# Patent

## Title
Oligonucleotides for detecting human papilloma virus in a test sample

## Abstract

Oligonucleotides targeted to HPV Type 16 and/or Type 18 nucleic acid sequences which are particularly useful to aid in detecting HPV type 16 and or 18 are described. The oligonucleotides can aid in detecting HPV Type 16 and/or Type 18 in different ways such as by acting as hybridization assay probes, helper probes, and/or amplification primers.

## Background
RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 10/601,913, filed Jun. 23, 2003, now U.S. Pat. No. 7,470,512 which is a continuation of U.S. application Ser. No. 08/749,955, filed Nov. 14, 1996, now U.S. Pat. No. 6,583,278, which claims the benefit under 35 U.S.C. §119(e) of U.S. provisional application No. 60/006,854, filed Nov. 15, 1995.


FIELD OF THE INVENTION
This invention relates generally to nucleic acid probes complementary to Human Papillomavirus (hereafter “HPV”) nucleic acids, methods of using such probes, and kits containing such probes. In particular, different types of oligonucleotide probes are described (including hybridization assay probes, helper oligonucleotides and amplification oligonucleotides) which are useful for detecting HPV Type 16 and/or Type 18 in a test sample, such as a vaginal swab, a cervical swab, a urethral swab, a tissue sample, a body fluid or an experimental solution.
BACKGROUND OF THE INVENTION
The following description of the background of the invention and references cited therein are not admitted to be prior art to the present invention.
Papillomaviruses are small DNA viruses. These viruses are associated with and/or thought to be the causative agent of a range of benign conditions (including benign lesions and benign tumors). Papillomaviruses have also been associated with malignancies such as squamous cell carcinoma in patients having the autosomal disease epidermodysplasia verricruciformis, and with genital cancers in both males and females.
There have now been at least 59 different types of HPV characterized, (see Manual of Clinical Microbiology; 998-1000; 5th ed. American Soc. for Microbiol. 1991). The genome of different HPV variants appears to be similar between all types (Van Ranst et al., J. Gen. Vir., 73:2653-60, 1992). Nonetheless, HPVs have been subject to differential typing, based on differences in the DNA sequences of different strains of the virus (Id.).
Among those HPV types associated with genital cancers are HPV types 16, 18, 31, 33 and 35. These five strains collectively are found in over 80% of all cervical tumors, suggesting a causative role.
Antigen detection of HPV types 16 and 18 has been described, but it is reported that commercially available sera react with antigens shared by all papillomaviruses (Roman and Fife, Clin. Microbiol. Rev. 2:166-190, 1989). In addition, the percentage of antigen-positive specimens is reported to decrease as the severity of the disease increases from mild dysplasia to carcinoma in situ, to invasive carcinoma (Id.).
In vivo, HPV DNA is found both episomally and integrated in the host genome. The HPV genome contains open reading frames encoding from 8 to 10 proteins, although not all of these proteins have been identified. Many of these open reading frames have been designated with the prefixes E or L, referring to “early” or “late” transcription events, although not all of those designated “early” are actually transcribed early, and vice versa.
Descriptions of certain primers and oligonucleotide probes for the detection of the E6 region of HPV types 16 and 18 are provided in Lucotte et al., Mol. Cell. Probes 7:339-344, 1993; De Britton et al., Obst. Gynec. 81:19-24, 1993; Nuovo, et al, Am. J. Pathol. 138:53-58, 1991; Van der Velde et al., J. Med. Virol. 36:279-282, 1992; Thompson et al., J. Med. Virol. 36:54-6, 1992; Cornelissen et al., J. Gen. Virol. 71:1243-1246, 1990, Hus and McNicol, Mol. Cell. Probes 6:459-466, 1992; Sang and Barbosa, Virol. 189:448-455, 1992; Joseph, European Pub. No. 0 477 972; Joannes et al, PCT Pub. No. WO 93/02217; Emery et al, PCT Pub. No. WO 92/01815; Hendricks, PCT Pub. No. WO 91/08312, PCT Pub. No. PCT/US90/07057; Manos et al., U.S. Pat. No. 5,182,377; Herzog, et alt, U.S. Pat. No. 4,983,728; Schwartz and Adams, PCT Pub. No. WO 89/02934; George and Groff, PCT Pub. No. WO 89/09940; Nur et al., PCT Pub. No. WO 92/14847; Mazzatente et al., European Pat. Pub. No. EPO 489 442; Shimada et al., European Pat. Pub. No. EPO 402 132; and Morris et al., PCT Pub. No. WO 88/06634; all of which are hereby incorporated herein by reference in their entirety (including drawings).
SUMMARY OF THE INVENTION
The present invention features oligonucleotides useful for detecting HPV Type 16 and/or Type 18, methods of making and using these oligonucleotides, and kits containing the oligonucleotides. The featured oligonucleotides include hybridization assay oligonucleotides, amplification oligonucleotides, and helper oligonucleotides. The different oligonucleotides can aid in the detection of HPV Type 16 and/or Type 18 in different ways.
Hybridization assay probe oligonucleotides are targeted to HPV Type 16 and/or Type 18 regions and preferably are labeled. These oligonucleotides are particularly useful for distinguishing between HPV Type 16 and/or Type 18 variants from other HPV variants, including HPV 6, 11, 31, 33, 35, 39, 45, 51, 52, or 58. The target region for the hybridization assay oligonucleotides includes nucleic acids specifically found in HPV Type 16 and/or Type 18, or a nucleic acid sequence complimentary thereto. Complimentary nucleic acid can be produced using standard well known nucleic acid amplification techniques.
The amplification primers can be used to initiate amplification reactions using HPV target nucleic acid. The primers are designed to hybridize to a region of the target nucleic acid 3′ of a target region. The primers can be used to initiate amplification synthesizing copies of nucleic acid complementary to the target region. Different types of amplification can be performed depending upon the amplification primer which is utilized. For example, pairs of amplification primers hybridizing to a region 3′ of the target sequence and to a region 3′ of a complimentary target sequence can be used in PCR amplification. Primers which hybridize to a region 3′ to the target sequence which have a promoter sequence recognized by a promoter (such as those used by bacteriophage T7, T3 or SP-6) can be used to synthesize multiple copies of nucleic acid complimentary to the target sequence.
Helper probes are particularly useful for facilitating the hybridization of a hybridization assay oligonucleotide to its target sequence. Helper probes aid in altering the secondary structure of nucleic acid in and around the target region. The use of helper probes is describe by Hogan and Milliman, U.S. Pat. No. 5,030,557, which is incorporated by reference herein in its entirety including any drawings. Also featured are probe mixes containing one or more labeled probes and at least one helper probe for use in hybridization assays for the detection of HPV and methods of detecting and amplifying HPV nucleic acids.
The probes, their complements or RNA equivalents, can be used to distinguish HPV Type 16 and/or Type 18 from closely related phylogenetic neighbors, by preferentially hybridizing to an HPV Type 16 and/or Type 18 target nucleic acid sequence region under selective hybridization assay conditions. The hybridization assay probes disclosed herein are particularly useful for detecting the presence of HPV Type 16 and/or Type 18 and/or for determining the quantity of HPV Type 16 and/or Type 18 present in a test sample, e.g., samples of sputum, urine, blood, tissue sections, urogenital secretions, urogenital swabs and other clinical samples.
Hybridization assay oligonucleotide probes contain a nucleotide sequence perfectly complementary, or substantially complementary, to an HPV target sequence. In addition to having a region designed to distinguish between HPV Type 16 and/or Type 18 on the one hand and different HPV variants on the other hand, hybridization assay probes can also have one or more additional nucleic acid sequences which are complementary to additional stretches of an HPV target nucleic acid or non-complementary nucleic acid sequences. For example, the additional sequences can be complementary to both HPV Type 16 and/or Type 18 and other HPV variants, they can be non-complementary to HPV Type 16 and/or Type 18, or HPV variants, or they can even have a slightly higher degree of complementarity to the HPV variants as long as the hybridization probe is able to distinguish HPV Type 16 and/or Type 18 from other HPV variants such as HPV types 6, 11, 31, 33, 35, 39, 45, 51, 52, or 58.
Hybridization assay probes are sufficiently complementary to nucleic acids containing a target sequence to form a stable and detectable hybrid probe:target duplex under stringent hybridization assay conditions. A hybridization assay probe is preferably between 10 and 100 nucleotides in length, more preferably between 14 and 50 nucleotides in length. Even more preferably the probe is between 18 and 40 nucleotides in length. Hybridization assay probes are preferably labeled with a reporter group moiety such as a radioisotope, a fluorescent moiety, a chemiluminescent moiety, an enzyme, or a ligand incorporated into the probe. The moiety can be used to detect or confirm probe hybridization to its target sequence. A hybridization assay probe is an oligonucleotide which can distinguish HPV type 16 and/or 18 from other HPV types and or common body flora, by preferentially hybridizing to an HPV type 16 and/or 18 target nucleic acid sequence region under stringent hybridization assay conditions.
I. Hybridization Assay Probes
Thus, in one aspect the invention features a hybridization assay probe containing an oligonucleotide able to hybridize to an HPV Type 16 and/or Type 18 target nucleic acid to form a detectable target:probe duplex under selective stringency hybridization conditions, but which preferably will not form a detectable non-target:probe duplex with nucleic acids from HPV Types 6, 11, 31, 33, 35, 39, 45, 51, 52, and/or 58. The oligonucleotide comprises a sequence of nucleic acids which is at least 70%, (preferably 80%, more preferably 90%, and most preferably 100% complementary) to a target sequence of 10 or more contiguous nucleotides present in a target region. The target regions can be better understood with reference to Table A below.











