TARGETED MYCOBACTERIUM PROBES PROBE BEHAVIOUR Genus Species Strain 2155 2156 2235 2257 2248 Citrobacter freundii 06B7 Escherichia coli 1665 4 Haemophilus influenza 33391 4 Klebβiella pneumoniae 1500 4 Bordetella pertussis 3513 4 Agrobacteriu tumefaciens 2021 4 Desulfovibrio desulfuricanε ATCC7757 4 Camp lσbacter jejuni 0022 Bacillus subtilis 0804 Clostridiu perfriπgens ATCC13124 Mycoplasma pneumonia FH Staphylococcus aureus 1711 Streptococcus faecalis 0406 2 Streptococcus pneumonia 040B P Streptococcus salivarius 0410 o Actiπomyces iβraelii 0005 Actiπomycec odontolyticulus 2195 Arthrobacter globifior is 2117 , Bifidobacterium dentium 0012 I tj τι Corynebacterium genitalium 0045 I Corynebacterium gluta icum 2120 o Corynebacterium pseudodiphtheriticum 2119 Corynebacterium pseudotuberculosis 2122 ri Corynebacterium pyogenes 2121 Corynebacterium xerosiε 0046 Corynebacterium diphtheriae 3511 Corynebacterium diphtheriae 3512 Jonesia deπitrifleans 0666 Micrococcuβ conoglomeratus ATCC0401 Micrococcus luteus ATCC03B1 Mycobacterium species 029B Nσcardia asteroides 2192 Nocardia albus DSM43109 Nocardia daβsonvillei DMS43235 Pimelobacter simplex DMS0B929 Propionobacteriu acnes 0363 Propionobacterium thoenii DMS20276 Rhodococcus equi 0665 Rhodococcus rhodochrous 4 Rhodococcus bronchialis 3473 4 TABLE 4a ( cont ' d ) DOT BLOT HYBRIDIZATION OF 16S rRNA-TARGETED MYCOBACTERIUM PROBES Genus Specieε Strain 2155 2156 2235 2257 224B GT# Rhodococcus εputi 3474 4-444 4- Rhodococcus obuensiε 3475 4444- 4- Rhodococcus aurantiacus 3476 4444 Rhodococcus erythopolis 3523 4444- Rhodococcus faεcians 3524 4444 Rhodococcus rhodochrous 35B9 4444 Rhodococcuε ketoglutanicum 35BB 4444 Streptomyces griseuε 3590 4 Streptomyces mutanε 0412 4 Streptomyces mitiε 3490 4 i Bifidobacterium dentium 0571 444 4 K rhinoεcleromitiε 1BB1 i 4 Fuεobacterium necrophorum 023B o E Spirochaeta aurantia i Bacteroideε fragilis ATCC29771 Chlorobium limicola Chloroflexuε aurantiacus Y0400 Deinococcuε radioduranε 2608 4 Normal stool 4 Human T-cells 4 Candida albicans Crytococcus neoformans Wheat germ A Inclusivity data was determined after four hour exposure and exclusivity data was determined after overninght exposure. AA Each organism is represented by either lOOng of CsTFA purified RNA. AAA 44-44- = positive level of hybridization; + = barely detectable and - = zero. TABLE 4a: DOT BLOT HYBRIDIZATION OF 16S rRNA-TARGETED MYCOBACTERIUM PROBES PROBE BEHA IOUR Genus Species Strain 2233 2240 2215 2213 2236 GT# itrobacter freundii Kscherichia coli Hae ophilus influenza Klebsiella pneumoniae Bordetella pertussis Agrobacterium tumefaciens D sulfovibrio desulfu icanβ Campylobacter j uni Bacillus subtilis Clostridium perfringens Mycoplaε a pneumonia Staphylococcus aureus o Streptococcus faecalis Streptococcus pneumonia o Streptococcus salivarius Actinomyces israelii Λctinomyceβ odontolyticulus Arthrobacter glσbifiormis Bifidσbacteriu dentium Corynebacterium genitalium Corynebacte ium gluta icum Corynebac erium pseudo iphthe i Corynebacterium pseudσtuberculo Corynebacterium pyogenes Corynebacterium xerosis 444 Corynebacterium diphtheriae Corynebacterium diphtheriae Jσneεia denitrificans Micrococcus cσnσglomeratus Micrococcus luteus Mycobacterium species Nocardia asteroides Nocardia albus Nocardia dassσnvillei 444 I'imelobacter simplex 444 Propionobacterium arnee Propionobacterium thoenii Rhodococcus equi Rhodococcus rhodochrnus Rhodococcus bronchia1 is TABLE 4a (cont'd): DOT BLOT HYBRIDIZATION OF 16S rRNA-TARGETED MYCOBACTERIUM PROBES PROBE BEHAVIOUR Genuε Species Strain 2233 2240 2215 2213 2236 GT# Rhodococcus sputi Rhodococcus obuensiε Rhodococcus aurantiacus Rhodococcus erythopolis Rhodococcus fascianε Rhodococcus rhodochrous Rhodococcus ketoglutanicum Streptomyces griseuε Streptomyces mutans j Streptomyces itiε Bifidobacterium dentium K rhiπoscleromitis cr> I Fuεobacterium necrophorum Spirochaeta aurantia Bacteroides fragiliε Chlorobium limicola Chloroflexus aurantiacus Deiπσcoccuε radiodurans Normal stool Human T-cellε Candida albicanε Crytococcuε neoformanε Wheat germ A Incluεivity data waε determined after four hour exposure and exclusivity data was determined after overninght exposure. AA Each organism is represented by either lOOng of CεTFA purified RNA. AAA 4-4-4-4- = poεitive level of hybridization; + = barely detectable and - = zero. TABLE 4b: DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM TUBERCULOSIS COMPLEX PROBES PROBE BEHAVIOUR Campylobacter jejuni 0022 Bacillus subtilis 0804 Clostridium perfringenε ATCC13124 Mycoplasaa pneumonia FH Staphylococcus aureus 1711 o Streptococcus faecalis 0406 Streptococcus pneumonia 040B Streptococcus salivarius 0410 O Actino yces israelii 0005 Actino yces odontolyticulus 2195 Arthrobacter globifiormis 2117 4444 I crz Bi idobacterium dentiu 0012 Ui ^ Corynebacterium genitalium 0045 4444 I Corynebacterium glutamicum 2120 4444 o Corynebacterium pseudodiphtheriticu 2119 rπ Coryneliacterium pseudotuberculosis 2122 Corynebacterium pyogenes 2121 4444 Corynebacterium xerosis 0046 4 4444 Corynebacterium diphtheriae 3511 4 +444 Corynebacterium diphtheriae 3512 4 4444 Jonesia denitrificanβ 0666 Micrococcus conoglomeratus ATCC0401 4444 Micrococcus luteus ATCC0381 4444 Mycobacterium species 029B 4444 Nocardia asteroides 2192 Nocardia albus DSM43109 Nocardia daβsonvillei DMS43235 Pi elobacter simplex DMS0B929 Propionobacterium acnes 0363 Propionobacterium thoenii DMS20276 Rhodococcus equi 0665 4444 Rhodococcus rhodochrous 4444 Rhodococcus bronchialis 3473 4444 TABLE 4b (cont'd) DOT BLOT HYBRIDIZATION OF 23S rRNA-TAHGETED MYCOBACTERIUM TUBERCULOSIS COMPLEX PROBES PROBE BEHAVIOUR Genus Species Strain 2364 2362 2366 2371 2368 2369 2372 CTf* Rhodococcus sputi 3474 4444 Rhodococcus obuensis 3475 4444 Rhodococcus aurantiacus 3476 4444 Rhodococcus erythopolis 3523 4444 Rhodococcus fascians 3524 4444 Rhodococcus rhodochrous 3589 4444 Rhodococcus ketoglutanicum 35BB 44+4 Streptomyceε griseus 3590 Streptomyces mutans 0412 Streptomyces itis 3490 O Bifidobacterium den ium 0571 O K rhinoscleromitis 1BB1 o Fu&obacterium necrophorum 023B Spirochaeta aurantia Bacteroides fragiliε ATCC29771 Chlorobium limicola ChloroflexuB aurantiacus Y0400 I Deinococcus radiodurans 260B OO o Normal stool -G- Human T-cells rt Candida albicans Crytococcus neoformans Wheat germ A Inclusivity data was determined after four hour exposure and excluεivity data was determined after overninght exposure. AA Each organism is represented by either lOOng of CsTFA purified RNA. AAA 4444 = positive level of hybridization; 4 = barely detectable and - = zero. TABLE 4c: DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM AVIUM COMPLEX PROBES PROBE BEHAVIOUR Genus Species Strain 2392 2425 242S GT# Citrobacter freundii 06B7 4 Esc eric ia coli 1665 44 Haemophiluε influenza 33391 Klebsiella pneumoniae 1500 Bordetella pertussis 3513 Agrobacterium tumefacienε 2021 Desulfovibrio desulfuricanε ATCC7757 Campylobacter jejuni 0022 Bacillus subtilis 0B04 Cloεtridium perfringens ATCC13124 Mycoplaε a pneumonia FH Staphylococcus aureuε 1711 Streptococcus faecaliε 0406 