Patent Publication Number: US-8993335-B2

Title: Methods for detection and analysis of polynucleotide-binding protein interactions

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     This application claims the benefit of U.S. Provisional Application No. 60/447,860, filed Feb. 13, 2003, which is hereby incorporated by reference in its entirety. 
    
    
     STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH 
     Work leading to this invention was performed under grant number GM62958-01 from the National Institutes of Health, grant number DMR-0097611 from the National Science Foundation and grant number N00014-1-1-0239 from the Office of Naval Research. The U.S. Government may have limited rights in this invention. 
    
    
     TECHNICAL FIELD 
     This invention relates to methods, articles and compositions for the detection and analysis of polynucleotides in a sample. 
     BACKGROUND OF THE INVENTION 
     Methods permitting polynucleotide analysis in real time and with high sensitivity are of great scientific and economic interest. 1,2,3  Their applications include medical diagnostics, identification of genetic mutations, gene delivery monitoring and specific genomic techniques. 4  Cationic organic dyes, such as ethidium bromide and thiazole orange, emit when intercalated into the grooves of double strand DNA (dsDNA), and serve as direct DNA hybridization probes, but lack sequence specificity. 5,6  Energy/electron transfer chromophore pairs for strand specific assays exist, but require chemical labeling of two nucleic acids, or dual modification of the same altered strand (for example, molecular beacons). 7,8  Difficulties in labeling two DNA sites result in low yields, high costs and singly labeled impurities, which lower detection sensitivity. 9    
     There is a need in the art for methods of detecting and analyzing particular polynucleotides in a sample, and for compositions and articles of manufacture useful in such methods. 
     SUMMARY OF THE INVENTION 
     Methods, compositions and articles of manufacture for detecting and assaying a target polynucleotide in a sample are provided. 
     In a first embodiment, a sample suspected of containing the target polynucleotide is contacted with a polycationic multichromophore and a sensor polynucleotide binding protein (PBP) that can bind to the target polynucleotide. The sensor PBP comprises a signaling chromophore. Without wishing to be bound by theory, in the presence of target polynucleotide in the sample, the signaling chromophore is believed to be brought into proximity with the cationic multichromophore by utilizing electrostatic interactions with the backbone of the target polynucleotide bound to the sensor PBP (see  FIG. 1 ). The signaling chromophore can then acquire energy from the excited polycationic multichromophore and emit light which can be detected. The target polynucleotide can be analyzed as it occurs in the sample, or can be amplified prior to or in conjunction with analysis. 
     Solutions are provided comprising reagents useful for performing the methods of the invention, as are kits containing such reagents. The methods can be used in multiplex settings where a plurality of different sensor PBPs are used to assay for a plurality of different target polynucleotides. The methods can optionally be performed on a surface, for example using a surface-associated polycationic multichromophore; the surface can be a sensor. The methods can also be provided in homogeneous formats. The methods and articles described herein can be used as alternatives to other techniques for detecting polynucleotides. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Patent and Trademark Office upon request and payment of the necessary fee. 
         FIG. 1  depicts the method of the invention, employing a polycationic polymer as the light-harvesting multichromophore. A sensor PBP (PBP-C*) comprises a signaling chromophore and a binding specificity for the target polynucleotide of interest. Upon contacting the target polynucleotide in a sample, the polycationic multichromophore is brought into proximity with the signaling chromophore by virtue of its own interactions with the target polynucleotide. Excitation of the multichromophore then produces light emission from the signaling chromophore. 
         FIG. 2  depicts the molecular structures of Tat-C* (SEQ ID NO: 1) used in the working examples (where C* is fluorescein), TAR RNA (SEQ ID NO: 2) and dTAR RNA (SEQ ID NO: 3). 
         FIG. 3  shows the optical spectra of polymer 1 and Tat-C*. Excitations were done at 380 nm and 480 nm for polymer 1 and Tat-C*, respectively. Assay conditions are TRIS EDTA buffer solution (10 mM) and pH=7.4. 
         FIG. 4  shows the optical spectra of oligomer 1 and Tat-C*. Excitations were done at 365 nm and 480 nm for oligomer 1 and Tat-C*, respectively. Assay conditions are TRIS EDTA buffer solution (10 mM) and pH=7.4. 
         FIG. 5  shows the optical spectra of oligomer 2 and Tat-C*. Excitations were done at 375 nm and 480 nm for oligomer 2 and Tat-C*, respectively. Assay conditions are TRIS EDTA buffer solution (10 mM) and pH=7.4. 
         FIG. 6  shows the emission spectra of Tat-C* in the presence of TAR RNA and dTAR RNA by excitation of oligomer 1 at 365 nm. Conditions are in TRIS EDTA buffer solution (10 mM) and pH=7.4. The spectra are normalized with respect to the emission of oligomer 1. 
         FIG. 7  shows the emission spectra of Tat-C* in the presence of TAR RNA and dTAR RNA by excitation of oligomer 2 at 375 nm. Conditions are in TRIS EDTA buffer solution (10 mM) and pH=7.4. The spectra are normalized with respect to the emission of oligomer 2. 
         FIG. 8  shows the emission spectra of Tat-C* in the presence of TAR RNA and dTAR RNA by excitation of polymer 1 at 380 nm. Conditions are in TRIS EDTA buffer solution (10 mM) and pH=7.4. The spectra are normalized with respect to the emission of polymer 1. 
         FIG. 9  shows the emission spectra of SH3-C* and Tat-C* in the presence of TAR RNA by excitation of oligomer 1 at 365 nm. Conditions are in TRIS EDTA buffer solution (10 mM) and pH=7.4. The spectra are normalized with respect to the emission of oligomer 1. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     Present technologies for DNA and RNA sensors (including “gene-chips” and “DNA-chips”) depend on the covalent attachment of fluorescent tags (lumophores ) to single strands of DNA. Most of these sensors are forced to rely on the labeling of the analyte sample, with unavoidable problems resulting from variations in the efficiency of the labeling reaction from sample to sample, requiring complex cross-calibrations. Other systems rely on the “molecular beacon” approach, requiring the attachment of lumophores and quenchers to precisely engineered sequences. 
     A method for polynucleotide analysis is provided comprising contacting a sample with at least two components; (a) a light harvesting, luminescent multichromophore system such as, for example, a conjugated polymer, semiconductor quantum dot or dendritic structure that is water soluble, and (b) a sensor PBP conjugated to a luminescent signaling chromophore (“PBP-C*”). The emission of a wavelength of light characteristic of the signaling chromophore-C* upon excitation of the multichromophore indicates the presence in solution of the target polynucleotide. By using multiple different sensor PBPs, each with a different base sequence and a different signaling chromophore (PBP1-C1*, PBP2-C2*, PBP3-C3*, PBP4-C4*, etc), multiple different polynucleotides can be independently detected and assayed. 
     The light harvesting chromophore and the signaling chromophore (C*) are chosen so that the absorption bands of the two chromophores have minimal overlap and so that the luminescent emission spectra of the two species are at different wavelengths. When prepared in aqueous solution, the light harvesting luminescent multichromophore system is positively charged, or cationic, and is preferably polycationic (for example a polycationic conjugated polyelectrolyte). The sensor PBP and multichromophore are chosen such that there is minimal interaction between them in the absence of target. Upon addition of a target polynucleotide that can bind to the sensor PBP, the target polynucleotide forms a complex with the sensor PBP. Because the target polynucleotide is negatively charged, the sensor PBP is brought into association with the polycationic multichromophore, permitting energy transfer from the polycationic multichromophore to the signaling chromophore, for example via the Förster energy transfer mechanism. When a polynucleotide that does not bind to the sensor PBP is added, complexation between the multichromophore and the sensor PBP does not occur. Because the average distance between the polycationic multichromophore and the signaling chromophore is too large for effective energy transfer in the absence of such complex formation, there is little or no emission from the signaling chromophore. The overall scheme serves to detect the presence of the target polynucleotide in the test solution. 
     In addition to the described method, the invention provides a predominantly aqueous solution comprising at least two components; (a) a cationic multichromophore, and (b) a “sensor PBP” (PBP-C*) comprising a polynucleotide binding protein conjugated to a signaling chromophore. 
     As demonstrated in the Examples, the optical amplification provided by a water soluble multichromophore such as a conjugated polymer can be used to detect polynucleotide binding to a PBP sensor. The amplification can be enhanced by using higher molecular weight water soluble conjugated polymers or other structures as the polycationic multichromophore as described herein. The invention can be provided in a homogeneous format that utilizes the ease of fluorescence detection methods. The invention can be used to detect amplified target polynucleotides or, because of the large signal amplification, as a stand alone assay, without need for polynucleotide amplification. 
     Unique advantages of the invention over present gene-chip technology thus include circumvention of the requirement to first label each sample to be analyzed by covalent coupling of lumophores or chromophores to the polynucleotides contained in or derived from the sample prior to analysis. Those coupling methods have inherent difficulties in reproducibility of coupling efficiency and result in the need for cross-calibration from sample to sample. 