TABLE A







Type






HPV 16,






HPV 18,





Seq.
Probe

DNA



ID
Primer
Sub-Type
or


Sequence
No.
Helper
1, 2 or 3
RNA







GACATTATTG TTATAGTTTG TATGGAAC
  1
HPV 16
2
DNA




primer




 


GTTCCATACA AACTATAACA ATAATGTC
  2


DNA


 


GACAUUAUUG UUAUAGUUUG UAUGGAAC
  3


RNA


 


GUUCCAUACA AACUAUAACA AUAAUGUC
  4


RNA


 


GAACAGCAAT ACAACAAACC GTTGTGTG
  5
HPV 16
3
DNA




probe




 


CACACAACGG TTTGTTGTAT TGCTGTTC
  6


DNA


 


GAACAGCAAU ACAACAAACC GUUGUGUG
  7


RNA


 


CACACAACGG UUUGUUGUAU UGCUGUUC
  8


RNA


 


GACGTGAGGT GTATTAACTG TCAAAAG
  9
HPV 16
2
DNA




probe




 


CTTTTGACAG TTAATACACC TCACGTC
 10


DNA


 


GACGUGAGGU GUAUUAACUG UCAAAAG
 11


RNA


 


CUUUUGACAG UUAAUACACC UCAGGUC
 12


RNA


 


CCATGCATGA TTACAGCTGG GTTTCTC
 13
HPV 16
2
DNA




primer




 


GAGAAACCCA GCTGTAATCA TGCATGG
 14


DNA


 


CCAUGCAUGA UUACAGCUGG GUUUCUC
 15


RNA


 


GAGAAACCCA GCUGUAAUCA UGCAUGG
 16


RNA


 


TACGTGTTCT TGATGATCTC ACGTCG
 17
HPV 16
2
DNA




probe




 


CGACGTGAGA TCATCAAGAA CACGTA
 18


DNA


 


UACGUGUUCU UGAUGAUCUC ACGUCG
 19


RNA


 


CGACGUGAGA UCAUCAAGAA CACGUA
 20


RNA


 


GTGTGTACTG CAAGCAACAG TTACTG
 21
HPV 16
2
DNA




primer




 


CAGTAACTGT TGCTTGCAGT ACACAC
 22


DNA


 


GUGUGUACUG CAAGCAACAG UUACUG
 23


RNA


 


CAGUAACUGU UGCUUGCAGU ACACAC
 24


RNA


 


CTTTTGACAG TTAATACACC TCACG
 25
HPV 16
3
DNA




probe




 


CGTGAGGTGT ATTAACTGTC AAAAG
 26


DNA


 


CUUUUGACAG UUAAUACACC UCACG
 27


RNA


 


CGUGAGGUGU AUUAACUGUC AAAAG
 28


RNA


 


AAAGTCATAT ACCTCACGTC GC
 29
HPV 16
2
DNA




probe




 


GCGACGTGAG GTATATGACT TT
 30


DNA


 


AAAGUCAUAU ACCUCACGUC GC
 31


RNA


 


GCGACGUGAG GUAUAUGACU UU
 32


RNA


 


GAAACCCAGC TGTAATCATG C
 33
HPV 16
1
DNA




probe




 


GCATGATTAC AGCTGGGTTT C
 34


DNA


 


GAAACCCAGC UGUAAUCAUG C
 35


RNA


 


GCAUGAUUAC AGCUGGGUUU C
 36


RNA


 


GATCATCAAG AACACGTAG
 37
HPV 16
1
DNA




primer




 


CTACGTGTTC TTGATGATC
 38


DNA


 


GAUCAUCAAG AACACGUAG
 39


RNA


 


CUACGUGUUC UUGAUGAUC
 40


RNA


 


GGAACTGAAC ACTTCACTGC AAGACATAGA
 41
HPV 18
3
DNA


AATAACC

primer




 


GGTTATTTCT ATGTCTTGCA GTGAAGTGTT
 42


DNA


CAGTTCC






 


GGAACUGAAC ACUUCACUGC AAGACAUAGA
 43


RNA


AAUAACC






 


GGUUAUUUCU AUGUCUUGCA GUGAAGUGUU
 44


RNA


CAGUUCC






 


GGAAAAACTA ACTAACACTG GGTTATACAA T
 45
HPV 18
1
DNA




probe




 


ATTGTATAAC CCAGTGTTAG TTAGTTTTTC C
 46


DNA


 


GGAAAAACUA ACUAACACUG GGUUAUACCA U
 47


RNA


 


AUUGUAUAAC CCAGUGUUAG UUAGUUUUUC C
 48


RNA


 


CATAGAAATA ACCTGTGTATA TTGCAAG
 49
HPV 18
2
DNA




primer




 


CTTGCAATAT ACACAGGTTAT TTCTATG
 50


DNA


 


CAUAGAAAUA ACCUGUGUAUA UUGCAAG
 51


RNA


 


CUUGCAAUAU ACACAGGUUAU UUCUAUG
 52


RNA


 


GACATTATTC AGACTCTGTGT ATGGAG
 53
HPV 18
2
DNA




primer




 


CTCCATACAC AGAGTCTGAAT AATGTC
 54


DNA


 


GACAUUAUUC AGACUCUGUGU AUGGAG
 55


RNA


 


CUCCAUACAC AGAGUCUGAAU AAUGUC
 56


RNA


 


GCAAGACAGT ATTGGAACTT ACAGAG
 57
HPV 18
3
DNA




probe




 


CTCTGTAAGT TCCAATACTG TCTTGC
 58


DNA


 


GCAAGACAGU AUUGGAACUU ACAGAG
 59


RNA


 


CUCTGUAAGU UCCAAUACUG UCUUGC
 60


RNA


 


CCTGTGTATA TTGCAAGACAG TATTG
 61
HPV 18
2
DNA




helper




 


CAATACTGTC TTGCAATATAC ACAGG
 62


DNA


 


CCUGUGUAUA UUGCAAGACAG UAUUG
 63


RNA


 