Streptococcus pneumonia 040B Streptococcus salivariuε 0410 Actinomyces israelii 0005 Actinomyces odontolyticuluε 2195 4 Arthrobacter globifiormis 2117 4444 Bifidobacterium dentiu 0012 Corynebacterium genitalium 0045 Corynebacterium glutamicum 2120 Corynebacterium pseudodiphtheriticum 2119 Corynebacterium pseudotuberculoεiε 2122 Corynebacterium pyogeneε 2121 4 Corynebacterium xeroεiε 0046 4 Corynebacterium diphtheriae 3511 4 Corynebacterium diphtheriae 3512 4 Joneεia denitrificanε 0666 444 Micrococcuε conoglomeratuε ATCC0401 Micrococcuε luteus ATCC03B1 4 Mycobacterium εpecieε 029B 4 Nocardia asteroideε 2192 Nocardia albuε DSM43109 Nocardia dassonvillei DMS43235 Pi elobacter simplex DMS0B929 4 Propionobacterium acnes 0363 4 Propionobacterium thoenii DMS20276 4 Rhodococcus equi 0665 444 Rhodococcus rhodochrous 4 Rhodococcuε bronchialis 3473 4 TABLE 4c (cont'd): DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM AVIUM COMPLEX PROBES PROBE BEHAVIOUR Genus Species Strain 2392 2425 2428 GT# Rhodococcus εputi 3474 44 Rhodococcuε obuenεiε 3475 44 Rhodococcuε aurantiacus 3476 44-4 Rhodococcuε erythopoliε 3523 44 Rhodococcus faεcianε 3524 44 Rhodococcuε rhodochrouε 3589 444 Rhodococcuε ketoglutanicum 35B8 44 Streptomyceε griεeuε 3590 4 Streptomyces mutanε 0412 Streptomyceε mitiε 3490 Bifidobacterium dentium 0571 K rhinoεclero itiε 1881 Fuεobacterium necrophoruπ 0238 Spirochaeta aurantia Bacteroides fragiliε ATCC29771 Chlorobiu limicola Chloroflexuε aurantiacus Y0400 De nococcuε radioduranε 2608 Normal εtool - - Human T-cells - Candida albicanε - - Crytococcuε neoformanε - Wheat germ - * Inclusivity data was determined after four hour exposure and exclusivity data was determined after overninght expoεure. ** Each orgaπiεm iε represented by either lOOng of CsTFA purified RNA. AA* ++44 = positive level of hybridization; 4 = barely detectable and - = zero. TABLE 4d: DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM KANSASII PROBES PROBE BEHAVIOUR Genus Species Strain 2382 238B 23B4 23E9 GT# Citrobaetβr freundii 0687 Escherichia coli 1665 Haβmophilus influenza 33391 Klebsiella pneumoniae 1500 Bordetella pertussis 3513 λgrobacteriua tuaβfaciβns 2021 Desul ovibrio desulfuricans ATCC7757 Campylobacter jejuni 0022 Bacillus subtilis 0804 4+ Cloβtridiua perfringens ATCC13124 Mycoplasma pneumonia FH Staphylococeuβ aureus 1711 Streptococcus faecalis 0406 Streptococcus pneumonia 040B Streptococcus salivarius 0410 Actinomyces iβraelii 0005 4 Actinomyces odontolyticulus 2195 +4 Arthrobaeter globif ormis 2117 Bifidobaeterium dentάum 0012 4 Corynebacterium genitalium 0045 44 Corynebacterium glutamicum 2120 4 Corynebacterium pseudodiphtheriticuxr. 2119 4+ Corynebacterium pseudotuberculosis 2122 ♦ Corynebacterium pyog ' eneβ 2121 +*•+ Corynebacterium xerosis 0046 Corynebacterium diphtheriae 3511 Corynebacterium diphtheriae 3512 Jonesia der.itrificans 06fc£ Micrococcus co oglomeratus ATCCD401 Micrococcus luteus ATCC03E1 Mycobacterium species 029B Nocardia asteroides 2192 Nocardia albus DSM43109 4+* Nocardia dassonvillei DMS43235 Pimelobacter ' simplex DMSCES25 Propionobacterium acnes 0363 Propionobacterium thoenii DMS2C276 Rhodococcus equi 0665 Rhodococcus rhodochrcus Rhodococcus bronchialis 3473 TABLE 4d (cont'd) DOT BLOT HYBRIDIZATION OF 23S rRNA-TARCETED MYCOBACTERIUM KANSASII PROBES PROBE BEHAVIOUR Genus Species Strain 23B2 23BB 23B4 23B9 GT# Rhodococcus sputi 3474 Rhodococcus obuensis 3475 4 Rhodococcus aurantiacus 3476 * Rhodococcus erythopolis 3523 44+ Rhodococcus fascians 3524 Rhodococcus rhodochrous 25B9 4+44 Rhodococcus etoglutanicuπ 35SB Streptomyces griseus 3590 Streptomyces utans 0412 Streptomyces mitis 3490 Bifidobacterium dentium 0571 K rhinosclero itis 1BB1 Fusobacterium necrophorum 023B Spirochaeta aurantia Bacteroides fragilis ATCC29771 Chioro um limicola Chloroflexus aurantiacus Y0400 Deinococcus radiodurans 2606 Normal stool Hunan T-cells Candida albicans Crytococcus neoformanε Wheat germ * Inclusivity data was determined after four hour exposure and exclusivity data was determined after overninght exposure. ** Each organism is represented by either lOOng of CsTFA purified RNA. *** +-r++ = positive level of hybridization; + = barely detectable and - = zero. TABLE 4d (cont'd): DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM KANSASII PROBES Genus Species Citrobacter freund i Eεcheric ia coli Haemophiluε influenza Klebεiella pneumoniae Bordetella pertuεεiε Agrobacterium tumefacienε Deεulfovibrio deεulfuricans Campylobacter jejuni Bacillus εubtiliε Clostridium perfringenε Mycoplaεma pneumonia Staphylococcuε aureuε Streptococcuε faecaliε Streptococcus pneumonia Streptococcuε salivariuε Actinomyces israelii Actinomyces odontolyticuluε Arthrobacter globifiormis Bifidobacteriu dentium Corynebacterium genitalium Corynebacterium glutam cum Corynebacterium pεeudodiphthe Corynebacterium pεeudotubercu Corynebacterium pyogeneε Corynebacterium xeroεis Corynebacterium diphtheriae Corynebacterium diphtheriae Joneεia denitrificanε Micrococcuε conoglomeratuε Micrococcuε luteuε Mycobacterium species Nocardia aεteroideε Nocardia albuε Nocardia dasεonvillei Pimelobacter simplex Propionobacterium acneε Propionobacterium thoenii Rhodococcuε egui Rhodococcuε rhodochrouε Rhodococcuε bronchialiε 3473 -6ώ- TABLE 4d (cont'd): DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM KANSASII PROBES PROBE BEHAVIOUR Genus Species Strain 2383 2390 2393 GT# Rhodococcus sputi 3474 Rhodococcus obuensis 3475 Rhodococcus aurantiacus 3476 Rhodococcus erythopolis 3523 Rhodococcus faεcians 3524 Rhodococcus rhodochrous 35B9 Rhodococcus ketoglutanicum 35B8 Streptomyces griseus 3590 Streptomyces mutanε 0412 Streptomyces itis 3490 Bifidobacterium dentium 0571 K rhinoεcleromitis 1BE1 444 Fusobacterium necrophorum 023E Spirochaeta aurantia Bacteroides fragilis ATCC29771 Chiorobium limicola Chloroflexus aurantiacus Y0400 Deinococcus radioduranε 260B Normal stool Human T-eelIs Candida albicanε Crytococcus neoformans Wheat germ * Inclusivity data was determined after four hour exposure and exclusivity data was determined after overninght exposure. ** Each organism is represented by either lOOng of CsTFA purified RNA. *** ■++++ = positive level of hybridization; * barely detectable and - = zero. TABLE 4e: DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM FORTUITUM PROBES PROBE BEHAVIOUR Genus Species 23B0 2376 2379 2365 Citrobacter freundii EEcherichia coli Haeaiophilus influenza KlebEiella pneuaoniae Bordetella pertussis Agrobacteriua tumefaciens Desulfovibrio desulfuricanε Caapylobacter jejuni Bacillus subtilis Clostridiua perfringenε Mycoplasaa pneumonia StaphylococcuE aureus Streptococcus faecaliβ Streptococcus pneumonia Streptococcus salivariuε Actinomyces israelii Actinomyces odontolyticuluε Arthrobacter globifiorais I Bi idobacteriua dentiua Corynebacteriua genitaliua Corynebacteriua glutaaicua Corynebacteriua pseudodiphth Corynebacteriua pεeudotuberc Corynebacteriua pyogenes Corynebacteriua xerosis Corynebacteriua diphtheriae 4 Corynebacteriua diphtheriae 4 Jonesia denitrificans Micrococcus conogloaeratus 4 Micrococcus