     The inventions described herein are useful for any assay in which a sample can be interrogated regarding a target polynucleotide. Typical assays involve determining the presence of the target polynucleotide in the sample or its relative amount, or the assays may be quantitative or semi-quantitative. 
     The methods of the invention can all be performed in multiplex formats. A plurality of different sensor PBPs can be used to detect corresponding different target polynucleotides in a sample through the use of different signaling chromophores conjugated to the respective sensor PBPs. Multiplex methods are provided employing 2, 3, 4, 5, 10, 15, 20, 25, 50, 100, 200, 400 or more different sensor PBPs which can be used simultaneously to assay for corresponding different target polynucleotides. 
     The methods can be performed on a substrate, as well as in solution, although the solution format is expected to be more rapid due to diffusion issues. Thus the assay can be performed, for example, in an array format on a substrate, which can be a sensor. This can be achieved by anchoring or otherwise incorporating an assay component onto the substrate, for example the sensor PBP, the polycationic multichromophore, or both. These substrates may be surfaces of glass, silicon, paper, plastic, or the surfaces of optoelectronic semiconductors (such as, but not confined to, indium-doped gallium nitride or polymeric polyanilines, etc.) employed as optoelectronic transducers. The location of a given sensor PBP may be known or determinable in an array format, and the array format may be microaddressable or nanoaddressable. 
     Before the present invention is described in further detail, it is to be understood that this invention is not limited to the particular methodology, devices, solutions or apparatuses described, as such methods, devices, solutions or apparatuses can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention. 
     Use of the singular forms “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, reference to “a target polynucleotide” includes a plurality of target polynucleotides, reference to “a signaling chromophore” includes a plurality of such chromophores, reference to “a sensor PBP” includes a plurality of sensor PBPs, and the like. Additionally, use of specific plural references, such as “two,” “three,” etc., read on larger numbers of the same subject unless the context clearly dictates otherwise. 
     Terms such as “connected,” “attached,” and “linked” are used interchangeably herein and encompass direct as well as indirect connection, attachment, linkage or conjugation unless the context clearly dictates otherwise. Where a range of values is recited, it is to be understood that each intervening integer value, and each fraction thereof, between the recited upper and lower limits of that range is also specifically disclosed, along with each subrange between such values. The upper and lower limits of any range can independently be included in or excluded from the range, and each range where either, neither or both limits are included is also encompassed within the invention. Where a value being discussed has inherent limits, for example where a component can be present at a concentration of from 0 to 100%, or where the pH of an aqueous solution can range from 1 to 14, those inherent limits are specifically disclosed. Where a value is explicitly recited, it is to be understood that values which are about the same quantity or amount as the recited value are also within the scope of the invention, as are ranges based thereon. Where a combination is disclosed, each subcombination of the elements of that combination is also specifically disclosed and is within the scope of the invention. Conversely, where different elements or groups of elements are disclosed, combinations thereof are also disclosed. Where any element of an invention is disclosed as having a plurality of alternatives, examples of that invention in which each alternative is excluded singly or in any combination with the other alternatives are also hereby disclosed; more than one element of an invention can have such exclusions, and all combinations of elements having such exclusions are hereby disclosed. 
     Unless defined otherwise or the context clearly dictates otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, the preferred methods and materials are now described. 
     All publications mentioned herein are for the purpose of describing the particular materials and methodologies for which the reference was cited. The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention. 
     Definitions 
     In describing the present invention, the following terms will be employed, and are intended to be defined as indicated below. 
     The terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and “nucleic acid molecule” are used interchangeably herein to refer to a polymeric form of nucleotides of any length, and may comprise ribonucleotides, deoxyribonucleotides, analogs thereof, or mixtures thereof. These terms refer only to the primary structure of the molecule. Thus, the terms includes triple-, double- and single-stranded deoxyribonucleic acid (“DNA”), as well as triple-, double- and single-stranded ribonucleic acid (“RNA”). It also includes modified, for example by alkylation, and/or by capping, and unmodified forms of the polynucleotide. 
     Whether modified or unmodified, the target nucleotide should have a polyanionic backbone, preferably a sugar-phosphate backbone, of sufficient negative charge to electrostatically interact with the polycationic multichromophore in the methods described herein, although other forces may additionally participate in the interaction. The sensor PBP is a polynucleotide binding protein which minimally interacts with the multichromophore in the absence of target. Suitable binding conditions for a given assay format can be determined by one of skill in the art; nonlimiting parameters which may be adjusted include concentrations of assay components, pH, salts used and their concentration, ionic strength, temperature, etc. 
     More particularly, the terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and “nucleic acid molecule” include polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), including tRNA, rRNA, hRNA, and mRNA, whether spliced or unspliced, any other type of polynucleotide which is an N- or C-glycoside of a purine or pyrimidine base, and other polymers containing a phosphate or other polyanionic backbone, and other synthetic sequence-specific nucleic acid polymers providing that the polymers contain nucleobases in a configuration which allows for base pairing and base stacking, such as is found in DNA and RNA. There is no intended distinction in length between the terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and “nucleic acid molecule,” and these terms are used interchangeably herein. These terms refer only to the primary structure of the molecule. Thus, these terms include, for example, 3′-deoxy-2′,5′-DNA, oligodeoxyribonucleotide N3′P5′ phosphoramidates, 2′-O-alkyl-substituted RNA, double- and single-stranded DNA, as well as double- and single-stranded RNA, and hybrids thereof including for example hybrids between DNA and RNA, and also include known types of modifications, for example, labels, alkylation, “caps,” substitution of one or more of the nucleotides with an analog, internucleotide modifications such as, for example, those with negatively charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), those containing pendant moieties, such as, for example, proteins (including enzymes (e.g. nucleases), toxins, antibodies, signal peptides, poly-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelates (of, e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotide or oligonucleotide. 
     It will be appreciated that, as used herein, the terms “nucleoside” and “nucleotide” will include those moieties which contain not only the known purine and pyrimidine bases, but also other heterocyclic bases which have been modified. Such modifications include methylated purines or pyrimidines, acylated purines or pyrimidines, or other heterocycles. Modified nucleosides or nucleotides can also include modifications on the sugar moiety, e.g., wherein one or more of the hydroxyl groups are replaced with halogen, aliphatic groups, or are functionalized as ethers, amines, or the like. The term “nucleotidic unit” is intended to encompass nucleosides and nucleotides. 
     Furthermore, modifications to nucleotidic units include rearranging, appending, substituting for or otherwise altering functional groups on the purine or pyrimidine base which form hydrogen bonds to a respective complementary pyrimidine or purine. The resultant modified nucleotidic unit optionally may form a base pair with other such modified nucleotidic units but not with A, T, C, G or U. Abasic sites may be incorporated which do not prevent the function of the polynucleotide; preferably the polynucleotide does not comprise abasic sites. Some or all of the residues in the polynucleotide can optionally be modified in one or more ways. 
     Standard A-T and G-C base pairs form under conditions which allow the formation of hydrogen bonds between the N3-H and C4-oxy of thymidine and the N1 and C6-NH2, respectively, of adenosine and between the C2-oxy, N3 and C4-NH2, of cytidine and the C2-NH2, N′-H and C6-oxy, respectively, of guanosine. Thus, for example, guanosine (2-amino-6-oxy-9-β-D-ribofuranosyl-purine) may be modified to form isoguanosine (2-oxy-6-amino-9-β-D-ribofuranosyl-purine). Such modification results in a nucleoside base which will no longer effectively form a standard base pair with cytosine. However, modification of cytosine (1-β-D-ribofuranosyl-2-oxy-4-amino-pyrimidine) to form isocytosine (1-β-D-ribofuranosyl-2-amino-4-oxy-pyrimidine) results in a modified nucleotide which will not effectively base pair with guanosine but will form a base pair with isoguanosine. Isocytosine is available from Sigma Chemical Co. (St. Louis, Mo.); isocytidine may be prepared by the method described by Switzer et al. (1993) Biochemistry 32:10489-10496 and references cited therein; 2′-deoxy-5-methyl-isocytidine may be prepared by the method of Tor et al. (1993) J. Am. Chem. Soc. 115:4461-4467 and references cited therein; and isoguanine nucleotides may be prepared using the method described by Switzer et al. (1993), supra, and Mantsch et al. (1993) Biochem. 14:5593-5601, or by the method described in U.S. Pat. No. 5,780,610 to Collins et al. Other nonnatural base pairs may be synthesized by the method described in Piccirilli et al. (1990) Nature 343:33-37 for the synthesis of 2,6-diaminopyrimidine and its complement (1-methylpyrazolo-[4,3]pyrimidine-5,7-(4H,6H)-dione). Other such modified nucleotidic units which form unique base pairs are known, such as those described in Leach et al. (1992) J. Am. Chem. Soc. 114:3675-3683 and Switzer et al., supra. 