CAAUACUGUC UUGCAAUAUAC ACAGG
 64


RNA


 


GAACTTACAG AGGTATTTGA ATTTGC
 65
HPV 18
3
DNA




probe




 


GCAAATTCAA ATACCTCTGT AAGTTC
 66


DNA


 


GAACUUACAG AGGUAUUUGA AUUUGC
 67


RNA


 


GCAAAUUCAA AUACCUCUGU AAGUUC
 68


RNA


 


CAACCGAGCA CGACAGGAACG AC
 69
HPV 18
2
DNA




primer




 


GTCGTTCCTG TCGTGCTCGGT TG
 70


DNA


 


CAACCGAGCA CGACAGGAACG AC
 71


RNA


 


GUCGUUCCUG UCGUGCUCGGU UG
 72


RNA


 


CCAACGACGC AGAGAAACAC AAG
 73
HPV 18
2
DNA




probe




 


CTTGTGTTTC TCTGCGTCGT TGG
 74


DNA


 


CCAACGACGC AGAGAAACAC AAG*
 75


RNA


 


CUUGUGUUUC UCUGCGUCGU UGG
 76


RNA


 


CTTACAGAGG TGCCTGCGGT GC
 77
HPV 18
3
DNA




probe




 


GCACCGCAGG CACCTCTGTA AG
 78


DNA


 


CUUACAGAGG UGCCUGCGGU GC
 79


RNA


 


GCACCGCAGG CACCUCUGUA AG
 80


RNA


 


GAACTTACAG AGGTGCCTGC GG
 81
HPV 18
3
DNA




probe




 


CCGCAGGCAC CTCTGTAAGT TC
 82


DNA


 


GAACUUACAG AGGUGCCUGC GG
 83


RNA


 


CCGCAGGCAC CUCUGUAAGU UC
 84


RNA


 


CAGGACACAG TGGCTTTTGA C
 85
HPV 16
3
DNA




primer




 


GTCAAAAGCC ACTGTGTCCT G
 86


DNA


 


CAGGACACAG UGGCUUUUGA C
 87


RNA


 


GUCAAAAGCC ACUGUGUCCU G
 88


RNA


 


GCTTTTTGTC CAGATGTCTT TGC
 89
HPV 16
2
DNA




primer




 


GCAAAGACAT CTGGACAAAA AGC
 90


DNA


 


GCUUUUUGUC CAGAUGUCUU UGC
 91


RNA


 


GCAAAGACAU CUGGACAAAA AGC
 92


RNA


 


GCAATGTAGG TGTATCTCCA TGC
 93
HPV 16
1
DNA




primer




 


GCATGGAGAT ACACCTACAC CGC
 94


DNA


 


GCAAUGUAGG UGUAUCUCCA UGC
 95


RNA


 


GCAUGGAGAU ACACCUACAC CGC
 96


RNA


 


AATTTAATAC GACTCACTAT AGGGAGA
 97
T7
1
DNA




Polymerase






primer




 


TCTCCCTATA GTGAGTCGTA TTAAATT
 98


DNA


 


AAUUUAAUAC GACUCACUAU AGGGAGA
 99


RNA


 


UCUCCCUAUA GUGAGUCGUA UUAAAUU
100


RNA


 


TCGTTTTTCATTAAGGTGTCTAAGTTTTTCTGCTG
101
HPV 18
1
DNA


GATTC

primer




 


GAATCCAGCAGAAAAACTTAGACACCTTAATGAA
102


DNA


AAACGA






 


UCGUUUUUCAUUAAGGUGUCUAAGUUUUUCUG
103


RNA


CUGGAUUC






 


GAAUCCAGCAGAAAAACUUAGACACCUUAAUGA
104


RNA


AAAACGA






 


GCAATGTTGC CTTAGGTCCA TGC
105
HPV 18
2
DNA




primer




 


GCATGGACCT AAGGCAACAT TGC
106


DNA


 


GCAAUGUUGC CUUAGGUCCA UGC
107


RNA


 


GCAUGGACCU AAGGCAACAU UGC
108


RNA


 


CGGTTTCTGG CACCGCAGGC AC
109
HPV 18
2
DNA




primer




 


GTGCCTGCGG TGCCAGAAAC CG
110


DNA


 


CGGUUUCUGG CACCGCAGGC AC
111


RNA


 


GUGCCUGCGG UGCCAGAAAC CG
112


RNA


 


GCAATGTAGC CGTATGTCCA TGC
113
HPV 18
2
DNA




primer




 


GCATGGACAT ACGGCTACAT TGC
114


DNA


 


GCAAUGUAGC CGUAUGUCCA UGC
115


RNA


 


GCAUGGACAU ACGGCUACAU UGC
116


RNA


 


CACTTCACTG CAAGACATAG AAATAACCTG
117
HPV 18
3
DNA


TGTATATT

HELPER




 


AATATACACA GGTTATTTCT ATGTCTTGCA
118


DNA


GTGAAGTG






 


CACUUCACUG CAAGACAUAG AAAUAACCUG
119


RNA


UGUAUAUU






 


AAUAUACACA GGUUAUUUCU AUGUCUUGCA
120


RNA


GUGAAGUG






 


TTATTAATAA GGTGCCTGCG GTGCCAGAAA CC
121
HPV 18
2
DNA




HELPER




 


GGTTTCTGGC ACCGCAGGCA CCTTATTAAT AA
122


DNA


 


UUAUUAAUAA GGUGCCUGCG GUGCCAGAAA
123


RNA


CC






 


GGUUUCUGGC ACCGCAGGCA CCUUAUUAAU
124


RNA


AA






 


GACTCTGTGT ATGGAGACAC ATT
125
HPV 18
1
DNA




HELPER




 


AATGTGTCTC CATACACAGA GTC
126


DNA


 


GACUCUGUGU AUGGAGACAC AUU
127


RNA


 