luteus 444 Mycobacteriua species 444 Nocardia asteroideε Nocardia albus 4 Nocardia dasβonvillei 4 Piaelobacter simplex 4 Propionobacterium acnes 44 Propionobacterium thoenii Rhodococcus equi 444 Rhodococcus rhσdochrous Rhodococcus bronchialis 3473 t t TABLE 4e (cont'd) DOT BLOT HYBRIDIZATION OF 23S rRNA-TARGETED MYCOBACTERIUM FORTUITUM PROBES Genus Species St Rhodococcus sputi 3474 Rhodococcus obuensiE 3475 Rhodococcus aurantiacus 3476 444 Rhodococcus erythopolis 3523 4 Rhodococcus fascians 3524 44 ' Rhodococcus rhodochrous 35B9 4 Rhodococcus ketoglutanicum 35BB 4 Streptomyces griεeuε 3590 4 Streptomyces mutans 0412 Streptomyces mitis 3490 Bifidobacterium dentium 0571 K rhinoscleromitis 1BB1 Fusobacterium necrophorum 0238 Spirochaeta aurantia . Bacteroides fragilis ATCC29771 Chlorobium limicola I Chloroflexus aurantiacus Y0400 DeinococcuE radioduranε 260B I Normal stool Human T-cells Candida albicans Crytocαccus neoformanε Wheat germ A Inclusivity data was determined after four hour exposure and exclusivity data was determined after overninght exposure. AA Each organism is represented by either lOOng of CsTFA purified RNA. AAA 4444 = positive level of hybridization; 4 = barely detectable and - = zero. TABLE «e (cont'd) i DOT BLOT HYBRIDIZATION OF 233 rRNA-TARCETED MYCOBACTERIUM FORTUITUM PROBES PROBE BEHAVIOUR Genus Species Strain 2375 2370 2377 2374 Citrobacter freundii 0607 4 ERcherichla coli 1665 4 Haemophilus influenza 33391 Klebβiella pneumonia 1500 Bordetella pertuβRis 351.1 Agrobacterium tumeTaciens 2021 Desulfσvibrio dι»κulfuricans ΛTCC7757 Campylobacter jejuni 0022 Bacillus εubtilis 0004 Clostridium perfringeπs ΛTCC1 124 Mycoplae a pneumonia FH Staphylococcue aurcui 1711 , Streptococcus faecalis 0406 Streptococcus pneumonia 0400 3 Streptococcus salivarius 0 10 . Actinomyces Israel11 0005 Actinomyces odontolytlculus 2195 Λrthrobacter globlfiormis 2117 Bifidσbacterium den ium 0012 Corynebacteriua genitaltun 0045 444 O Corynebacterium glutaaicum 2120 Corynebacterium pβeudodiphtheri cum 2119 rj Corynebacteriua pseudotuberculORis 2122 Corynebacteriua pyogenes 2121 4 44 Corynebacteriua xerσsis 0046 4 Corynebacteriua diphtheriae 3511 4 4 Corynebacterium diphtheriae 3512 4 4 Jonesia denitrificans 0666 Micrococcus conoglomeratus ATCC0 01 Micrococcus luteuβ ΛTCC0301 4 44 Mycobacterium species 0290 4 44 Nocardia asterσides 2192 Nocardia lbus DSM43109 44 Nocardia dassonvillei DMS43235 Pimelσbacter simplex ΠMΠOΘ9Z9 4 Propionobacterium acnes 0.161 4 Propionobacterium thoenii DMS2027b 444 Rhodocncrus equi f.65 444 Hhoilococrus rhodochrouu Hhotlnrorcus bronchia1 in 3473 TABLE 4e (cont'd) I DOT BLOT HYBRIDIZATION OF 235 rRNA-TARGETED MYCOBACTERIUM FORTUITUM PROBES PROBE BEHAVIOUR Genus Species 237B 2377 2374 Rhodococcus sputl 4 Rhodococcus obuensis Rhodococcus aurantiacus 44 Rhodococcus erythopolis Rhodococcus fascians Rhodococcus rhodochrous 44 Rhodococcus etoglutanicum Streptomyces griseus Streptomyceε mutans StreptoMyces stitis Bifidobacterium dentium K rhinoscleroMitis Fusobacterium necrσphorusi Spirochaeta aurantia Bacteroides fragilis Chlorobium limicola Chloroflexus aurantiacus Deinococcus radiodurans O Normal stool Hunan T-cells Candida albicans Crytococcus neoformans Wheat germ A Inclusivity data was determined after four hour exposure and exclusivity data was determined after overninght exposure. AA Each organism is represented by either lOOng of CsTFA purified RNA. AAA ++++ = positive level of hybridization; 4 = barely detectable and - = zero. TABLE 4a (cont'd): DOT BLOT HYBRIDIZATION OF 16S rRNA-TARGETED MYCOBACTERIUM PROBES PROBE BEHAVIOUR Genus Species Strain 2214 2234 2247 GT# Citrobacter freundii 0687 Eεcherichia coli 1665 Hae ophiluε influenza 33391 Klebεiella pneu oniae 1500 Bordetella pertussis 3513 Agrobacterium tumefaciens 2021 Deεulfovibrio desulfuricanε ATCC7757 Camp lobacter jejuni 0022 Bacillus εubtilis 0B04 Cloεtridium perfringenε ATCC13124 Mycoplaε a pneumonia FH Staphylococcuε aureuε 1711 Streptococcuε faecaliε 0406 Streptococcus pneumonia 0408 Streptococcus salivarius 0410 Actinomyces iεraelii 0005 Actinomyces odontolyticulus 2195 Arthrobacter globifior iε 2117 Bifidobacterium dentium 0012 Corynebacterium genitalium 0045 Corynebacterium glutamicum 2120 Corynebacterium pεeudodiphtheriticu 2119 Corynebacterium pseudotuberculoεiε 2122 Corynebacterium pyogeneε 2121 Corynebacterium xerosis 0046 Corynebacterium diphtheriae 3511 Corynebacterium diphtheriae 3512 Joneεia denitrificans 0666 Micrococcus conogloπeratus ATCC0401 Micrococcuε luteuε ATCC03B1 Mycobacterium species 0298 Nocardia asteroideε 2192 Nocardia albuε DSM43109 Nocardia daεεonvillei DMS43235 Fimelobacter simplex DMS08929 Propionobacterium acneε 0363 Propionobacterium thoenii DMS20276 Rhodococcus equi 0665 Rhodococcuε rhodochrouε Rhodococcuε bronchialiε 3473 4-444 TABLE 4a (cont'd): DOT BLOT HYBRIDIZATION OF 16S rRNA-TARCETED MYCOBACTERIUM PROBES Cenus Specie* Rhodococcus sputi Rhodococcus obυβnsiβ Rhodococcus aurantiacus Rhodococcus erythopol s Rhodococcus fascians Rhodococcus rhodoehrous Rhodococcus kctoglutanieu Streptoayees griβeus Streptomyees autanβ Streptoayees aitis Bi dobaetβriua entium X rhinoscleronitis Fusobaeteriua nβcrophorua Spirochaeta aurantia Bacteroides fragilis Chiorob ua liaieola Chloroflexus aurantiacus Dβinococcus radiodurans Normal stool . . . Hunan T-cβllβ - Candida albicans . . . Crytococcuβ nβoforaans . . . Wheat gβra - * Inclusivity data was determined after four hour exposure and exclusivity data was deterained after overninght exposure. ** Each organism is represented by either lOOng of CsTFA purified RNA. A*A +♦«.«. s positive level of hybridization; ♦ ■ barely detectable and - ■ zero. SEQUSNCE LISTING (1) GENERAL INFORMATION: (i) APPLICANT: Shah, Jyotsna S. Niβtupβki, Raymond M. Liu, Jing (ii) TITLE OF INVENTION: Oligonucleotides Complementary to Mycobacterial Nucleic Acids (iii) NUMBER OF SEQUENCES: 133 (iv) CORRESPONDENCE ADDRESS: (A) ADDRESSEE: Amoco Corporation (B) STREET: 200 East Randolph Drive, P.O. Box 87703 (C) CITY: Chicago (D) STATE: Illinois (E) COUNTRY: U.S.A. (F) ZIP: 60680 (v) COMPUTER READABLE FORM: (A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS (D) SOFTWARE: Patentln Release #1.0, Version #1.25 (vii) PRIORITY APPLICATION DATA: (A) APPLICATION NUMBER: US 07/744,282 (B) FILING DATE: 13-AUG-1991 (C) CLASSIFICATION: (viii) ATTORNEY/AGENT INFORMATION: (A) NAME: Galloway, Norval B. (B) REGISTRATION NUMBER: 33,595 (C) REFERENCE/DOCKET NUMBER: CN 5851 (ix) TELECOMMUNICATION INFORMATION: (A) TELEPHONE: 312-856-7180 (B) TELEFAX: 312-856-4972 (2) INFORMATION FOR SEQ ID NO:l: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 55 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:l: GUCUGGGAAA CUGCCUGλUG GAGGGGGAUλ ACUACUGGAA ACGGUAGCUA AUACC 55 (2) INFORMATION FOR SEQ ID NO:2: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 33 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: AGTTTCCCAG GCTTATCCCG AAGTGCAGGG CAG 33 (2) INFORMATION FOR SEQ ID NO:3: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 29 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: TAGACCCAGT TTCCCAGGCT TATCCCGGA 29 (2) INFORMATION FOR SEQ ID NO:4: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 56 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: ACGUGGGUGA UCUGCCCUGC ACUUCGGGAU AAGCCUGGGA AACUGGGUCU AAUACC 56 (2) INFORMATION FOR SEQ ID NO:5: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 56 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5: ACGUGGGCAA UCUGCCCUGC ACUUCGGGAU AAGCCUGGGA AACUGGGUCU AAUACC 56 (2) INFORMATION FOR SEQ ID NO:6: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 56 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA ( i) SEQUENCE DESCRIPTION: SEQ ID NO:6: ACGUGGGCAA UCUGCCCUGC ACACCGGGAU AAGCCUGGGA AACUGGGUCU AAUACC 56 (2) INFORMATION FOR SEQ ID NO:7: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 56 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:7: ACGUGGGUAA UCUGCCCUGC ACUUUGGGAU AAGCCUGGGA AACUGGGUCU AAUACC 56 (2) INFORMATION FOR SEQ ID NO:8: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 90 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8: CGGGUUGUAA AGUACUUUCλ GCGGGGAGGA AGGGAGUAAA GUUAAUACCU UUGCUCAUUG 60 ACGUUACCCG CAGAAGAAGC λCCGGCUλλC 90 (2) INFORMATION FOR SEQ ID NO:9: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 38 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9: CAATCCGAGA GAACCCGGAC CTTCGTCGAT GGTGAAAG 38 (2) INFORMATION FOR SEQ ID NO:10: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 44 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:10: CTTCTCCACC TACCGTCAAT CCGAGAGAAC CCGGACCTTC GTCC 44 (2) INFORMATION FOR SEQ ID NO:11: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 30 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11: CTTCTCCACC TACCGTCAAT CCGAGAGAAC 30 (2) INFORMATION FOR SEQ ID NO:12: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 82 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12: CGGGUNGUAA ACCUCUUUCA CCAUCGACGA AGGUCCGGGU UCUCUCGGAU UGACGGUAGG 60 UGGAGAAGAA GCACCGGCCA AC 82 (2) INFORMATION FOR SEQ ID NO:13: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 82 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13: CGGGUNGUAA ACCUCUUUCA CCAUCGACGA AGGUCCGGGU UUUCUCGGAU UGACGGUAGG 60 UGGAGAAGλλ GCACCGGCCA AC 82 (2) INFORMATION FOR SEQ ID NO:14: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 82 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14: CGGGUUGUAA ACCUCUUUCA CCAUCGACGA AGGUCCGGGU UCUCUCGGAU UGACGGUAGG 60 UGGAGAAGAA GCACCGGCCA AC 82 (2) INFORMATION FOR SEQ ID NO:15: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 70 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:15: CGGGUNGUAA ACCGUUUUCA AUAGGGACGA AGCGCAAGUG ACGGUACCUA UAGAAGAAGG 60 ACCGGCCAAC 70 (2) INFORMATION FOR SEQ ID NO:16: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 100 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:16: GGGCGUAAAG CGCACGCAGG CGGUUUGUUA AGUCAGAUGU GAAAUCCCCG GGCUCAACCU 60 GGGAACUGCA UCUGAUACUG GCAGCUUGAG UCUCGUAGAG 100 (2) INFORMATION FOR SEQ ID NO:17: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 33 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:17: ATTTCACGAλ CAACGCGACλ AACCACCTAC GAG 33 (2) INFORMATION FOR SEQ ID NO:18: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 38 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:18: CTCACAGTTA AGCCGTGAGA TTTCACGAAC AACGCGAC 38 (2) INFORMATION FOR SEQ ID NO:19: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 36 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19: ATCGCCCGCA CGCTCACAGT TAAGCCGTGA GATTTC 36 (2) INFORMATION FOR SEQ ID NO:20: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:20: CCTGCAGTAC TCTAGT 16 (2) INFORMATION FOR SEQ ID NO:21: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 97 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:21: GGGCGUAAAG AGCUCGUAGG UGUUUGUCGC GUGUUCGUGA AAUCUCACGG CUUAACUGUG 60 AGCGUGCGGG CGAUCGGGCλ GACUAGAGUA CUGCGGG 97 (2) INFORMATION FOR SEQ ID NO:22: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 97 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:22: GGGCGUAAAG AGCUOGUAGG UGUUUGUCGC GUUUCGUGAA AUCUCACGGC UUAAGUGUGA 60 GCGUGCGGGC GAUACGGGCA GACUAGAGUA CUGCAGG 97 (2) INFORMATION FOR SEQ ID NO:23: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 99 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:23: GGGCGUAAAG AGCUCGUAGG UGGUUUGUCG OGUUGUUCGU GAAAUCUCAC GGCUUAACUG 60 UGAGCGUGCG GCGAUACGGG CAGACUAGAG UACUGCAGG 99 (2) INFORMATION FOR SEQ ID NO:24: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 95 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:24: GGGCGUAAAG AGCUCGUAGG UGUUUGUCGC GUUUCGUGAA AACUCACAGC UUACUGUGGG 60 CGUGCGGGCG λUλCGGGCAG ACUAGAGUAC UGCGG 95 (2) INFORMATION FOR SEQ ID NO:25: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 26 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:25: GGGGGUAGAA UUCCAGGUGU AGCGGU 26 (2) INFORMATION FOR SEQ ID NO:26: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 17 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:26: CAGGAATTCC AGTCTCC 17 (2) INFORMATION FOR SEQ ID NO:27: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 26 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:27: GGAGGCUGGλ AUUCCUGGUG UAGCGG 26 (2) INFORMATION. FOR SEQ ID NO:28: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 26 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: βingli (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:28: GGAGACUGGλ AUUCCUGGUG UAGCGG 26 (2) INFORMATION FOR SEQ ID NO:29: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 26 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:29: GGAGACUGGA AUUCCUGGUG UAGCGG 26 (2) INFORMATION FOR SEQ ID NO:30: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 26 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:30: GGAGACUGGA AUUCCUGGUG UAGCGG 26 (2) INFORMATION FOR SEQ ID NO:31: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 81 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:31: UACCUGGUCU UGACAUCCAC GGAAGUUUUC AGAGAUGAGA AUGUGCCUUC GGGAλCCGUG 60 AGACAGGUGC UGCλUGGCUG U 81 -80- (2) INFORMATION FOR SEQ ID NO:32: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 33 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:32: CTGCACACAG GCCλCλλGGG AACGCCTATC TCT 33 (2) INFORMATION FOR SEQ ID NO:33: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 43 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:33: GGCCACAAGG GAACGCCTAT CTCTAGACGC GTCCTGTGCA TAT 43 (2) INFORMATION FOR SEQ ID NO:34: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 29 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:34: GCACCACCTG CACACAGGCC ACλλGGGAA 29 (2) INFORMATION FOR SEQ ID NO:35: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 80 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA ( i) SEQUENCE DESCRIPTION: SEQ ID NO:35: -81- UACCUGGGUU UGλCλUGCλC λGGUCGCGUC UλGλGλUλGG OGUUCCCUUG UGGCCUGUGU 60 GCAGGUGGUG CλUGGCUGUC 80 (2) INFORMATION FOR SEQ ID NO:36: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 81 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:36: UACCUGGGUU UGλCλUGCλC