     “Complementary” or “substantially complementary” refers to the ability to hybridize or base pair between nucleotides or nucleic acids, such as, for instance, between a sensor polynucleotide binding protein and a target polynucleotide. Complementary nucleotides are, generally, A and T (or A and U), or C and G. Two single-stranded polynucleotides are said to be substantially complementary when the bases of one strand, optimally aligned and compared and with appropriate insertions or deletions, pair with at least about 80% of the bases of the other strand, usually at least about 90% to 95%, and more preferably from about 98 to 100%. 
     Alternatively, substantial complementarity exists when a polynucleotide or PNA will hybridize under selective hybridization conditions to its complement. Typically, selective hybridization will occur when there is at least about 65% complementary over a stretch of at least 14 to 25 bases, preferably at least about 75%, more preferably at least about 90% complementary. See, M. Kanehisa Nucleic Acids Res. 12:203 (1984). 
     “Preferential binding” or “preferential hybridization” refers to the increased propensity of one member of a binding pair to bind to its binding partner as compared to another component of the sample. 
     Hybridization conditions will typically include salt concentrations of less than about 1M, more usually less than about 500 mM and preferably less than about 200 mM. In the case of hybridization between a peptide nucleic acid and a polynucleotide, the hybridization can be done in solutions containing little or no salt. Hybridization temperatures can be as low as 5° C., but are typically greater than 22° C., more typically greater than about 30° C., and preferably in excess of about 37° C. Longer fragments may require higher hybridization temperatures for specific hybridization. Other factors may affect the stringency of hybridization, including base composition and length of the complementary strands, presence of organic solvents and extent of base mismatching, and the combination of parameters used is more important than the absolute measure of any one alone. Other hybridization conditions which may be controlled include buffer type and concentration, solution pH, presence and concentration of blocking reagents to decrease background binding such as repeat sequences or blocking protein solutions, detergent type(s) and concentrations, molecules such as polymers which increase the relative concentration of the polynucleotides, metal ion(s) and their concentration(s), chelator(s) and their concentrations, and other conditions known in the art. 
     “Multiplexing” herein refers to an assay or other analytical method in which multiple analytes can be assayed simultaneously. 
     “Optional” or “optionally” means that the subsequently described event or circumstance may or may not occur, and that the description includes instances where the event or circumstance occurs and instances in which it does not. 
     A polynucleotide sensor is provided comprising two components; (a) a light harvesting, luminescent water-soluble polycationic multichromophore, such as a conjugated polymer, oligomer or dendritic molecule; (b) a sensor polynucleotide binding protein or a binding fragment thereof labeled with a luminescent signaling chromophore (PBP-C*). The binding of PBP-C* to a target polynucleotide results in the formation of a complex of sufficient negative charge to interact with the polycationic multichromophore. Electrostatic (and hydrophobic) interactions with the cationic light harvesting molecule bring the signaling chromophore (C*) in close proximity to the light harvesting molecule. Excitation of the light harvesting molecule at the appropriate frequency results in energy transfer to the signaling chromophore. Emission from C* confirms binding between PBP-C* and the target polynucleotide. If the sensor-target interactions are specific, then C* emission corresponds to the presence of a specific DNA or RNA sequence in solution. 
     A schematic of the sensor operation is shown in  FIG. 1 . In aqueous solution, there is minimal interaction between the cationic light harvesting molecules (shown in black) and the probe PBP-C* (shown in red). The PBP and the light harvesting molecule are chosen so that they do not interact significantly in the absence of target. Upon addition of a sample containing polynucleotides, two situations can take place. Situation A shows the results of the signaling PBP-C* binding to the target polynucleotide (in blue). Under these conditions the negatively charged DNA-PBP-C* or RNA-PBP-C* complex associates by multiple electrostatic interactions with the positively charged light harvesting conjugated molecules. The ensuing close proximity results in energy transfer from the light harvesting conjugated molecules to the signaling chromophore of PBP-C*, for example via the Förster energy transfer mechanism. 10,11  The emission of light with wavelength characteristic of signaling C* indicates the recognition between the protein and RNA or DNA. When a polynucleotide is present which does not interact with the PBP-C* (shown in green), the PBP-C* is not adjacent to a negatively charged macromolecule and the distance between the cationic light harvesting molecule and C* is too large for energy transfer (situation B). 
     As a specific working example of the sensor we have used the following two components: (a) a light harvesting, luminescent water-soluble conjugated molecules, such as conjugated polymers and conjugated oligomers; (b) a 16-residue peptide labeled with a luminescent signaling chromophore at the N-terminus (Tat-C*). The light harvesting molecules and the signaling chromophore (C*) are chosen so that the luminescent emission spectra of the two species are at different wavelengths and so that the absorption of C* overlaps the emission of the light harvesting species. Upon addition of TAR RNA, the signaling peptide Tat-C* specifically binds with TAR RNA. The negatively charged TAR RNA/Tat-C* complex then associates with the positively charged light harvesting conjugated molecules (situation A). The ensuing close proximity results in energy transfer from the light harvesting conjugated molecules to the signaling chromophore of Tat-C*. The emission of light with wavelength characteristic of signaling Tat-C* indicates the presence of HIV TAR RNA. When an RNA which does not interact with Tat is used, the RNA and the cationic molecule interact, however there is no energy transfer to C*. 
     Developing reliable technologies for detecting human immunodeficiency virus type 1 (HIV-1) is of significant clinical interest. 12,13,14,15  The traditional detection technologies for HIV infection is an ELISA test for the HIV antibody, in which viral antigens are adsorbed onto a solid phase. 22,16  A western blot assay coupling electrophoretic separation with radioisotopic detection is also common for this task. 22,17  The drawbacks of these technologies include complex instrumentation, the time required for the assay and complications caused by the short half-life and hazardous nature of radiolabeled probes. Simple, high sensitive, specific and real-time methods are highly desired for detecting HIV virus. 
     The transactivation responsive element RNA sequence (TAR) of HIV is expressed at high levels by virally infected cells. 18  The ability to conveniently monitor TAR RNA in real-time as described herein provides a viable method for the rapid detection for the presence of the HIV virus. Extensive studies demonstrate that the transactivator protein (Tat) binds the TAR RNA with great specificity and approximately 1 nM affinity, to form a stable, well-defined complexes. 19,20,21  The specific binding of Tat to TAR RNA thus triggers signal transduction for the clinically relevant real-time detection of HIV using the methods described herein. 
     The working examples demonstrate a novel HIV bio-optical sensor which couples the specificity of Tat peptide binding and folding to TAR RNA with the large optical amplification of conjugated polymers and oligomers. The HIV RNA sensor comprises two components: (a) light harvesting, luminescent water-soluble conjugated molecules, such as conjugated polymers and conjugated oligomers; (b) a 16-residue peptide being labeled with a luminescent signaling chromophore at N-terminus (Tat-C*). The binding of the probe peptide and luminescent conjugated molecules to the TAR RNA results in the formation of a complex and introduces energy transfer from conjugated molecules to Tat-C*. The emission of light with wavelength characteristic of the signaling Tat-C* indicates the presence of HIV-1 TAR RNA. 
     As demonstrated in the Examples, the optical amplification of water soluble conjugated molecules can be used to detect the presence of HIV TAR RNA. This invention can be used in a homogeneous format that utilizes the ease of fluorescence detection methods and the specific binding behavior found in protein-polynucleotide interactions such as Tat-TAR RNA interactions and provides the ability to detect TAR RNA in real time. The structures of Tat peptide, TAR RNA and dTAR RNA used in the working examples are shown in  FIG. 2  (with amino acids shown in single letter code for Tat-C*). 
     As shown by Förster 22 , dipole-dipole interactions lead to long-range resonance energy transfer (FRET) from a donor chromophore to an acceptor chromophore. The energy transfer efficiency (E) is proportional to 1/r 6 , where r is the donor-acceptor distance, and the overlap integral, as shown in Equation 1. 
                     E   ∝       1     r   6       ⁢           ·           ⁢         ∞                       o     ⁢         F   D     ⁡     (   λ   )       ⁢       ɛ   A     ⁡     (   λ   )       ⁢     λ   4     ⁢     ⅆ   λ                 0             ⁢                   (   1   )               
The distance requirement for energy transfer in the methods described herein will be controlled by the interactions in  FIG. 1 . The overlap integral expresses the spectral overlap between the emission of the donor and the absorption of the acceptor 23 . As exemplified herein, the components of the sensor can be chosen so that their optical properties meet this requirement.
 