AAUGUGUCUC CAUACACAGA GUC
128


RNA









Preferably, the target region comprises a sequence selected from the group consisting of those set forth in SEQ ID NOs: 9-12, 17-20, 29-32, 33-36, 45-48, and 73-76, or wherein said target region consists of a sequence present in a sequence selected from the group of consisting of those set forth in SEQ ID NOs: 5-8, 25-28, 57-60, 65-68, 77-80, and 81-84. Preferred oligonucleotides have, consist essentially of, consist of, or are substantially similar to the sequences set forth in SEQ ID NOs SEQ ID NOs: 5-12, 17-20, 25-36, 45-48, 57-60, 65-68 and 73-84.
The probes are isolated nucleic acids. The term “isolated nucleic acid” means an oligonucleotide or nucleic acid molecule which is present in a form not found in nature without human intervention (e.g., recombined with foreign nucleic acid, synthesized, isolated, or purified to some extent). Preferably an isolated nucleic acid is at least 75% homogenous. The probes may also contain additional nucleotides complementary to nucleic acid sequences contiguous to the target region and may also contain nucleotides not complementary to the targeted region, so long as such additional nucleotides do not prevent hybridization under stringent hybridization conditions. Non-complementary sequences, such as a promoter sequence, a binding site for RNA transcription, a restriction endonuclease recognition site, or sequences which will confer a desired secondary or tertiary structure such as a catalytic active site can be used to facilitate detection and/or amplification.
By “oligonucleotide,” “nucleotide polymer” or “nucleic acid” is meant two or more nucleotide subunits covalently joined together. The sugar groups of the nucleotide subunits may be ribose, deoxyribose, or modified derivatives thereof such as 2′O-methyl ribose. The nucleotide bases may be modified by non-nucleotide moieties, that do not prevent preferential hybridization of the oligonucleotide to its complementary target nucleic acid. The nucleotide subunits may be joined by linkages such as phosphodiester linkages, modified linkages or by non-nucleotide moieties, that do not prevent preferential hybridization of the oligonucleotide to its complementary target nucleic acid. Modified linkages include those linkages in which a standard phosphodiester linkage is replaced with a different linkage, such as a phosphothionate linkage, or methylphosphonate linkage.
By “selective stringency hybridization conditions” is meant a set of parameters which allows the probes and target sequences of the invention to hybridize to one another forming a detectable probe:target duplex which can be used to distinguish HPV type 16 and or 18 from HPV types 6, 11, 31, 33, 35, 39, 45, 51, 52, or 58 or other HPV variants. A detailed description of these parameters is provided below in the “Description of the Preferred Embodiments” subsection IC. entitled, “Construction and Use of Hybridization Assay Probes.” As but one example, the selective stringency hybridization conditions may preferably comprise 0.10M to 0.14M phosphate buffer containing approximately equimolar amounts of Na2HPO4 and NaH2PO4, approximately 1 mM EDTA, and 0.01 to 0.03% sodium dodecyl sulfate at 60 to 70° C.
In preferred embodiments the target region:
(a) comprises a sequence selected from the group consisting of those set forth in SEQ ID 9-12, 17-20, 29-32, and 33-36 or consists of a sequence selected from the group of consisting of those set forth in SEQ ID NOs: 5-8, and 25-28;
(b) comprises a sequence selected from the group consisting of those set forth in SEQ ID NOs: 45-48, and 73-76, or consists of a sequence selected from the group of consisting of those set forth in SEQ ID NOs: 57-60, 65-68, 77-80, and 81-84;
(c) is DNA or RNA;
(d) comprises a sequence selected from the group of consisting of those set forth in SEQ ID NOs: 33-36, and 45-48,
(e) comprises a sequence selected from the group consisting of those set forth in SEQ ID NOs: 9-12, 17-20, 29-32, and 73-76; and/or
(f) consists of a sequence selected from the group consisting of those set forth in SEQ ID NOs: 5-8, 25-28, 57-60, 65-68, 77-80, and 81-84.
In other especially preferred embodiments the probe preferentially hybridizes to nucleic acid of HPV Type 16 and/or Type 18 and not to HPV Types 6, 11, 31, 33, 35, 39, 45, 51, 52, and/or 58 at 50 to 60° C. in 0.04M to 0.06M lithium succinate buffer containing between 0.9 and 1.1% lithium lauryl sulfate, wherein said hybrid is stable for the detection of HPV Type 16 and/or Type 18 and not for the detection of HPV Types 6, 11, 31, 33, 35, 39, 45, 51, 52, and/or 58.
The term “preferentially hybridize” is meant to indicate that under stringent hybridization assay conditions, hybridization assay probes can hybridize to their target nucleic acids to form stable probe:target hybrids which can be detected to indicate the presence of the target nucleic acid while the probes do not form a sufficient number of stable probe:non-target hybrids under these conditions to indicate the presence of a closely related non-target nucleic acid. Organisms “closely related” to HPV Types 16 and/or Type 18 include HPV Types 6, 11, 31, 33, 35, 39, 45, 51, 52, or 58 (see, Van Ranst et al., J. Gen Vir., 73:2653-60, 1992).
Preferably the oligonucleotide comprises a sequence which is at least 90% complementary to said target sequence of 10 or more contiguous nucleotides, more preferably the oligonucleotide comprises a sequence which is 100% complementary to said target sequence of 10 or more contiguous nucleotides. In yet other preferred embodiments the oligonucleotide is 10 to 100 nucleotides in length, 14 to 50 bases in length, up to 40 nucleotides in length, 23-40 bases in length. The oligonucleotide may be linked to a second oligonucleotide sequence which is recognized by an RNA polymerase or which enhances initiation or elongation by an RNA polymerase.
II. Nucleic Acid Hybrids
Another aspect of the present invention relates to compositions containing detectable nucleic acid hybrids made up of a hybridization assay probe and an HPV nucleic acid molecule having a nucleic acid sequence substantially complementary thereto. The hybrid is a stable nucleic acid structure comprising a double-stranded, hydrogen-bonded region, preferably 10 to 100 nucleotides in length. The term “hybrids” include RNA:RNA, RNA:DNA, or DNA:DNA duplex molecules. The hybridization probe present in the nucleic acid hybrid has one of the sequences noted above.
The term “substantially complementary” means that the nucleic acid sequence is able to preferentially hybridize under stringent hybridization assay conditions to a target nucleic acid region. Preferably, the probe has a region of at least 10 contiguous nucleotide bases which are complementary to the corresponding target region. More preferably, the probe has a region of at least 14 contiguous nucleotide bases which are complementary to the corresponding target region.
The hybrid preferably is stable for the detection of HPV Type 16 and/or Type 18 and not for the detection of HPV Types 6, 11, 31, 33, 35, 39, 45, 51, 52, and/or 58 and may further comprise a site for the initiation of nucleic acid synthesis. Under stringent hybridization conditions said oligonucleotide preferably hybridizes specifically to nucleic acid of HPV Type 16 and/or Type 18 and not to HPV Types 6, 11, 31, 33, 35, 39, 45, 51, 52, or 58.
III. Helper Probes
In another aspect the invention features helper probes comprising an oligonucleotide, wherein said oligonucleotide comprises a sequence which will hybridize to a target sequence, wherein said target sequence has, consists essentially of, consists of, or is substantially similar to a sequence selected from the group consisting of SEQ ID NOs: 62, 64, 118, 120, 122, 124, 126, and 128.
In preferred embodiments, the oligonucleotide is substantially identical to (at least 70%) at least 10 contiguous nucleotides in a sequence selected from the group consisting of SEQ ID NOs: 61, 63, 117, 119, 121, 123, 125, and 127. In particular preferred embodiments the helper probes consist of these sequences.