λGGACGCGUC UAGλGλGλGG OGUUCCCUUG UAGCCλUGUG 60 UGCAGGUGGU GCAUGGCUGU C 81 (2) INFORMATION FOR SEQ ID NO:37: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 80 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:37: UACCUGGGUU UGλCλUGCλC λGGACGCGUC UλGλGλUλGG CGUUCCCUUG UGGCCUGUGU 60 GCAGGUGGUG CλUGGCUGUC 80 (2) INFORMATION FOR SEQ ID NO:38: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 80 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNλ (xi) SEQUENCE DESCRIPTION: SEQ ID NO:38: UACCUGGGUU UGλCλUGCλC AGGACGCCGU CUλGλGλUλU OGGUUCCCUU GUGCCUGUGU 60 GCAGGUGGUG CλUGGCUGUC 80 (2) INFORMATION FOR SEQ ID NO:39: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 68 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 9: AACGAGCGCA λCCCUUλUCC UUUGUUGCCλ GCGGUCCGGC CGGGΛACUCA AλGGλGλCUG 60 CCAGUGAU 68 (2) INFORMATION FOR SEQ ID NO:40: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 28 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:40: CGAGTCCCCA CCATTACGTG CTGGCAAC 28 (2) INFORMATION FOR SEQ ID NO:41: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 28 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:41: CGAGTCCCCG GCATTACCCG CTGGCAAC 28 (2) INFORMATION FOR SEQ ID NO:42: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 68 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:42: CGAGCGCAAC CCUUGUCUCA UGUUGCCAGC ACGUAAUGGU GGGGACUCGU AGAGACUGCC 60 GGGGUUλλ 68 (2) INFORMATION FOR SEQ ID NO:43: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 66 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 3: CGAGCGCAλC CUUGUCUCλU GUUGCCλGCG GGUλUGCCGG GGλCUCGUλG λGλCUGCCGG 60 GGUCAA 66 (2) INFORMATION FOR SEQ ID NO:44: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 69 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:44: CGAGCGCAAC CCUUGUCUCλ UGUUGCCAGC GGGUAAUGCC GGGGACUCGU GAGAGACUGC 60 CGGGGUCAλ 69 (2) INFORMATION FOR SEQ ID NO: 5: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 69 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 5: CGAGCGCAλC CCUUGUCUCλ UGUUGCCAGC λCGUUλUGGU GGGGACUCGU GλGλGλCUGC 60 CGGGGUCλλ 69 (2) INFORMATION FOR SEQ ID NO:46: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 58 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:46: UUAAUUGAUG GGGUUAGCGC AAGCGAAGCU CUUGλUCGλλ GCCCCGGUAA ACGGCGGC 58 (2) INFORMATION FOR SEQ ID NO:47: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 35 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 7: GGGCTTAAAT TCTCCGCTTC ACCTTGCGGG TTAAC 35 (2) INFORMATION FOR SEQ ID NO:48: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 61 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:48: UUAAGAGGAC CCGUUAACCC GCAAGGUGAA GCGGAGAAUU UAAGCCCCAG UAAACGGCGG 60 U 61 (2) INFORMATION FOR SEQ ID NO:49: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 36 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:49: GGGCTTAAAT TCTCCGCTTC ACCCTTGCGG GTTAAC 36 (2) INFORMATION FOR SEQ ID NO:50: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 62 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:50: GUUAAGAGGA CCCGUUAλCC OGCAAGGGUG λλGCGGλGλλ UUUλλGCCCC AGUAAACGGC 60 GG 62 (2) INFORMATION FOR SEQ ID NO:51: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 35 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:51: GGGCTTAAAT TCTCTGCTTC ACCCCGλλGG TTλλC 35 (2) INFORMATION FOR SEQ ID NO:52: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 61 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:52: GUUAAGAGGA CCUGUUλλCC UUCGGGGUGλ λGCλGλGλλU UUλλGCCCCλ GUλλλCGGCG 60 G 61 (2) INFORMATION FOR SEQ ID NO:53: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 34 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:53: GGGCTTAAAC TTCCTGCTTC ACTTACGGGT TAλC 34 (2) INFORMATION FOR SEQ ID NO:54: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 60 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:54: GUUAAGAGGA CCCGUUAλCC CGUAAGUGAA GCAGGAAGUU UAAGCCCCAG UAAACGGCGG 60 (2) INFORMATION FOR SEQ ID NO:55: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 60 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:55: GUAGGAUAGG UGGGAGGCUU UGAAGUGUGG ACGCCAGUCU GAUGGAGCCG ACCUUGAAAU 60 (2) INFORMATION FOR SEQ ID NO:56: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 35 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:56: CTCCGCCCCλ λCTGGCGTCG AGGTTTCACλ GTCTC 35 (2) INFORMATION FOR SEQ ID NO:57: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 61 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:57: GUλGGλUλGG UGGGλGλCUG UGλλλCCUCG λCGCCλGUUG GGGCGGλGUC GUUGUUGλλλ 60 C 61 (2) INFORMATION FOR SEQ ID NO:58: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 35 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:58: CTCCACCCCA λCTGGCGTTG λGGTTTCλCλ GTCTC 35 (2) INFORMATION FOR SEQ ID NO:59: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 61 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:59: GUAGGAUAGG UGGGAGλCUG UGλλλCCUCA λCGCCλGUUG GGGUGGλGUC GUUGUUGAAA 60 U 61 (2) INFORMATION FOR SEQ ID NO:60: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 35 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:60: CTCCACAACC λCTGGCGTGG CTGCTTCACλ GTCTC 35 (2) INFORMATION FOR SEQ ID NO:61: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 61 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:61: GUAGGAUAGG UGGGλGλCUG UGλλGCλGCC λCGCCλGUGG UUGUGGAGUC GUUGUUGAλλ 60 U 61 (2) INFORMATION FOR SEQ ID NO:62: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 36 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:62: CTCCACACAA ACTGGGCGTC TGTGCTTCAA AGTCTC 36 (2) INFORMATION FOR SEQ ID NO:63: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 62 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:63: GUAGGAUMGG YSGGAGλCUU UGλλGCACAG ACGCCCAGUU UGUGUGGλGU CGUUGUUGλλ 60 AU 62 (2) INFORMATION FOR SEQ ID NO:64: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 60 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:64: GAAAGCUAUU UλGGUλGCGC CUCGUGλλUU CλUCUCCGGG GGUλGλGCλC UGUUUCGGCλ 60 (2) INFORMATION FOR SEQ ID NO:65: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 61 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: Single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:65: GAAAUGCAUU UAGGUGCλGC GUUGCGUGGU UCλCCGCGGλ GGUλGλGCUλ CUGGAUGCCG 60 A 61 (2) INFORMATION FOR SEQ ID NO:66: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 61 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:66: GAAAUGCAUU UAGGUGCλGC GUUGCGUGUU UCλCCλCGGλ GGUλGλGCUλ CUGGλUGCCG 60 A 61 (2) INFORMATION FOR SEQ ID NO:67: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 35 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:67: CTCTACCTCC AACΛAGAAΛC λTGTGλCGCT GCACC 35 (2) INFORMATION FOR SEQ ID NO:68: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 61 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: βingli (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:68: GAAAUGCAUU UAGGUGCAGC GUCλCλUGUU UCUUGUUGGλ GGUλGλGCUλ CUGGλUGCCG 60 A 61 (2) INFORMATION FOR SEQ ID NO:69: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 51 