The Sample
 
     The portion of the sample comprising or suspected of comprising the target polynucleotide can be any source of biological material which comprises polynucleotides that can be obtained from a living organism directly or indirectly, including cells, tissue or fluid, and the deposits left by that organism, including viruses, mycoplasma, and fossils. The sample may comprise a target polynucleotide prepared through synthetic means, in whole or in part. Typically, the sample is obtained as or dispersed in a predominantly aqueous medium. Nonlimiting examples of the sample include blood, urine, semen, milk, sputum, mucus, a buccal swab, a vaginal swab, a rectal swab, an aspirate, a needle biopsy, a section of tissue obtained for example by surgery or autopsy, plasma, serum, spinal fluid, lymph fluid, the external secretions of the skin, respiratory, intestinal, and genitourinary tracts, tears, saliva, tumors, organs, samples of in vitro cell culture constituents (including but not limited to conditioned medium resulting from the growth of cells in cell culture medium, putatively virally infected cells, recombinant cells, and cell components), and a recombinant library comprising polynucleotide sequences. 
     The sample can be a positive control sample which is known to contain the target polynucleotide or a surrogate therefor. A negative control sample can also be used which, although not expected to contain the target polynucleotide, is suspected of containing it (via contamination of one or more of the reagents) or another component capable of producing a false positive, and is tested in order to confirm the lack of contamination by the target polynucleotide of the reagents used in a given assay, as well as to determine whether a given set of assay conditions produces false positives (a positive signal even in the absence of target polynucleotide in the sample). 
     The sample can be diluted, dissolved, suspended, extracted or otherwise treated to solubilize and/or purify any target polynucleotide present or to render it accessible to reagents which are used in an amplification scheme or to detection reagents. Where the sample contains cells, the cells can be lysed or permeabilized to release the polynucleotides within the cells. One step permeabilization buffers can be used to lyse cells which allow further steps to be performed directly after lysis, for example a polymerase chain reaction. 
     The Target Polynucleotide and Amplification Products Produced Therefrom 
     The target polynucleotide can be single-stranded, double-stranded, or higher order, and can be linear or circular. Exemplary single-stranded target polynucleotides include mRNA, rRNA, tRNA, hnRNA, ssRNA or ssDNA viral genomes, although these polynucleotides may contain internally complementary sequences and significant secondary structure. Exemplary double-stranded target polynucleotides include genomic DNA, mitochondrial DNA, chloroplast DNA, dsRNA or dsDNA viral genomes, plasmids, phage, and viroids. The target polynucleotide can be prepared synthetically or purified from a biological source. The target polynucleotide may be purified to remove or diminish one or more undesired components of the sample or to concentrate the target polynucleotide. Conversely, where the target polynucleotide is too concentrated for the particular assay, the target polynucleotide may be diluted. 
     Following sample collection and optional nucleic acid extraction, the nucleic acid portion of the sample comprising the target polynucleotide can be subjected to one or more preparative reactions. These preparative reactions can include in vitro transcription (IVT), labeling, fragmentation, amplification and other reactions. mRNA can first be treated with reverse transcriptase and a primer to create cDNA prior to detection and/or amplification; this can be done in vitro with purified mRNA or in situ, e.g. in cells or tissues affixed to a slide. Nucleic acid amplification increases the copy number of sequences of interest such as the target polynucleotide. A variety of amplification methods are suitable for use, including the polymerase chain reaction method (PCR), the ligase chain reaction (LCR), self sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), the use of Q Beta replicase, reverse transcription, nick translation, and the like. 
     Where the target polynucleotide is single-stranded and is to be amplified, the first cycle of amplification forms a primer extension product complementary to the target polynucleotide. If the target polynucleotide is single-stranded RNA, a polymerase with reverse transcriptase activity is used in the first amplification to reverse transcribe the RNA to DNA, and additional amplification cycles can be performed to copy the primer extension products. The primers for a PCR must, of course, be designed to hybridize to regions in their corresponding template that will produce an amplifiable segment; thus, each primer must hybridize so that its 3′ nucleotide is paired to a nucleotide in its complementary template strand that is located 3′ from the 3′ nucleotide of the primer used to replicate that complementary template strand in the PCR. 
     The target polynucleotide is typically amplified by contacting one or more strands of the target polynucleotide with a primer and a polymerase having suitable activity to extend the primer and copy the target polynucleotide to produce a full-length complementary polynucleotide or a smaller portion thereof. Any enzyme having a polymerase activity which can copy the target polynucleotide can be used, including DNA polymerases, RNA polymerases, reverse transcriptases, enzymes having more than one type of polymerase activity, and the enzyme can be thermolabile or thermostable. Mixtures of enzymes can also be used. Exemplary enzymes include: DNA polymerases such as DNA Polymerase I (“Pol I”), the Klenow fragment of Pol I, T4, T7, Sequenase® T7, Sequenase® Version 2.0 T7, Tub, Taq, Tth, Pfx, Pfu, Tsp, Tfl, Tli and  Pyrococcus  sp 
     GB-D DNA polymerases; RNA-polymerases such as  E. coli , SP6, T3 and T7 RNA polymerases; and reverse transcriptases such as AMV, M-MuLV, MMLV, RNAse H-MMLV (SuperScript® polymerase), SuperScript® II polymerase, ThermoScript® polymerase, HIV-1, and RAV2 reverse transcriptases. All of these enzymes are commercially available. Exemplary polymerases with multiple specificities include RAV2 and Tli(exo-)polymerases. Exemplary thermostable polymerases include Tub, Tag, Tth, Pfx, Pfu, Tsp, Tfl, Tli and  Pyroccoccus  sp. GB-D DNA polymerases. 
     Suitable reaction conditions are chosen to permit amplification of the target polynucleotide, including pH, buffer, ionic strength, presence and concentration of one or more salts, presence and concentration of reactants and cofactors such as nucleotides and magnesium and/or other metal ions (e.g., manganese), optional cosolvents, temperature, thermal cycling profile for amplification schemes comprising a polymerase chain reaction, and may depend in part on the polymerase being used as well as the nature of the sample. Cosolvents include formamide (typically at from about 2 to about 10%), glycerol (typically at from about 5 to about 10%), and DMSO (typically at from about 0.9 to about 10%). Techniques may be used in the amplification scheme in order to minimize the production of false positives or artifacts produced during amplification. These include “touchdown” PCR, hot-start techniques, use of nested primers, or designing PCR primers so that they form stem-loop structures in the event of primer-dimer formation and thus are not amplified. Techniques to accelerate PCR can be used, for example centrifugal PCR, which allows for greater convection within the sample, and comprising infrared heating steps for rapid heating and cooling of the sample. One or more cycles of amplification can be performed. An excess of one primer can be used to produce an excess of one primer extension product during PCR; preferably, the primer extension product produced in excess is the amplification product to be detected. A plurality of different primers may be used to amplify different target polynucleotides or different regions of a particular target polynucleotide within the sample. 
     Amplified target polynucleotides may be subjected to post amplification treatments. For example, in some cases, it may be desirable to fragment the target polynucleotide prior to hybridization in order to provide segments which are more readily accessible. Fragmentation of the nucleic acids can be carried out by any method producing fragments of a size useful in the assay being performed; suitable physical, chemical and enzymatic methods are known in the art. 
     An amplification reaction can be performed under conditions which allow the sensor PBP to bind to the amplification product during at least part of an amplification cycle. When the assay is performed in this manner, real-time detection of this hybridization event can take place by monitoring for a change in light emission from the signaling chromophore that occurs upon such hybridization during the amplification scheme. 
     The Polycationic Multichromophore 
     Light harvesting multichromophore systems have been demonstrated to be efficient light absorbers by virtue of the multiple chromophores they comprise. Examples include, but are not limited to, conjugated polymers, aggregates of conjugated molecules, luminescent dyes attached via side chains to saturated polymers, semiconductor quantum dots and dendritic structures. For example, each repeat unit on a conjugated polymer can be considered as a contributing chromophore, quantum dots are made up of many atoms, a saturated polymer can be functionalized with many luminescent dye molecules on side chains, and dendrimers can be synthesized containing many covalently bonded individual chromophores. Attachment of chromophore assemblies onto solid supports, such as polymer beads or surfaces, can also be used for light harvesting. 
     Light harvesting multichromophore systems can efficiently transfer energy to nearby luminescent species (e.g., “signaling chromophores”). Mechanisms for energy transfer include, for example, resonant energy transfer (Förster (or fluorescence) resonance energy transfer, FRET), quantum charge exchange (Dexter energy transfer) and the like. Typically, however, these energy transfer mechanisms are relatively short range; that is, close proximity of the light harvesting multichromophore system to the signaling chromophore is required for efficient energy transfer. Under conditions for efficient energy transfer, amplification of the emission from the signaling chromophore occurs when the overall absorptive ability of the multichromophore exceeds that of the signaling chromophore, for example when the number of individual chromophores in the light harvesting multichromophore system is large; that is, the emission from the signaling chromophore is more intense when the incident light (the “pump light”) is at a wavelength which is absorbed by the light harvesting multichromophore system than when the signaling chromophore is directly excited by the pump light. 
     Conjugated polymers (CPs) are characterized by a delocalized electronic structure and can be used as highly responsive optical reporters for chemical and biological targets. 24,25  Because the effective conjugation length is substantially shorter than the length of the polymer chain, the backbone contains a large number of conjugated segments in close proximity. Thus, conjugated polymers are efficient for light harvesting and enable optical amplification via Förster energy transfer. 26  Water-soluble CPs show exceptional fluorescence quenching efficiencies in the presence of oppositely charged acceptors and are of particular interest for transduction of biological recognition events. 27,28    
     Spontaneous interpolymer complexation between cationic polyelectrolytes and DNA has been described and is largely the result of cooperative electrostatic forces. 29,30,31  Hydrophobic interactions between aromatic polymer units and DNA bases were also recently recognized. 32,33  The free energy of polyelectrolyte/DNA interactions is controlled by the structure of the participating species used in conjunction with solution variables such as pH, ionic strength, and temperature. 34  The strength and specificity of these interactions has recently been coordinated to recognize the tertiary structure of plasmid DNA. 35    
     The multichromophores used in the present invention are polycationic so that they can interact with a target polynucleotide electrostatically and thereby bring a signaling chromophore on an uncharged sensor PBP into energy-receiving proximity by virtue of binding between the sensor PBP and the target polynucleotide. Any polycationic multichromophore that can absorb light and transfer energy to a signaling chromophore on a sensor PBP can be used in the methods described. Exemplary multichromophores which can be used include conjugated polymers, saturated polymers or dendrimers incorporating multiple chromophores in any viable manner, and semiconductor nanocrystals (SCNCs). The conjugated polymers, saturated polymers and dendrimers can be prepared to incorporate multiple cationic species or can be derivatized to render them polycationic after synthesis; semiconductor nanocrystals can be rendered polycationic by addition of cationic species to their surface. 
     In a preferred embodiment, a conjugated polymer is used as the polycationic multichromophore. 
     Exemplary polycationic multichromophores are shown below, where the cationic water soluble conjugated molecules are polymer 1 (where n=2-100,000), oligomer 1 and oligomer 2. This specific molecular structure is not critical; any water soluble cationic light harvesting molecules can be used. 
     