It is also preferred that the oligonucleotide is at least 90% complementary to said subsequence of 10 or more contiguous nucleotides and more preferably is 100% complementary to said subsequence of 10 or more contiguous nucleotides. The oligonucleotide is preferably 10 to 100 nucleotides in length, 15 to 50 bases in length, up to 40 nucleotides in length, or 23-40 bases in length.
The preferred oligonucleotides have, consist essentially of, consist of, or are substantially similar to the sequences set forth in SEQ ID NOs: 61, 63, 117, 119, 121, 123, 125 and 127.
IV. Probe Mixes
Another aspect of the invention features probe mixes containing at least one hybridization probe and at least one helper probe for use in a hybridization assay. Helper probes can be used to facilitate hybridization of the probe:target duplex in a hybridization assay. Helper probes facilitate hybridization by enhancing the kinetics and/or the Tm of the target:hybridization probe duplex. Helper probes are described in Hogan and Milliman, U.S. Pat. No. 5,030,557, which is incorporated by reference herein in its entirety, including any drawings.
Specifically, helper oligonucleotides are designed to bind to the target nucleic acid and impose a different secondary and tertiary structure on the target to facilitate binding of the assay probe to the target. The resulting hybrid of assay probe and target nucleic acid also exhibits a higher Tm than the hybrid which results from addition of the probe in the absence of helper oligonucleotides. Because a substantial portion of this secondary and tertiary structure is not lost under conditions normally employed for nucleic acid hybridization, e.g., elevated temperature, presence of salt, presence of accelerators and the like, this residual structure can sterically inhibit, or even block, hybrid formation between a nucleotide multimer, for example a DNA or RNA oligomer being used as a probe, and its complementary sequence in the ribosomal RNA or other single-stranded nucleic acid such as mRNA or DNA which the probe targets. This inhibition can be reduced and even eliminated, by use of a “helper” oligonucleotide which binds to a portion of the RNA or DNA other than that being targeted by the probe, and which imposes new secondary and tertiary structure on the targeted region of the single-stranded nucleic acid whereby the rate of binding of the probe is accelerated. Thus, the rate of hybridization can be substantially increased and even permit hybridization to occur at a rate and under conditions otherwise adequate for an assay where, without the use of the helper, no substantial hybridization can occur.
In a preferred embodiment, nucleic acid hybridization assay probe component of the probe mix can detect the presence of HPV Type 16 and/or Type 18 and comprises a first oligonucleotide 10 to 100 bases in length having at least 14 out of 17 contiguous bases perfectly complementary to a first nucleic acid target region that consist of a sequence selected from the group consisting of those set forth in SEQ ID NOs: 9, 11, 17, 19, 29, 31, 33, 35, 45, 47, 73, and 75 or consists of a sequence selected from the group of consisting of those set forth in SEQ ID NOs: 5, 7, 25, 27, 57, 59, 65, 67, 77, 79, 81, and 83. The hybridization assay probe preferably distinguishes HPV Type 16 and/or Type 18 from HPV Types 6, 11, 31, 33, 35, 39, 45, 51, 52, and/or 58 under selective hybridization conditions, i.e., under said conditions said hybridization assay probe hybridizes to HPV Type 16 and/or Type 18 RNA or DNA to form a detectable probe:target duplex, but does not hybridize to non-target nucleic acid from HPV 6, 11, 31, 33, 35, 39, 45, 51, 52, and/or 58 to form a detectable probe:non-target duplex.
Also in preferred embodiments the helper probe component of the probe mix comprises a second oligonucleotide which is at least 70% complementary to a second target sequence that comprises a sequence selected from the group consisting of those set forth in SEQ ID NOs: 61, 63, 121, 123, 125 and 127 or consists of a sequence selected from the group of consisting of those set forth in SEQ ID NOs: 117 and 119.
With respect to a hybridization assay probe or a helper probe, a “substantially similar” nucleotide sequence is a nucleotide sequence identical to, or having no more than a 10% nucleotide base difference than an identified nucleotide sequence (excluding substitution of a RNA or DNA equivalent nucleotide, e.g., substituting T for U or U for T) and which enables a hybridization assay probe or helper probe to hybridize to HPV Type 16 and/or Type 18 nucleic acid under stringent hybridization conditions used to detect HPV Type 16 and/or Type 18. With respect to amplification oligonucleotides, a “substantially similar” nucleotide sequence is a nucleotide sequence identical to, or having no more than a 20% nucleotide base difference than an identified nucleotide sequence (excluding substitution of a RNA or DNA equivalent nucleotide, e.g., substituting T for U or U for T) and which enables an amplification oligonucleotide to prime or initiate the amplification of HPV target nucleic acid under amplification conditions.
The phrases “consists essentially of” or “consisting essentially of” mean that the oligonucleotide has a nucleotide sequence substantially similar to a specified nucleotide sequence and is preferably no more than four additional nucleotides longer or two nucleotides shorter. Thus, these phrases contain both a sequence length limitation and a sequence variation limitation. Any additions, substitutions or deletions of an oligonucleotide consisting essentially of the specified nucleotide sequence do not deprive it of its basic and novel properties, vis, the ability to specifically hybridize with its target and function as a probe or a primer. For instance, with respect to hybridization and helper probes, any additions, substitutions or deletions would not prevent these probes from being able to preferentially hybridize under stringent hybridization assay conditions to its target nucleic acid over non-target nucleic acids. With respect to an amplification oligonucleotide, any additions, substitutions or deletions would not prevent it from being able to prime amplification reactions producing target HPV nucleic acid under amplification conditions.
V. Amplification Oligonucleotides
In another aspect, the invention features an amplification oligonucleotide for amplifying HPV Type 16 and/or Type 18 nucleic acid sequences. The oligonucleotide comprises a sequence of nucleic acids which has a region that is at least 70% complementary to a subsequence of 10 or more contiguous nucleic acids present in target sequence. The target sequence has, consists essentially of, consists of, or is substantially similar to a sequence selected from the group consisting of those set forth in SEQ ID NOs: 2, 4, 14, 16, 22, 24, 38, 40, 42, 44, 50, 52, 54, 56, 70, 72, 86, 88, 90, 92, 94, 96, 102, 104, 106, 108, 110, 112, 114, and 116.
In preferred embodiments, the oligonucleotide is DNA or RNA at least 70% identical to a subsequence of 10 or more contiguous nucleotides present in: (a) a sequence selected from the group of consisting of those set forth in SEQ ID NOs: 37, 39, 93, 95, 101, and 103; (b) a sequence selected from the group consisting of those set forth in SEQ ID NOs: 1, 3, 9, 11, 13, 15, 21, 23, 49, 51, 53, 55, 69, 71, 89, 91, 105, 107, 109, 111, 113, and 115; or (c) a sequence selected from the group consisting of those set forth in SEQ ID NOs: 41, 43, 85, and 87. The oligonucleotide is preferably at least 90% identical to said subsequence of 10 or more contiguous nucleotides, more preferably 100% identical to said subsequence of 10 or more contiguous nucleotides. The oligonucleotide is preferably 10 to 100 nucleotides in length, 15 to 50 bases in length, up to 40 nucleotides in length, or 23-40 bases in length.