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:69: CAAACUGCGA AUACCGGAGA AUGUUAUCAC GGGAGACACA CGGCGGGUGC U 51 (2) INFORMATION FOR SEQ ID NO:70: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 50 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:70: CAAACUCCGA AUGCCGUGGU GUAAAGCGUG GCAGUGAGAC GGCGGGGGλU 50 (2) INFORMATION FOR SEQ ID NO:71: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 50 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:71: CAAACUCCGA AUGCCGUGGU GUλUλGCGUG GCλGUGλGλC GGCGGGGKΛU 50 (2) INFORMATION FOR SEQ ID NO:72: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 35 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNλ (xi) SEQUENCE DESCRIPTION: SIQ ID NO:72: CGTCTCλCTG CCλCλCTCTT GGλCTTGTCG GCλTT 35 (2) INFORMATION FOR SEQ ID NO:73: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 53 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:73: CAAACUCCGA AUGCCGλCλλ GUCCλλGλGU GUGGCλGUGλ GλCGGCGGGG GλU 53 (2) INFORMATION FOR SEQ ID NO:74: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 54 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:74: AAGCUGCGGC AGCGλCGCUU λUGCGUUGUU GGGUλGGGGλ GCGUUCUGUλ λGCC 54 (2) INFORMATION FOR SEQ ID NO:75: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 35 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:75: CTACCCACAC CCλCCACλλG GTGGλTGTGC CGCGG 35 (2) INFORMATION FOR SEQ ID NO:76: (i) SEQUENCE CHARACTERIS ICS: (A) LENGTH: 55 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:76: AAGCCGCGGC λCλUCCλCCU UGUGGUGGGU βUGGGUAGGG GλGCGUCCCU CλUUC 55 (2) INFORMATION FOR SEQ ID NO:77: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 31 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:77: GCTCCCCTAC CCAACCTTGC GGTTGTCGCG G 31 (2) INFORMATION FOR SEQ ID NO:78: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 45 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:78: AAGCCGCGAC AλCCGCλλGG UUGGGUλGGG GλGCGUCCCU CλUUC 45 (2) INFORMATION FOR SEQ ID NO:79: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 33 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:79: GCTCCCCTAC CCλλCGλTλλ ATCGTTGCCG CGG 33 (2) INFORMATION FOR SEQ ID NO:80: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 47 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:80: AAGCCGCGGC λλCGλUUUλU CGUUGGGUλG GGGλGCGUCC UGCλUCC 47 (2) INFORMATION FOR SEQ ID NO:81: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 42 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:81: GCTCCCCTλC CCλCλTCCAC CGTAAAGATG λλTGTGCCGC GG 42 (2) INFORMATION FOR SEQ ID NO:82: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 56 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:82: AAGCCGCGGC λCAUUCAUCU UUλCGGUGGλ OGUGGGUλGG GGλGCGUCCC CCλUUC 56 (2) INFORMATION FOR SEQ ID NO:83: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 50 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:83: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CλGλGGCGλU 50 (2) INFORMATION FOR SEQ ID NO:84: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:84: CAACAAAAAC CAλλGλλTAT TGCλCAAAGA λCλCGCC 37 (2) INFORMATION FOR SEQ ID NO:85: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 64 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA . (xi) SEQUENCE DESCRIPTION: SEQ ID NO:85: CUGCCGGCUA GCGGUGGCGU GUUCUUUGUG CAAUAUUCUU UGGUUUUUGU UGUGUUUGUλ 60 AGUG 64 (2) INFORMATION FOR SEQ ID NO:86: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:86: CAAAAACCAλ AGAATAAAAT TGCλCAAAAG AλCλCGC 37 (2) INFORMATION FOR SEQ ID NO:87: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 64 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:87: GCGUUGCUAC GGGUλGCGUG UUCUUUUGUG CλλUUUUλUU CUUUGGUUUU UGUGUUUGUλ 60 AGUG 64 (2) INFORMATION FOR SEQ ID NO:88: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:88: CAAAAACCAλ AAATGAGTTT AAAAGAAATT GCλCλTC 37 (2) INFORMATION FOR SEQ ID NO:89: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 62 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:89: UGGUUUUGUG UGUUGAUGUG CλλUUUCUUU UλλλCUCλUU UUUGGUUUUU GUGUUGUAAG 60 UG 62 (2) INFORMATION FOR SEQ ID NO:90: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 38 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:90: AGCGGCGAGC GλλCGGGGλG CλGCCCλGλG CCUGλλUC 38 (2) INFORMATION FOR SEQ ID NO:91: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:91: GGTTACCCAT GCGTGCGGTT TAGCCTGTTC CGCGTTC 37 (2) INFORMATION FOR SEQ ID NO:92: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 58 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:92: AGUGGCGAGC GAACSGλλCλ GGCUAAACCG CACGCAUGGG UAACCGGGUA GGGGUUGC 58 (2) INFORMATION FOR SEQ ID NO:93: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 59 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:93: AGUGGCGAGC GAACGCGλλC AGGCUAAACC GCACGCλUGG GUλλCCGGGU λGGGGUUGU 59 (2) INFORMATION FOR SEQ ID NO:94: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:94: GGTTACCCAT GCGTGCGGTT TAGCCATGTT CCGGTTC 37 (2) INFORMATION FOR SEQ ID NO:95: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 60 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:95: AGUGGCGAGC GλλCCGGλλC λUGGCUλλλC CGCλCGCλUG GGUλλCCGGG UλGGGGUUGU 60 (2) INFORMATION FOR SEQ ID NO:96: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:96: GGTATCACλT GCλTλCGGTT TλGCCλTCCC TTCTTTC 37 (2) INFORMATION FOR SEQ ID NO:97: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 60 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:97: AGUGGCGAGC GλλλGλλGGG λUGGCUλλλC CGUλUGCλUG UGλUλCCGGG UλGGGGUUGU 60 (2) INFORMATION FOR SEQ ID NO:98: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 13 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:98: AGUGUGUGUG UUA 13 (2) INFORMATION FOR SEQ ID NO:99: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 42 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:99: CTGACTGCCT CTCAGCCGGG TAGCGCTGAG ACATATCCTC CC 42 (2) INFORMATION FOR SEQ ID NO:100: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 71 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:100: UGUGUGCGGG GUUGUGGGAG GAUAUGUCUC AGCGCUACCG GCUGAGAGGC AGUCAGAAAG 60 UGUCGUGGUU A 71 (2) INFORMATION FOR SEQ ID NO:101: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 70 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNλ (xi) SEQUENCE DESCRIPTION: SEQ ID NO:101: GUGUGCGGGG UUGUGGGλGλ UλUGUCUCAG UGCUACCCGG CUGΛGAGGCA GUCλGλλλGU 60 GUCGUGGUUλ 70 (2) INFORMATION FOR SEQ ID NO:102: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 43 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:102: CTGACTGCCC CTCAGCCGGG TλGλGCTGλG λCGKΛTCGTλ CCC 43 (2) INFORMATION FOR SEQ ID NO:103: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 72 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:103: GUGUGCGGGG UUGUGGGAUC GAUMCGUCUC λGCUCUλCCC GGCUGAGGGN CAGUCAGAAA 60 GUGUCGUGGU UA 72 (2) INFORMATION FOR SEQ ID NO:104: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 42 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:104: CTGACTACCC TCCAGCCAGG TAGAACTGGA AAAACAGGTC CC 42 (2) INFORMATION FOR SEQ ID NO:105: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 