       
         
         
             
             
         
       
     
     Molecular structure of water-soluble, cationic, luminescent conjugated molecules. 
     Another example is shown in polymer 3 where the cationic water soluble conjugated polymer is poly((9,9-bis(6′-N,N,N-trimethylammonium)-hexyl)-fluorene phenylene) with iodide counteranions (denoted in the following as polymer 3). 36  The particular size of this polymer is not critical, so long as it is able to absorb light and transfer energy to signaling chromophores brought into proximity. Typical values of “n” fall within the range of two to about 100,000. This specific molecular structure is not critical; any water soluble cationic conjugated polymer with relatively high luminescence quantum efficiency can be used. 
     
       
         
         
             
             
         
       
     
     Water soluble conjugated oligomers can also be used as the polycationic multichromophore. An example of such a water soluble, cationic, luminescent conjugated oligomer with iodide counterions is shown below (denoted herein as oligomer 4): 
     
       
         
         
             
             
         
       
     
     Although the smaller oligomer 4 does not display the large signal amplification characteristic of a high molecular weight polymer, such smaller molecules are useful to deconvolute structure property relationships, which are difficult to determine with the inherent polydispersity and batch-to-batch variations found in polymers. Further, in aqueous media oligomers such as 4 are more soluble than their polymeric counterparts, and hydrophobic interactions are expected to be less important for 4 than for polymer structures. Assemblies of oligomers may thus be desired for specific applications. 
     The Sensor PBP 
     A sensor PBP is provided that binds to the target polynucleotide to be assayed. Chemical methods for attaching the signaling chromophore to the sensor PBP are known. Specific sensor PBP structures, including structures conjugated to chromophores, can be custom-made using commercial sources or chemically synthesized. 
     Any protein which can bind to a target polynucleotide of interest can be employed in the methods disclosed. Non-limiting examples of PBPs include DNA-binding proteins including transcription factors, splicing-factors, poly(A) binding proteins, chromatin components, viral proteins, proteins which detect viral infection, replication factors, and proteins involved in mitotic and/or meiotic cell division. RNA-protein interactions mediate important cellular processes including transcription, posttranscriptional modifications, RNA splicing, and translation 37,38,39,40 . The replication cycle of many pathogenic viruses, such as the human immunodeficiency virus type 1 (HIV-1) 41 , picornaviruses 42  and influenza viruses 43 , rely on specific RNA-protein interactions. The specificity of such interactions can be used as the basis for sequence specific sensors for utility in medical diagnostics and genomic studies. Exemplary polynucleotide binding proteins include zinc-finger proteins, homeodomain proteins, winged-helix (forkhead) proteins, leucine-zipper proteins, helix-loop-helix proteins, helix-turn-helix proteins, and histone-like proteins. 
     The PBPs may be isolated from a cell source, or may be produced in vitro, for example through in vitro transcription/translation methods or through completely synthetic methods. The PBPs can be naturally occurring proteins, mutants of naturally occurring proteins, randomly produced proteins produced, for example, by molecular evolution methods, or suspected polynucleotide binding proteins of unknown binding specificity. 
     One reason that monitoring RNA/protein interactions can be significant is that protein structures can serve as antibiotics that inhibit RNA function. One example is the interaction of the regulatory protein, Rev, with the Rev Responsive Element (RRE, a subdomain of the viral RNA) which is central to the human immunodeficiency virus (HIV) replication. Rev, which contains 116 amino acids, facilitates expression by inducing the accumulation of incompletely spliced viral mRNA transcripts in the cytoplasm. Protein/DNA binding and interactions are important because these events regulate various functions and metabolism of DNA. Proteins that exhibit this property are called sequence-specific DNA binding proteins. They mediate DNA replication, recombination, strand scission and transcription. 
     The Tat peptide used in the working examples is easily synthesized by the solid phase method and can be purified by HPLC and characterized by MALDI-TOF mass spectrum and amino acid analysis. The chemical methods for attaching the signaling chromophore to the peptide to form the signaling sensor PBP-C* are known. 44  A specific example is the signaling Tat-C* with fluorescein at the N-terminus. Specific PBP-C* structures can be made to order by commercial sources. 
     Other examples of PBP&#39;s which can be used include the matrix protein (M1, with a sequence of “DPNNMDKAVKLYRKLKR” SEQ ID NO: 4; in single letter code) which binds to Type A influenza virus RNA, and hnRNP U protein (“MRGGNFRGGAPGNRGGYNRRGN” SEQ ID NO: 5; in single letter code) which binds to pre-ribosomal RNA. For example, M1 can be used in an assay to detect influenza virus in a sample, similar to the working example shown for HIV. 
     The Signaling Chromophore 
     Chromophores useful in the inventions described herein include any substance which can receive energy from an excited polycationic multichromophore in an appropriate solution and emit light. For multiplexed assays, a plurality of different signaling chromophores can be used with detectably different emission spectra. The chromophore can be a lumophore or a fluorophore. Typical fluorophores include fluorescent dyes, semiconductor nanocrystals, lanthanide chelates, and green fluorescent protein. 
     Exemplary fluorescent dyes include fluorescein, 6-FAM, rhodamine, Texas Red®, tetramethylrhodamine, a carboxyrhodamine, carboxyrhodamine 6G, carboxyrhodol, carboxyrhodamine 110, Cascade Blue®dye, Cascade Yellow™ dye, coumarin, Cy2® dye, Cy3® dye, Cy3.5® dye, Cy5® dye, Cy5.5® dye, Cy-Chrome™ dye, phycoerythrin, PerCP™ dye (peridinin chlorophyll-a Protein), PerCP-CY™ 5.5dye, JOE(6-carboxy-4′,5′-dichloro-2′,7′dimethoxyfluorescein), NED™ dye, ROX™ dye (5-(and 6)-carboxy-X-rhodamine), HEX™ dye, Lucifer Yellow, Marina Blue™ dye, Oregon Green® 488 dye, Oregon Green® 500 dye, Oregon Green® 514 dye, Alexa Fluor® 350 dye, Alexa Fluor® 430 dye, Alexa Fluor® 488 dye, Alexa Fluor® 532 dye, Alexa Fluor® 546 dye, Alexa Fluor® 568 dye, Alexa Fluor® 594 dye, Alexa Fluor® 633 dye, Alexa Fluor® 647 dye, Alexa Fluor® 660 dye, Alexa Fluor® 680 dye, 7-amino-4-methylcoumarin-3-acetic acid, BODIPY® FL dye, BODIPY® FL-BR 2  dye, BODIPY® 530/555 dye, BODIPY® 558/568 dye, BODIPY® 564/570 dye, BODIPY® 576/589 dye, BODIPY® 581/591 dye, BODIPY® 630/650 dye, BODIPY® 650/665 dye, BODIPY® R6G dye, BODIPY® TMR dye, BODIPY® TR dye, conjugates thereof, and combinations thereof. Exemplary lanthanide chelates include europium chelates, terbium chelates and samarium chelates. 