In another aspect, the invention features amplification oligonucleotides useful for binding to, extending through, or transcribing HPV target regions. Located at the 5′ end of the amplification oligonucleotide, which acts as a promoter sequence, is a sequence which is recognized by an RNA polymerase or which enhances initiation or elongation by an RNA polymerase. Located at the 3′ end of the same amplification oligonucleotide, is one or more sequences which acts as a target hybridizing region to HPV type 16 and or 18.
“RNA and DNA equivalent nucleotides” refer to RNA and DNA molecules having the equivalent base pair hybridization properties. RNA and DNA equivalents have different sugar groups (i.e., ribose versus deoxyribose), and may differ by the presence of uracil in RNA and thymine in DNA. The difference between RNA and DNA equivalents do not contribute to differences in substantially similar nucleic acid base sequences.
Amplification oligonucleotides are preferably 10 to 100 nucleotides in length, more preferably 22 to 44 nucleotides. Amplification oligonucleotides may have modifications, such as blocked 3′ and/or 5′ termini or additions including, but not limited to, specific nucleic acid sequences recognized by an RNA polymerase, (e.g., the promoter sequence for T7, T3, or SP6 RNA polymerase) sequences enhancing initiation or elongation of RNA transcription by an RNA polymerase (Kacian et al., U.S. Pat. No. 5,399,491 incorporated herein in its entirety including drawings).
Amplification oligonucleotides can be used in nucleic acid amplification procedures, such as the polymerase chain reaction or transcription associated amplification reactions, such as that using RNA polymerase, and reverse transcriptase, as described by Kacian and Fultz, supra. Other transcription based amplification systems are described in Sninsky et al., U.S. Pat. No. 5,079,351. Both of these references are hereby incorporated by reference herein. Preferably, promoters which are recognized by an RNA polymerase such as T7, T3 or SP6 RNA polymerase are used for the transcription-based amplification.
The term “amplification” means increasing the number of nucleic acid molecules having at least one specific target nucleic acid sequence. In order to increase the amplification of oligonucleotides containing target sequences, applicants preferably employ amplification systems in which target-template strands containing a double-stranded promoter region are produced to serve as templates for RNA polymerase. The target-template amplification is preferably carried out using a primer recognized by the DNA polymerase activity of reverse transcriptase.
VI. Methods of Amplification and Detection
In another aspect the invention provides a method for selectively amplifying HPV Type 16 and/or Type 18 nucleic acid in a sample by amplifying the nucleic acid with one or more probes of the invention.
In yet another aspect the invention features a method for detecting HPV Type 16 and/or Type 18 in a sample potentially containing the HPV Type 16 and/or Type 18 comprising the steps of:
a) providing to said sample one or more nucleic acid hybridization assay probes of the invention; and
b) detecting the formation of said detectable probe:target duplex which is indicative of the presence of HPV Type 16 and/or Type 18.
In a preferred embodiment the target nucleic acid is amplified with an amplification probe and detected with a detection probe. Examples of most preferred combinations of a particular amplification probe with a particular detection probe (i.e., the best-mix combination) are shown in the examples presented herein.
In other aspects, methods are described for using the hybridization assay probes, helper probes and amplification oligonucleotides to detect HPV Type 16 and/or Type 18 and to distinguish HPV Type 16 and/or Type 18 from closely related organisms. These amplification assays involve amplifying target nucleic acid in a sample to be tested, contacting the amplified sequences under stringent hybridization assay conditions with a hybridization assay probe which preferentially hybridizes with HPV Type 16 and/or Type 18 nucleic acid over nucleic acids present in closely related organisms, and detecting or measuring the hybridized probe.
The sample is preferably a clinical sample such as sputum, urine, blood, uro-genital secretion, clinical swabs, tissue sections or nucleic acid isolated from a clinical sample. More preferably, the amplification assay will be used to detect HPV Type 16 and/or Type 18 directly from a clinical sample. Detection directly from a clinical sample means that culture of the sample is not required prior to carrying out the amplification assay.
Preferably the amplification assay utilizes a hybridization probe consisting of one those listed above.
Helper probes for use in preferred embodiments of the amplification assay have, or are substantially similar to sequences selected from the group of Seq ID NOS: 117-128.
VII. Kits
The present invention also features a kit containing one or more of the hybridization assay probes or probe mixes of the invention. A kit contains all the necessary reagents to carry out the methods of detection described herein, for example one or amplification oligonucleotides or helper probes described herein. The kit may contain a one or more container means, a product insert label, and/or a buffer solution. Those skilled in the art will recognize that the probes of the present invention can readily be incorporated into one of the established kit formats which are well known in the art.
The oligonucleotides targeted to HPV offer a rapid, objective and sensitive method of identification and quantitation of HPV by detecting the presence of specific nucleic acid sequences unique to different species and strains of HPV Type 16 and/or Type 18. The probes of this invention can be used to identify, in hybridization assays, HPV from clinical samples. Combining an amplification step with a hybridization assay in the amplification assay increases the amount of target and thus the sensitivity of the assay. Both HPV type 16 and 18 can be amplified and detected in the same reaction vessel. A specially designed mismatch primer can amplify HPV Type 16 and/or Type 18 separately or simultaneously in the same reaction vessel. Probes can detect unspliced and heterogenous mRNA splices of HPV Type 16 and/or Type 18. Some of the probes of the present invention have been designed to exclude detection of mRNA targets which may be advantageous in certain applications.
Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.
DESCRIPTION OF THE PREFERRED EMBODIMENTS
Following is description of HPV nucleic acids, methods of making and using oligonucleotide probes, and kits containing such probes. In particular, different types of oligonucleotide probes are described (including hybridization assay probes, helper oligonucleotides and amplification oligonucleotides) which are useful for detecting HPV Type 16 or Type 18 in a clinical sample, such as a vaginal swab, a cervical swab, a urethral swab, a tissue sample, a body fluid or an experimental solution.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1 and 2 are representations respectively of the E6 region in the HPV Type 16 and HPV Type 18 genome. The top line represents that portion of the genome between the designated base pairs (vertical lines). Subsequently lower lines show splice acceptor sites and that portion of mRNA excised during transcription to produce either the E6* or E6** species of mRNA (area excised underlies triangle; i.e. in FIG. 1 the area between bases 233-416 of the HPV type 18 RNA is excised during transcription resulting in the E6*mRNA). Still lower lines represent preferred probes, primers, and amplifying oligonucleotides (rectangles with SEQ ID NOS. adjacent) that were used in the Examples section below, i.e., which were used in amplifying and detecting either HPV type 16 or HPV type 18 E6, E6*, or E6** mRNA (specific example numbers located left of line).