71 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:105: GUGUGCGGGG UUGUGGGACC UGUUUUUCCλ GUUCUλCCUG GCUGGλGGGU λGUCλGλλλλ 60 UGUCGUGGUU λ 71 (2) INFORMATION FOR SEQ ID NO:106: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 54 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:106: UACAAGCAGU GGGλGCλCGC UUλGGCGUGU GλCUGCGUλC CUUUUGUλUλ λUGG 54 (2) INFORMATION FOR SEQ ID NO:107: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 39 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:107: CCATCACCAC CCTCCTCCGG AGAGGAAAAG GAGGCTCTG 39 (2) INFORMATION FOR SEQ ID NO:108: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 68 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:108: UACAAUCCGU CAGAGCCUCC UUUUCCUCUC CGGAGGAGGG UGGUGλUGGC GUGCCUUUUG 60 AAGAAUGA 68 (2) INFORMATION FOR SEQ ID NO:109: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 67 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:109: UCAAUCCGUC AGλGCCUCCU UUUCCUCUCC GGλGGλGGGU GGUGλUGGCG UGCCUUUUGλ 60 AGAAUGA 67 (2) INFORMATION FOR SEQ ID NO:110: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 30 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNλ (xi) SEQUENCE DESCRIPTION: SEQ ID NO:110: GGCACGCCAT CACCCCACGA λλGGGCTCTG 30 (2) INFORMATION FOR SEQ ID NO:111: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 53 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:111: UACAAUCCGU CAGλGCCCUU UCGUGGGGUG λUGGCGUGCC UUUUGλAGAλ UGA 53 (2) INFORMATION FOR SEQ ID NO:112: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 37 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:112: GGCACGCCAT CACCCCλCCλ CλλλGTCGλλ GGCTCTG 37 (2) INFORMATION FOR SEQ ID NO:113: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 60 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:113: UACAAUCCGU CAGAGCCUUC GλCUUUGUCG UGGGGUGλUG GCGUGCCUUU UGλλGλλUGλ 60 (2) INFORMATION FOR SEQ ID NO:114: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 56 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:114: GGGAAACCGA GUCUUAACUG GGCGUUAAGU UGCAGGGUAU AGλCCCGλAA CCCGGU 56 (2) INFORMATION FOR SEQ ID NO:115: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 50 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:115: GAACACGCCA CTATTCACAC GCGCGTATGC GTGTGGGTCG CCCTATTCAG 50 (2) INFORMATION FOR SEQ ID NO:116: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 79 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:116: GCGAAAGCGA GUCUGAAUAG GGCGACCCΛC ACGCAUACGC GCGUGUGAAU AGUGGCGUGU 60 UCUGGACCCG AAGCGGAGU 79 (2) INFORMATION FOR SEQ ID NO:117: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 78 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:117: GCGAAAGCGA GUCUGλλUλG GGCGλCCCλC λSCλUλCGCG CGUGUGλλUλ GUGGCGUGUU 60 CUGGλCCCGλ AGCGGAGU 78 (2) INFORMATION FOR SEQ ID NO:118: (i) SEQUENCE CHARλCTERISTICS: (A) LENGTH: 46 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:118: CCAGAλCλCC CλCTλCλCλC GCTCGCGCGC GλTλCGCCCT λTTCλG 46 (2) INFORMATION FOR SEQ ID NO:119: (i) SEQUENCE CHARλCTERISTICS: (λ) LENGTH: 73 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNλ (xi) SEQUENCE DESCRIPTION: SEQ ID NO:119: GCGAAAGCGA CUCUGλλUλG GGCGUλUCGC GCGCGλGCGU GUGUλGUGGC GUGUUCUGGλ 60 CCCGλAGCGG AGU 73 (2) INFORMATION FOR SEQ ID NO:120: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 50 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:120: CCAGAACACA CCλCTλCλCC λCλCACTACT GTGCGGATλC CCCTATTCAG 50 (2) INFORMATION FOR SEQ ID NO:121: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 76 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:121: GCGAAAGCGA GUCUGλλUλG GGGUλUCCGC λCλGUλGUGU GUGGUGUAGU GGUGUGUUCU 60 GGACCCGAAG CGGAGU 76 (2) INFORMATION FOR SEQ ID NO:122: (i) SEQUENCE CHARλCTERISTICS: (λ) LENGTH: 42 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA . (xi) SEQUENCE DESCRIPTION: SEQ ID NO:122: CCAGAACACG CAACTACλCC CCAAGGGATG CGCCCTATTC AG 42 (2) INFORMATION FOR SEQ ID NO:123: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 68 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: RNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:123: GCGAAAGCGA GUCUGλλUλG GGCGCλUCCU UNGGGGUGUλ GUUGCNUGUU CUGGλCCCGλ 60 AGCGGAGU 68 (2) INFORMATION FOR SEQ ID NO:124: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 17 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:124: AAGGAGGTGA TCCAGCC 17 (2) INFORMATION FOR SEQ ID NO:125: (i) SEQUENCE CHARλCTERISTICS: (λ) LENGTH: 18 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:125: AGAGTTTGAT CCTGGCTC 18 (2) INFORMATION FOR SEQ ID NO:126: (i) SEQUENCE CHARλCTERISTICS: (λ) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:126: TGYACλCλCC GCCCGT 16 (2) INFORMATION FOR SEQ ID NO:127: (i) SEQUENCE CHARACTERISTICS: (λ) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:127: ATTGGCCTTT CλCCCC 16 (2) INFORMATION FOR SEQ ID NO:128: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 18 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:128: GAACTGλλλC ATCTWλGT 18 (2) INFORMATION FOR SEQ ID NO:129: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 15 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:129: TTAGCMTTTC ACCCC 15 (2) INFORMATION FOR SEQ ID NO:130: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: eingle (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:130: CTTAGATGCY TTCAGC 16 (2) INFORMATION FOR SEQ ID NO:131: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 15 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:131: TTGGCMTTTC ACCCC 15 (2) INFORMATION FOR SEQ ID NO:132: (i) SEQUENCE CHARλCTERISTICS: (λ) LENGTH: 16 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: singll (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:132: AGGGRAACAR CCCAGA 16 (2) INFORMATION FOR SEQ ID NO:133: (i) SEQUENCE CHARλCTERISTICS: (λ) LENGTH: 39 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (xi) SEQUENCE DESCRIPTION: SEQ ID NO:133: CCGAATTCGT CGλCλλCCλG GCTTλGCTTC CGGGTTCGG 39

Claims: -108- 1. A substantially inclusive nucleic acid sequence, the substantially inclusive nucleic acid sequence having a nucleotide sequence which is substantially complementary to ribosomal RNA and ribosomal DNA from members of the genus Mycobacteria within the region corresponding approximately to nucleotide sequences of the E. coli ribosomal RNA, the E. coli nucleotide sequences selected from the group consisting of nucleotide sequence numbers: a) 578-609 of the 16S ribosomal RNA genome; b) 606-641 of the 16S ribosomal RNA genome; c) 995-1038 of the 16S ribosomal RNA genome; and d) 1012-1047 of the 16S ribosomal RNA genome. 2. A substantially inclusive nucleic acid sequence of Claim 1, selected from the group consisting of: a) SEQ ID NO: 17; b) SEQ ID NO: 19; c) SEQ ID NO: 32; and d) SEQ ID NO: 33 e) oligonucleotides of a) through d) wherein ϋ is substituted for T; f) complements of a} through e) ; and g) homologs of a) through f) . 