     A wide variety of fluorescent semiconductor nanocrystals (“SCNCs”) are known in the art; methods of producing and utilizing semiconductor nanocrystals are described in: PCT Publ. No. WO 99/26299 published May 27, 1999, inventors Bawendi et al.; U.S. Pat. No. 5,990,479 issued Nov. 23, 1999 to Weiss et al.; and Bruchez et al., Science 281:2013, 1998. Semiconductor nanocrystals can be obtained with very narrow emission bands with well-defined peak emission wavelengths, allowing for a large number of different SCNCs to be used as signaling chromophores in the same assay, optionally in combination with other non-SCNC types of signaling chromophores. 
     The term “green fluorescent protein” refers to both native  Aequorea  green fluorescent protein and mutated versions that have been identified as exhibiting altered fluorescence characteristics, including altered excitation and emission maxima, as well as excitation and emission spectra of different shapes (Delagrave, S. et al. (1995) Bio/Technology 13:151-154; Heim, R. et al. (1994) Proc. Natl. Acad. Sci. USA 91:12501-12504; Heim, R. et al. (1995) Nature 373:663-664). Delgrave et-al. isolated mutants of cloned  Aequorea victoria  GFP that had red-shifted excitation spectra. Bio/Technology 13:151-154 (1995). Heim, R. et al. reported a mutant (Tyr66 to His) having a blue fluorescence (Proc. Natl. Acad. Sci. (1994) USA 91:12501-12504). 
     The Substrate 
     For those variations of the assay performed on a substrate, the substrate can comprise a wide range of material, either biological, nonbiological, organic, inorganic, or a combination of any of these. For example, the substrate may be a polymerized Langmuir Blodgett film, functionalized glass, Si, Ge, GaAs, GaP, SiO 2 , SiN 4 , modified silicon, or any one of a wide variety of gels or polymers such as (poly)tetrafluoroethylene, (poly)vinylidenedifluoride, polystyrene, cross-linked polystyrene, polyacrylic, polylactic acid, polyglycolic acid, poly(lactide coglycolide), polyanhydrides, poly(methyl methacrylate), poly(ethylene-co-vinyl acetate), polysiloxanes, polymeric silica, latexes, dextran polymers, epoxies, polycarbonates, or combinations thereof. Conducting polymers and photoconductive materials can be used. 
     Substrates can be planar crystalline substrates such as silica based substrates (e.g. glass, quartz, or the like), or crystalline substrates used in, e.g., the semiconductor and microprocessor industries, such as silicon, gallium arsenide, indium doped GaN and the like, and includes semiconductor nanocrystals. 
     The substrate can take the form of a photodiode, an optoelectronic sensor such as an optoelectronic semiconductor chip or optoelectronic thin-film semiconductor, or a biochip. The location(s) of the individual sensor PBP(s) on the substrate can be addressable; this can be done in highly dense formats, and the location(s) can be microaddressable or nanoaddressable. 
     Silica aerogels can also be used as substrates, and can be prepared by methods known in the art. Aerogel substrates may be used as free standing substrates or as a surface coating for another substrate material. 
     The substrate can take any form and typically is a plate, slide, bead, pellet, disk, particle, microparticle, nanoparticle, strand, precipitate, optionally porous gel, sheets, tube, sphere, container, capillary, pad, slice, film, chip, multiwell plate or dish, optical fiber, etc. The substrate can be any form that is rigid or semi-rigid. The substrate may contain raised or depressed regions on which an assay component is located. The surface of the substrate can be etched using well known techniques to provide for desired surface features, for example trenches, v-grooves, mesa structures, or the like. 
     Surfaces on the substrate can be composed of the same material as the substrate or can be made from a different material, and can be coupled to the substrate by chemical or physical means. Such coupled surfaces may be composed of any of a wide variety of materials, for example, polymers, plastics, resins, polysaccharides, silica or silica-based materials, carbon, metals, inorganic glasses, membranes, or any of the above-listed substrate materials. The surface can be optically transparent and can have surface Si—OH functionalities, such as those found on silica surfaces. 
     The substrate and/or its optional surface are chosen to provide appropriate optical characteristics for the synthetic and/or detection methods used. The substrate and/or surface can be transparent to allow the exposure of the substrate by light applied from multiple directions. The substrate and/or surface may be provided with reflective “mirror” structures to increase the recovery of light. 
     The substrate and/or its surface is generally resistant to, or is treated to resist, the conditions to which it is to be exposed in use, and can be optionally treated to remove any resistant material after exposure to such conditions. 
     Assay components can be fabricated on or attached to the substrate by any suitable method, for example the methods described in U.S. Pat. No. 5,143,854, PCT Publ. No. WO 92/10092, U.S. patent application Ser. No. 07/624,120, filed Dec. 6, 1990 (now abandoned), Fodor et al., Science, 251: 767-777 (1991), and PCT Publ. No. WO 90/15070). Techniques for the synthesis of arrays using mechanical synthesis strategies are described in, e.g., PCT Publication No. WO 93/09668 and U.S. Pat. No. 5,384,261. 
     Still further techniques include bead based techniques such as those described in PCT Appl. No. PCT/US93/04145 and pin based methods such as those described in U.S. Pat. No. 5,288,514. 
     Additional flow channel or spotting methods applicable to attachment of sensor PBPs to the substrate are described in U.S. patent application Ser. No. 07/980,523, filed Nov. 20, 1992, and U.S. Pat. No. 5,384,261. Reagents are delivered to the substrate by either (1) flowing within a channel defined on predefined regions or (2) “spotting” on predefined regions. A protective coating such as a hydrophilic or hydrophobic coating (depending upon the nature of the solvent) can be used over portions of the substrate to be protected, sometimes in combination with materials that facilitate wetting by the reactant solution in other regions. In this manner, the flowing solutions are further prevented from passing outside of their designated flow paths. 
     Typical dispensers include a micropipette optionally robotically controlled, an ink-jet printer, a series of tubes, a manifold, an array of pipettes, or the like so that various reagents can be delivered to the reaction regions sequentially or simultaneously. 
     Excitation and Detection of the Chromophores 
     Any instrument that provides a wavelength that can excite the polycationic multichromophore and is shorter than the emission wavelength(s) to be detected can be used for excitation. The excitation source preferably does not significantly excite the signaling chromophore directly. The source may be: a broadband UV light source such as a deuterium lamp with an appropriate filter, the output of a white light source such as a xenon lamp or a deuterium lamp after passing through a monochromator to extract out the desired wavelengths, a continuous wave (cw) gas laser, a solid state diode laser, or any of the pulsed lasers. The emitted light from the signaling chromophore can be detected through any suitable device or technique; many suitable approaches are known in the art. For example, a fluorimeter or spectrophotometer may be used to detect whether the test sample emits light of a wavelength characteristic of the signaling chromophore upon excitation of the multichromophore. 