I. Construction and Use of Hybridization Assay Probes
A. Probe Design
Strands of deoxyribonucleic acid (“DNA”) or ribonucleic acid (“RNA”) are formed from nucleotide units joined in a specific arrangement, or sequence. Nucleotides each contain one “base” structure and are distinguished from one another by the base which they contain. Bases include adenine (A), cytosine (C), thymine (T), guanine (G), uracil (U), or inosine (I)).
The structures of the bases in the nucleotides permit certain pairs of bases to interact with one another through the formation of hydrogen bonds. Generally, A is hydrogen bonded to T or U, while G is hydrogen bonded to C. At any point along the chain, therefore, one may find the classical base pairs AT or AU, TA or UA, GC, or CG. One may also find AG, GU and other “wobble” or mismatched base pairs. Bases which can hydrogen bond are said to be complementary to one another.
Two single strands of DNA or RNA may specifically align and associate (“hybridize”) to form a double stranded structure in which the two strands are held together by the hydrogen bonds which form between pairs of complementary bases. When a first single-strand of nucleic acid contains sufficient contiguous complementary bases to a second, and those two strands are brought together under conditions promoting their hybridization, double-stranded nucleic acid results. Under appropriate conditions, double-stranded DNA/DNA, RNA/DNA, or RNA/RNA hybrids may be formed. Conditions which decrease the likelihood of forming a given double-stranded hybrid are said to be more stringent conditions than conditions in which hybrid formation is less likely.
A probe is generally a single-stranded nucleic acid having a base sequence which is complementary to some degree to a nucleic acid oligonucleotide “target region” comprising, consisting essentially of, or consisting of a “target sequence” sought to be detected. It may contain a detectable moiety such as a radioisotope, antigen or chemiluminescent moiety. A background description of the use of nucleic acid hybridization as a procedure for the detection of particular nucleic acids is described by Hogan et al., International Patent Application No. PCT/US87/03009, entitled “Nucleic Acid Probes for Detection and/Or Quantitation of Non-Viral Organisms,” incorporated by reference herein in its entirety, including any drawings.
Using methods known to those skilled in the art, and described herein, regions of RNA or DNA sequences from HPV Type 16 and/or Type 18 were identified. Nucleic acids from different organisms and having different nucleotide sequences can be aligned in regions of homology based on a conserved primary sequence. Potential target sequences for the hybridization assay probes described herein were identified by noting variations in the homology of the aligned sequences.
The sequence evolution at each of the regions is mostly divergent. Because of this divergence, corresponding DNA regions of more distant phylogenetic relatives of HPV Type 16 and/or Type 18 show greater differences from HPV Type 16 and/or Type 18 RNA or DNA than do the DNAs of phylogenetically closer relatives. Sufficient variation between HPV Type 16 and/or Type 18 and its closest know phylogenetic relatives, HPV 6, 11, 31, 33, 35, 39, 45, 51, 52, or 58, was observed to allow identification of prospective target sites and to design hybridization assay probes useful for distinguishing between the nucleic acids of these organisms.
B. Oligonucleotide Probes
We have designed hybridization assay probes specific for HPV Type 16 and/or Type 18, and we have successfully used those probes in a specific assay for the detection of HPV Type 16 and/or Type 18, distinguishing the strains from each other and what are believed to be their most closely related taxonomic or phylogenetic neighbors. These probes have also been shown to function in an amplification assay for HPV Type 16 and/or Type 18. In addition, in a more preferred embodiment, we have used the probes in an amplification assay to detect HPV Type 16 and/or Type 18 directly from clinical samples such as vaginal swabs, sputum, biopsies, tissues, uro-genital fluid, uro-genital washes. In addition, the probes can be used to detect HPV Type 16 and/or Type 18 in other clinical samples such as blood, and tissue sections, and in other samples such as swabs, secretions or biopsies. The featured probes preferably comprises, consists essentially of, or consist of one of the sequences identified above.
As illustrated by examples described below, the described hybridization assay probes can detect HPV Type 16 and/or Type 18 and distinguish it from HPV 6, 11, 31, 33, 35, 39, 45, 51, 52, or 58.
C. Hybridization
Hybridization assay probes and helper probes hybridize to their target sequence under stringent hybridization conditions. Oligonucleotides acting as helper probes or amplification oligonucleotides do not need to be able to preferentially hybridize to HPV Type 16 and/or Type 18 nucleic acid.
Preferential hybridization of hybridization assay probes to their target nucleic acids can be accomplished by choosing the appropriate hybridization assay conditions and proper probe design. The stability of the probe:target nucleic acid hybrid should be chosen to be compatible with the assay and washing conditions so that stable, detectable hybrids form only between nucleic acids having highly complementary sequences. Manipulation of one or more of the different assay parameters determines the exact sensitivity and specificity of a particular hybridization assay probe.
Preferential hybridization occurs under stringent hybridization assay conditions. In general, reducing the degree of complementarity of an oligonucleotide targeted region to its target sequence region decreases the degree or rate of hybridization of the probe oligonucleotide to its target sequence region.
Preferential hybridization can be measured using techniques known in the art and described herein, such as in the examples provided below. Preferably, there is at least a 100-fold difference between target and non-target hybridization signals, more preferably at least a 1,000-fold difference, even more preferably at least a 10,000-fold difference. Also preferably, non-target hybridization signals are not more than background level.
The following guidelines are useful for designing probes and determining specific stringent hybridization assay conditions. Because the sensitivity and specificity of hybridization reactions such as those described herein are affected by a number of factors, including the hybridization assay probe nucleotide sequence and length, the sequence of the target sequence region, the degree of homology between the target sequence and the analogous aligned HPV nucleic acid sequences from closely related organisms, the hybridization temperature, and the composition of hybridization reagents, the manipulation of one or more of those factors will determine the exact sensitivity and specificity of a particular probe, whether perfectly complementary to its target or not. The importance and effect of various hybridization assay conditions, explained further herein, are known to those skilled in the art.
First, the stability of the probe:target nucleic acid hybrid should be chosen to be compatible with the assay conditions so that stable, detectable hybrids form only between nucleic acids having highly complementary sequences. Probes should be designed to have an appropriate melting temperature (Tm). This may be accomplished by varying the probe length and nucleotide composition (percentage of G+C versus A+T). The probe length and nucleotide composition are preferably chosen to correspond to a Tm about 2-10° C. higher than the temperature at which the final assay will be performed. For instance, the Tm can be increased by avoiding long A and T rich sequences, or by terminating the hybrids with G:C base pairs. The beginning and end points of the probe should be chosen so that the length and % G+C content result in a Tm about 2-10° C. higher than the temperature at which the final assay will be performed.
In general, the optimal hybridization temperature for an oligonucleotide is approximately 5° C. below the melting temperature for a given duplex. Incubation at temperatures below the optimum temperature may allow mismatched base sequences to hybridize and can therefore decrease specificity. The longer the oligonucleotide, the more base pairs are present to hydrogen bond and, in general, the higher the Tm. The base composition of the probe is significant because G-C base pairs exhibit greater additional hydrogen bonding and therefore greater thermal stability than A-T base pairs. (See, e.g., Sambrook, et al., Molecular Cloning: A Laboratory Manual, 2:11 (2d ed. 1989) [hereinafter Molecular Cloning]) Thus, hybridization involving complementary nucleic acids of higher G-C content will be stable at higher temperatures.
To ensure specificity of a hybridization assay probe for its target, it is preferable to design probes which hybridize with target nucleic acids and not with non-target nucleic acids under conditions of high stringency. Under high stringency conditions only highly complementary nucleic acid hybrids will form. Accordingly, the stringency of the assay conditions determines the amount of complementarity which should exist between two nucleic acid strands in order to form a hybrid under those conditions. Stringency should be chosen to maximize the difference in stability between the probe:target hybrid and potential probe: non-target hybrids.
In addition, proper specificity may be achieved by minimizing the length of the hybridization assay probe having perfect complementarity to sequences of non-target organisms by minimizing the length of perfect complementarity to non-target organisms, avoiding G and C rich regions of homology to non-target sequences, and by constructing the probe to contain as many destabilizing mismatches to non-target sequences as possible. Whether a probe sequence is appropriate for detecting only a specific type of organism depends largely on the thermal stability difference between probe:target hybrids and probe:non-target hybrids. In designing probes, the differences in these Tm values should be as large as possible (e.g., at least 2° C. and preferably 5° C. or more).
The length of the target nucleic acid sequence and, accordingly, the length of the probe sequence can also be important. In some cases, there may be several sequences from a particular region, varying in location and length, which will yield probes with the desired hybridization characteristics. In other cases, one sequence may be significantly better than another which differs from it merely by a single base. While it is possible for nucleic acids that are not perfectly complementary to specifically hybridize, the longest stretch of perfectly homologous base sequence generally determines hybrid stability.
Third, regions of RNA which are known to form strong internal structures inhibitory to hybridization are less preferred target regions. Likewise, probes with extensive self-complementarity should be avoided. If a strand is wholly or partially involved in an intramolecular or intermolecular hybrid it will be less able to participate in the formation of a new intermolecular probe:target hybrid, Ribosomal RNA molecules are known to form very stable intramolecular helices and secondary structures by hydrogen bonding. By designing a probe to a region of the target nucleic acid which remains substantially single-stranded under hybridization conditions, the rate and extent of hybridization between probe and target may be increased.