3. A partially inclusive nucleic acid sequence, the partially inclusive nucleic acid sequence having a nucleotide sequence which is substantially complementary to ribosomal RNA and ribosomal DNA from members of the genus Mycobacteria within a region corresponding approximately to nucleotide sequences of -109- the E. coli ribosomal RNA, the E. coli nucleotide sequences selected from the group consisting of nucleotide sequence numbers: a) 143-171 of the 16S ribosomal RNA genome; b) 436-481 of the 16S ribosomal RNA genome; c) 446-497 of the 16S ribosomal RNA genome; d) 459-501 of the 16S ribosomal RNA genome; e) 592-629 of the 16S ribosomal RNA genome; f) 254-281 of the 23S ribosomal RNA genome; g) 535-559 of the 23S ribosomal RNA genome; h) 535-565 of the 23S ribosomal RNA genome; i) 640-666 of the 23S ribosomal RNA genome; j) 640-669 of the 23S ribosomal RNA genome; k) 1159-1191 of the 23S ribosomal RNA genome; 1) 1159-1197 of the 23S ribosomal RNA genome; m) 1864-1894 of the 23S ribosomal RNA genome; n) 2126-2160 of the 23S ribosomal RNA genome; o) 923-946 of the 23S ribosomal RNA genome; and p) 281-284 of the 23S ribosomal RNA genome. 4. A partially inclusive oligonucleotide of Claim 3 selected from the group consisting of: -110- 5. A substantially inclusive non-exclusive nucleic acid sequence, the substantially inclusive detection oligonucleotide having a nucleotide sequence which is substantially complementary to ribosomal RNA of the genus Mycobacteria within a region corresponding approximately to nucleotide sequences of the E. coli ribosomal RNA, the E. coli nucleotide sequences selected from the group consisting of nucleotide sequence numbers: 132-164 of the 16S ribosomal RNA genome; 649-680 of the 16S ribosomal RNA genome; and 2126-2160 of the 23S ribosomal RNA genome. 6. A substantially inclusive detection oligonucleotide of Claim 5, selected from the group consisting of: a) SEQ ID NO: 2; b) SEQ ID NO: 26; c) SEQ ID NO: 56; d) SEQ ID NO: 81; -111- e) oligonucleotides of a) through d) wherein U is substituted for T; f) complements of a) through e) ; and g) ho ologs of a) through f) . 7. A partially inclusive non-exclusive oligonucleotide, the partially inclusive detection oligonucleotide having a nucleotide sequence which is substantially complementary to ribosomal RNA of the genus Mycobacteria within a region corresponding approximately to nucleotide sequences of the E. coli ribosomal RNA, the E. coli nucleotide sequences selected from the group consisting of nucleotide sequence numbers: 1121-1147 of the 16S ribosomal RNA genome; 1159-1197 of the 23S ribosomal RNA genome; 2126-2160 of the 23S ribosomal RNA genome; 830-864 of the 23S ribosomal RNA genome; and 281-284 of the 23S ribosomal RNA genome. 8. A partially inclusive non-exclusive oligonucleotide o Claim 7, selected from the group consisting of: a) SEQ ID NO: 40; b) SEQ ID NO: 41; c) SEQ ID NO: 77; d) SEQ ID NO: 79; e) SEQ ID NO: 60; f) SEQ ID NO: 67; g) SEQ ID NO: 102; h) oligonucleotides of a) through g) wherein U is substituted for T; i) complements of a) through h) ; and j) homologs of a) through i) . 9. A substantially inclusive oligonucleotide, the substantially inclusive oligonucleotide having a nucleotide sequence which is substantially complementary to ribosomal RNA of the Mycobacterium tuberculosis complex subgenus within the region corresponding approximately to nucleotide sequences of the E. coli ribosomal RNA, the E. coli nucleotide sequences selected from the group consisting of nucleotide sequence numbers: 535-559 of the 23S ribosomal RNA; and 640-666 of the 23S ribosomal RNA. 10. A substantially inclusive oligonucleotide of Claim 9, selected from the group consisting of: a) SEQ ID NO: 107; b) SEQ ID NO: 115; c) oligonucleotides of a) through b) wherein U is substituted for T; d) complements of a) through c) ; and e) homologs of a) through d) . 11. A substantially inclusive oligonucleotide, the substantially inclusive oligonucleotide having a nucleotide sequence which is substantially complementary to ribosomal RNA of the slow growing class of Mycobacteria within the region corresponding approximately to nucleotide sequences of the E. coli ribosomal RNA, the E. coli nucleotide sequences selected from the group consisting of nucleotide sequence numbers: 1864-1894 of the 23S ribosomal RNA; and 281-284 of the 23S ribosomal RNA. 12. A substantially inclusive oligonucleotide of Claim 11, selected from the group consisting of: a) SEQ ID NO: 47; b) SEQ ID NO: 99; c) oligonucleotides of a) through b) wherein U is substituted for T; 13. -114- X) SEQ ID NO: 58; y) SEQ ID NO: 72; z) SEQ ID NO: 99; aa) SEQ ID NO: 104; ab) oligonucleotides of a) through aa) wherein U is substituted for T; ac) complements of a) through ab) ; and ad) homologs of a) through ac) . 14. A capture/detection oligonucleotide set, the capture oligonucleotide selected from the group of oligonucleotides consisting of: -115- 15. A kit for the identification of bacteria of the genus Mycobacteria, the kit comprising a hybridization vessel, hybridization buffer, wash buffer and an oligonucleotide selected from the group consisting of a) SEQ ID NO: 17; b) SEQ ID NO: 19; c) SEQ ID NO: 32; d) SEQ ID NO: 33; -116- e) oligonucleotides of a) through d) wherein U is substituted for T; 16. -117- z) SEQ ID NO: 99; aa) SEQ ID NO: 104; ab) oligonucleotides of a) through aa) wherein U is substituted for T; ac) complements of a) through ab) ; and ad) homologs of a) through ac) . 17. A kit for the identification of bacteria of the genus Mycobacteria, the kit comprising a hybridization vessel, hybridization buffer, wash buffer and a capture/detection oligonucleotide set wherein; the capture oligonucleotide selected from the group consisting of: 17; 19; : 32; 33; 3; 9; 10; : 11; 18; 91; 94; 96; : 107; 110; 112; 115; 122; 120; 75; 62; 47; 49; -118- w) SEQ ID NO: 51; x) SEQ ID NO: 58; y) SEQ ID NO: 72; z) SEQ ID NO: 99; aa) SEQ ID NO: 104; ab) oligonucleotides of a) through aa) wherein U is substituted for T; ac) complements of a) through ab) ; and ad) homologs of a) through ac) ; and the detection oligo- nucleotide is selected from the group consisting of: a) SEQ ID NO: 2; b) SEQ ID NO: 26; c) SEQ ID NO: 56; d) SEQ ID NO: 81; e) SEQ ID NO: 40; f) SEQ ID NO: 41; g) SEQ ID NO: 77; h) SEQ ID NO: 79; i) SEQ ID NO: 60; j) SEQ ID NO: 67; k) SEQ ID NO: 102; 1) oligonucleotides of a) through k) wherein U is substituted for T; m) complements of a) through 1) ; and n) homologs of a) through m) . 18. A method for detecting the presence of bacteria of the genus mycobacteria comprising the steps of: a) providing a bacterial culture to be tested for the presence of Mycobacteria; b) isolating nucleic acid from the culture; c) fixing the nucleic acid to a solid support; d) contacting the support-bound nucleic acid with a solution containing a probe selected from the group listed in Claim 2; e) washing the support-bound nucleic acid to remove non-specifically bound probe; and f) detecting specifically bound probe.

Inventors: LIU JING, NIETUPSKI RAYMOND MARK, SHAH JYOTSNA SUDHIR, LIU, JING, NIETUPSKI, RAYMOND, MARK, SHAH, JYOTSNA, SUDHIR
Applicants: AMOCO CORP, AMOCO CORPORATION
Application year: 1992
Main classification: C12Q1
IPC codes: C12N15, C12Q1