     Kits 
     Kits comprising reagents useful for performing the methods of the invention are also provided. In one embodiment, a kit comprises a sensor PBP that binds to a target polynucleotide of interest and a polycationic multichromophore. The sensor PBP is conjugated to a signaling chromophore. In the presence of the target polynucleotide in the sample, the sensor PBP is brought into proximity to the multichromophore upon binding to the target, which associates electrostatically with the polycationic multichromophore. 
     The components of the kit are retained by a housing. Instructions for using the kit to perform a method of the invention are provided with the housing, and can be provided in any fixed medium. The instructions may be located inside the housing or outside the housing, and may be printed on the interior or exterior of any surface forming the housing which renders the instructions legible. The kit may be in multiplex form, containing pluralities of one or more different sensor PBPs which can bind to corresponding different target polynucleotides. 
     EXAMPLES 
     The following examples are set forth so as to provide those of ordinary skill in the art with a complete description of how to make and use the present invention, and are not intended to limit the scope of what is regarded as the invention. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperature, etc.) but some experimental error and deviation should be accounted for. Unless otherwise indicated, parts are parts by weight, temperature is degree centigrade and pressure is at or near atmospheric, and all materials are commercially available. The TAR RNA and dTAR RNA oligonucleotides described below were purchased from Dharmacon Research Inc. (Lafayette, USA). The polypeptides modified by fluorescein on the N-terminus (Tat-C* and SH3-C*) were custom-made by Sigma-Genosys (Texas, USA). The polymer 1 and oligomer 2 are prepared as described in the literature 45 . All the fluorescence and FRET experiments were carried out using a PTI Quantum Master fluorometer equipped with a Xenon lamp excitation source in tris-EDTA buffer solution (10 mM, pH=7.4). 
     Example 1 
     The emission spectra of the polymer 1, Tat-C* and the absorption spectra of Tat-C* are shown in  FIG. 3 . The data show that there is excellent overlap between the emission of polymer 1 and the absorption of Tat-C* to ensure fluorescence resonance energy transfer. 
     Example 2 
     The emission spectra of the oligomer 1, Tat-C* and the absorption spectra of Tat-C* are shown in  FIG. 4 . The data show that there is excellent overlap between the emission of oligomer 1 and the absorption of Tat-C* to ensure fluorescence resonance energy transfer. 
     Example 3 
     The emission spectra of the oligomer 2, Tat-C* and the absorption spectra of Tat-C* are shown in  FIG. 5 . The data show that there is excellent overlap between the emission of oligomer 2 and the absorption of Tat-C* to ensure fluorescence resonance energy transfer. 
     Example 4 
     The Tat-C* probe ([Tat-C*]=1.0×10-8 M) was mixed with an equimolar amount of the TAR RNA at room temperature, and in an identical fashion with a non-specific dTAR RNA. It is known that a bulge structure in TAR RNA is a requirement for Tat peptide binding to TAR RNA.46,47 dTAR RNA is closely related in structure to TAR RNA, lacking the three base bulge structure necessary for Tat binding. 
     Addition of oligomer 1 in water ([oligomer 1]=8.0×10-8 M) and subsequent comparison of the resulting fluorescence of Tat-C* obtained by excitation at 365 nm ( FIG. 6 ) reveals an intensity ratio &gt;10 times higher for the Tat-C*/TAR RNA, relative to the non-specific Tat-C*/dTAR RNA pair. These FRET differences demonstrate the specificity of the HIV TRA RNA sensor for a specific RNA. Furthermore, the fluorescein emission is more than 25 times larger than that obtained from direct Tat-C* excitation at the absorption maximum of fluorescein in the absence of oligomer 1. The increased Tat-C* emission in the energy transfer complex indicates that optical amplification is provided by the conjugated oligomer 1. 
     Example 5 
     The Tat-C* probe ([Tat-C*]=1.0×10 −8  M) was mixed with an equimolar amount of the TAR RNA at room temperature, and in an identical fashion with a non-specific dTAR RNA. Addition of oligomer 2 in water ([oligomer 2]=6.0×10 −8  M) and subsequent comparison of the resulting fluorescence of Tat-C* obtained by excitation at 375 nm ( FIG. 7 ) reveals an intensity ratio 15 times higher for the Tat-C*/TAR RNA, relative to the non-specific Tat-C*/dTAR RNA pair. These FRET differences demonstrate the specificity of the HIV TRA RNA sensor of this invention to a specific RNA. Furthermore, the fluorescein emission is more than 30 times larger than that obtained from direct Tat-C* excitation in the absence of oligomer 2. The increased Tat-C* emission in the energy transfer complex indicates that optical amplification is provided by the conjugated oligomer 2. 
     Example 6 
     The water soluble conjugated polymer 1 (average n=app. 15) was utilized as the light harvesting chromophore. The Tat-C* probe ([Tat-C*]=1.0×10 −8  M) was mixed with an equimolar amount of the TAR RNA at room temperature, and in an identical fashion with a non-specific dTAR RNA. Addition of polymer 1 in water ([polymer 1]=4.8×10 −7  M) into the mixture of Tat-C* and TAR RNA results in fluorescence of Tat-C* ( FIG. 8 ) with an intensity ratio &gt;15 times higher than that of the non-specific Tat-C*/dTAR RNA and 10 times larger than that obtained from direct Tat-C* excitation in the absence of polymer 1. Thus, significantly higher FRET ratios and correspondingly higher sensitivities can be achieved. Titration of 1 against the mixture of Tat-C* and TAR RNA revealed that the FRET ratio increased with the concentration of 1 until the ratio of charges from 1 to TAR RNA was close to 4:1, after which the FRET ratio was found to decrease. A similar pattern was observed for oligomer 2. 
     Example 7 
     Another peptide sequence labeled with fluorescein at N-terminus (SH3-C * ; AKPRPPRPLPVAC SEQ ID NO: 6; in single letter code) which cannot specifically binding to TAR RNA was also utilized as the signal probe.  FIG. 9  ([SH3-C* or Tat-C*]=1.0×10 −8  M, [TAR RNA]=1.0×10 −8  M and [oligomer 1] =8.0×10 −8  M) shows C* emission only when the Tat-C* was present. These FRET differences demonstrate that the HIV TRA RNA sensor of this invention depends on the specific interaction of Tat peptide sequence with TAR RNA. 
     Although the invention has been described in some detail with reference to the preferred embodiments, those of skill in the art will realize, in light of the teachings herein, that certain changes and modifications can be made without departing from the spirit and scope of the invention. Accordingly, the invention is limited only by the claims. 
     REFERENCES 
     
         
           1 Wang, J.  Nucleic Acid Res.  2000 28 3011. 
           2 Umek, R. M.; Lin, S. W.; Vielmetter, J.; Terbrueggen, R. H.; Irvine, B.; Yu, C. J.; Kayyem, J. F.; Yowanto, H.; Blackburn, G. F.; Farkas, D. H.; Chen, Y. P.  J. Mol. Diag.  2001 3 74. 
           3 Schork N. J.; Fallin D.; Lanchbury J. S.  Clini. Genet.  2000 58 250. 
           4 Balakin, K. V.; Korshun, V. A.; Mikhalev, I. I.; Maleev, G. V.; Malakhov A. D.; Prokhorenko, I. A.; Berlin, Yu. A.  Biosensors and Bioelectronics  1998 13 771. 
           5 LePecg, J. B.; Paoletti, C.  J. Mol. Biol.  1967 27 87. 
           6 Petty, J. T.; Bordelon, J. A.; Robertson, M. E.  J. Phys. Chem. B  2000 104 7221. 
           7 Cardullo, R. A.; Agrawal, S.; Flores, C.; Zamechnik, P. C.; Wolf, D. E. Proc.  Natl. Acad. Sci.  1988 85 8790. 
           8 Castro, A.; Williams, J. G. K.  Anal. Chem.  1997-69 3915. 
           9 Knemeyer, J.; Marmè, N.; Sauer, M.  Anal. Chem.  2000 72 3717. 
           10 N. J. Turro,  Modern Molecular Photochemistry , University Science Books: Sausalito, Calif. 1991. 
           11 J. R. Lakowicz,  Principles of fluorescence spectroscopy , Kluwer Academic/Plenum Publishers, New York, 1999. 
           12 R. Gallo, L. Montagnier,  Sci. Am.  1988, 259 (10), 41. 
           13 J. Wang, X. Cai, G. Rivas, H. Shiraishi, P. A. M. Farias, N. Dontha,  Anal. Chem.  1996, 68, 2629.N. R. Isola, D. L. Stokes, T. Vo-Dinh,  Anal. Chem.  1998, 70, 1352. 
           14 J. Kuby,  Immunology , W. Freeman Inc.: New York, 1991. 
           15 D. S. Hage,  Anal. Chem.  1999, 71, 294R. 
           16 P. Nishanian, K. Huskins, S. Stehn, R. Detels, J. Fahey,  J. Infect. Dis.  1990, 162, 21. 
           17 J. Karn, M. J. Churcher, K. Rittner, A. Kelly, P. J. G. Butler, D. A. Mann, M. J. Gait,  HIV, a practical approach , J. Karn, Ed., pp 147-165, IRL Press, New York, 1995. 
           18 L. Chen, A. D. Frankel,  Proc. Natl. Acad. Sci. USA.  1995, 92, 5077. 
           19 A. D. Frankel,  Prot. Sci.  1992, 1, 1539. 
           20 C. Matsumoto, K. Hamasaki, H. Mihara, A. Ueno,  Bioorg. Med. Chem. Lett.  2000, 10, 1857. 
           21 I. C. Kwon, Y. H. Bae, S. W. Kim,  Nature,  1991, 354,-291. 
           22 D. Frankel,  Prot. Sci.  1, 1539 (1992). 
           23 K. M. Weeks, C. Ampe, S. C. Schultz, T. A. Steitz, D. M. Crothers,  Science  249, 1281 (1 990). 
           24 McQuade, D. T.; Pullen. A. E.; Swager, T. M.  Chem. Rev.  2000 100 2537. 
           25 Chen, L.; McBranch, D. W.; Wang, H.-L.; Helgeson, R.; Wudl, F.; Whitten, D. G.  Proc. Natl. Acad. Sci. U.S.A.  1999 96 12287. 
           26 Dogariu, A., Gupta, R., Heeger, A. J., Wang, H.  Synthetic Metals  1999 100 95. 
           27 Wang, J.; Wang, D.; Miller, E. K.; Moses, D.; Bazan, G. C.; Heeger, A. J.  Macromolecules  2000 33 5153. 
           28 Stork, M. S.; Gaylord, B. S.; Heeger, A. J.; Bazan, G. C.  Adv. Mater.  2002 14 361. The molecular weight of polymer 1 was determined to be 8,600 g/mole (M n ). 
           29 Kabanov, A. V.; Felgner, P.; Seymour, L. W., Eds.  Self-Assembling Complexes for Gene Delivery. From Laboratory to Clinical Trial ; John Wiley: Chichester, 1998. 
           30 Kircheis, R.; Blessing, T.; Brunner, S.; Wightman, L.; Wagner, E.  J. Controlled Release  2001 72 165. 
           31 Wolfert, M. A.; Dash, P. R.; Navarova, O.; Oupicky, D.; Seymour, L. W.; Smart, S.; Strohalm, J.; Ulbrich, K.  Bioconjugate Chem.  1999 10 993. 
           32 Ganachaud, F.; Elaïssari, A.; Pichot, C.; Laayoun, A. ; Cros, P.  Langmuir  1997 13 701. 
           33 Smith, J. O.; Olson, D. A.; Armitage, B. A.  J. Am. Chem, Soc.  1999 121 2628. 
           34 Harada, A.; Kataoka, K. Science 1999 283 65. 
           35 Bronich, T. K.; Nguyen, H. K.; Eisenberg, A.; Kabanov, A. V.  J. Am. Chem. Soc.  2000 122 8339. 
           36 Stork, M. S.; Gaylord, B. S.; Heeger, A. J.; Bazan, G. C. Adv. Mater. 2002 14 361. 
           37 K. Nagai, I. W. Mattay, RNA-Protein Interactions. Frontiers in Molecular Biology Series (Oxford University Press, Oxford, UK, 1994). 
           38 G. Varani,  Acc. Chem. Res.  30, 189 (1997). 
           39 Y. N. Vaishnav, F. Wong-Staal,  Ann. Rev. Biochem.  60, 577 (1991). 
           40 C. Jain. J. G. Belasco,  Methods Enzymol.  318, 309 (2000). 
           41 B. A. Sullenger, E. Gilboa,  Nature  418, 252 (2002). 
           42 E. V. Pilipenko et al.,  Genes Dev.  14, 2028 (2000). 
           43 Portela, P. Digard,  J. Gen. Virol.  83, 723 (2001). 
           44 G. T. Hermanson,  Bioconjugate Techniques , Academic Press, San Diego, 1996. 
           45 J. Futami et al.,  J. Biochem.  132, 223 (2002). 
           46 S. Richter, H. Cao, T. M. Rana,  Biochemistry  41, 6391 (2002). 
           47 J. D. Puglisi, R. Tan, B. J. Calnan, A. D. Frankel, J. R. Williamson,  Science  257, 76 (1992).