HPV target sequences may initially be present as part of a nucleic acid duplex. For example, a genomic DNA target occurs naturally in a double stranded form. The polymerase chain reaction (PCR) and transcription-based amplification systems can also give rise to a double stranded product. These double-stranded targets require denaturation prior to hybridization. Appropriate denaturation and hybridization conditions are known in the art (e.g., E. M. Southern, J. Mol. Biol. 98:503 (1975)).
The rate of hybridization may be measured by determining the C0T1/2. The rate at which a probe hybridizes to its target is a measure of the thermal stability of the target secondary structure in the probe region. The standard measurement of hybridization rate is the C0T1/2 which is measured as moles of nucleotide per liter times seconds. Thus, the C0T1/2 value is the concentration of probe times the half-life of hybridization at that concentration. This value is determined by hybridizing various amounts of probe to a constant amount of hybrid for a fixed time.
In one example, 0.05 pmol of target is incubated with 0.0012, 0.025, 0.05, 0.1 and 0.2 pmol of probe for 30 minutes. The amount of hybrid after 30 minutes is preferably measured by using Hybridization Protection Assay as described below. The signal is then plotted as the logarithmic unit of the percent of maximum Relative Light Units (RLU) (from the highest probe concentration) versus probe concentration (moles of nucleotide per liter). RLU are a measurement of the quantity of photons emitted by the labeled-probe measured by the luminometer. The C0T1/2 is found graphically from the concentration corresponding to 50% of maximum hybridization multiplied by the hybridization time in seconds. These values range from 9.0×10−6 to 9×10−5 with the preferred values being less than 3.5×10−5.
Other methods of nucleic acid reassociation can be used. For example, Kohne and Kacian, EP 229442, entitled “Accelerated Nucleic Acid Reassociation Method,” describes a method to accelerate nucleic acid reassociation.
A preferred method to determine Tm measures hybridization using a hybridization protection assay (HPA) according to Arnold, et al., U.S. Pat. No. 5,283,171, entitled “Homogeneous Protection Assay.” Tm can be measured using HPA in the following manner. Probe molecules are labeled with an acridinium ester. Probe:target hybrids are formed in a lithium succinate buffer (0.1 M lithium succinate buffer, pH 5.0, 2 mM EDTA, 2 mM EGTA, 10% (w/v) lithium lauryl sulfate) using an excess amount of target. Aliquots of the solution containing the nucleic acid hybrids are then diluted in the lithium succinate buffered solution and incubated for five minutes at various temperatures starting below that of the anticipated Tm (typically 55° C.) and increasing in 2-5° increments. This solution is then diluted with a mild alkaline borate buffer (0.15 M sodium tetraborate, pH 7.6, 5% (v/v) polyoxethylene ether (TRITON® X-100)) and incubated at a lower temperature (for example 50° C.) for ten minutes.
Under these conditions the acridinium ester attached to the single-stranded probe is hydrolyzed, while the acridinium ester attached to hybridized probe is relatively protected from hydrolysis. Thus, the amount of acridinium ester remaining after hydrolysis treatment is proportional to the number of hybrid molecules. The remaining acridinium ester can be measured by monitoring the chemiluminescence produced from the remaining acridinium ester by adding hydrogen peroxide and alkali to the solution. Chemiluminescence can be measured in a luminometer (e.g., the Gen-Probe LEADER® I or LEADER® 50). The resulting data is plotted as percent of maximum signal (usually from the lowest temperature) versus temperature. The Tm is defined as the temperature at which 50% of the maximum signal remains. In addition to the method above, Tm may be determined by isotopic methods known to those skilled in the art (see e.g., Hogan et al., supra).
The Tm for a given hybrid varies depending on the nature of the hybridization solution used. Factors such as the concentration of salts, detergents, and other solutes can affect hybrid stability during thermal denaturation (see J. Sambrook, et al., supra). Conditions such as ionic strength and incubation temperature under which a probe will be used should be taken into account in constructing a probe. It is known that the thermal stability of a hybrid nucleic acid increases with the ionic strength of the reaction mixture. On the other hand, the addition of chemical reagents which disrupt hydrogen bonds, such as formamide, urea, DMSO and alcohols, can greatly reduce hybrid thermal stability and thereby increase the stringency of hybridization. In general, optimal hybridization for synthetic oligonucleotide probes of about 10-50 bases in length occurs approximately 5° C. below the melting temperature for a given duplex. Incubation at temperatures below the optimum may allow mismatched base sequences to hybridize and can therefore result in reduced specificity.
Examples of specific stringent hybridization conditions for hybridization assay probes are provided in the examples described below. Additional sets of stringent hybridization conditions can be determined based on the present disclosure by those of ordinary skill in the art. (See e.g., Molecular Cloning, supra.)
D. Oligonucleotide Synthesis
Defined oligonucleotides may be produced by any of several well known methods, including automated solid-phase chemical synthesis using cyanoethylphosphoramidite precursors. Barone et al., Nucleic Acids Res. 12:4051 (1984). In addition, other well-known methods for construction of synthetic oligonucleotides may be employed. Molecular Cloning, supra (2:11). Following synthesis and purification of an oligonucleotide, several different procedures may be utilized to determine the acceptability of the oligonucleotide in terms of size and purity. Such procedures include polyacrylamide gel electrophoresis and high pressure liquid chromatography, both of which are known to those skilled in the art.
Once synthesized, selected oligonucleotide hybridization assay probes may also be labeled with a reporter group by an of several well known methods. Molecular Cloning, supra (2:11). Useful labels include radioisotopes as well as non-radioactive reporting groups. Isotopic labels include 3H, 35S, 32P, 125I, Cobalt and 14C. Isotopic labels can be introduced into an oligonucleotide by techniques known in the art such as nick translation, end labeling, second strand synthesis, reverse transcription, and by chemical methods. When using radio-labeled probes, hybridization can be detected by autoradiography, scintillation counting, or gamma counting. The chosen detection method depends on the hybridization conditions and the particular radio-isotope used for labeling.
Non-isotopic materials can also be used for labeling, and may be introduced internally between nucleotides or at an end of the oligonucleotide. Modified nucleotides may be incorporated enzymatically or chemically. Chemical modifications of the probe may be performed during or after synthesis of the probe, for example, by the use of non-nucleotide linker groups as described by Arnold et al., entitled “Non-Nucleotide Linking Reagents for Nucleotide Probes,” European Pat. Appl. No. 88308766.0, Pub. No. 313219, incorporated by reference herein in its entirety including any drawings. Non-isotopic labels include fluorescent molecules, chemiluminescent molecules, enzymes, cofactors, enzyme substrates, haptens or other ligands.
Preferably, the hybridization assay probes are labeled with an acridinium ester. Acridinium ester labeling may be performed as described by Arnold et al., U.S. Pat. No. 5,185,439 entitled “Acridinium Ester Labeling and Purification of Nucleotide Probes” issued Feb. 9, 1993 and incorporated by reference herein in its entirety including any drawings.
II. Hybrids Containing a Hybridization Assay Probe and a Hpv Target Sequence
Another aspect of this invention is a hybrid formed by a hybridization assay probe and a target sequence from HPV Type 16 and/or Type 18. The formed hybrid is useful for detecting the presence of the target. For example, acridinium ester (“AE”) present in hybrid is resistant to hydrolysis in alkali solution while acridinium ester present in single-stranded nucleic acid is hydrolyzed in alkali solution. Thus, binding of AE-labeled probe to target can be detected, after hydrolysis of the unbound AE-labeled probe, by measuring chemiluminescence of acridinium ester remaining in the nucleic acid hybrid. Additionally, the formed hybrid can be used to as a basis to separate hybridized target from unhybridized probe, thereby removing background due to unhybridized probe. For example, hybrid molecules can be selectively retained on hydroxyapatite columns or filters under conditions not permitting retention of single-stranded probe using methods well known to those skilled in the art (See, e.g., Sambrook, supra).
III. Mixes of Hybridization Assay Probes and Helper Probes
Mixes of hybridization assay probes and helper probes can be used in the detection of HPV Type 16 and/or Type 18. Helper probes are used to enhance the rate of nucleic acid hybridization of an assay probe with its target nucleic acid and to facilitate the hybridization of the hybridization assay probe to its target. In addition, helper probes are sufficiently complementary to their target nucleic acid sequence to form a helper probe:target duplex under stringent hybridization assay conditions. The stringent hybridization assay conditions used with a given helper probe are determined by the conditions in which a hybridization assay probe is used to preferentially hybridize to its target sequence.
Regions of single stranded RNA and DNA can be involved in secondary and tertiary structures even under stringent hybridization assay conditions. Such structures can sterically inhibit, or even block hybridization of a hybridization assay probe to its target region. Hybridization of the helper probe alters the secondary and tertiary structure of the target nucleic acid, thereby rendering the hybridization assay probe target region more accessible. As a result helper probes enhance the kinetics and/or the Tm of the target:hybridization probe duplex. Helper probes are generally selected to hybridize to nucleic acid sequences located near the hybridization assay probe target region.
Helper probes which can be used with the hybridization assay probes of the present invention are targeted to nucleic acid sequence regions of the HPV genome and will preferably contain at least 14 nucleotides of which at least 12 out of the 14 nucleotides are perfectly complementary to a nucleic acid sequence present in the HPV target region.
IV. Amplification Oligonucleotides and Amplification Assay Conditions
Methods of amplifying the number of target sequences in a sample can be combined with the use of probe sequences to increase the sensitivity of the detection assay. (Miller, et al., Evaluation of Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test and PCR for Direct Detection of Mycobacterium tuberculosis in Clinical Specimens, J. Clin. Micro. 1994: 393-397; Reddy, et al., Mol. Cell. Probes 7: 121-126, 1993).
Amplification oligonucleotides can act as primers and may be part of promoter-primer combinations (i.e., a primer having an attached promoter sequence) to amplify a HPV Type 16 and/or Type 18 target sequence. Preferably the amplification oligonucleotide will have one of the following sequences: SEQ ID NOs: 1, 3, 13, 15, 21, 23, 37, 39, 41, 43, 49, 51, 53, 55, 69, 71, 89, 91, 93, 95, 101, 103, 105, 107, 109, 111, 113 and 115. In a more preferred embodiment, the amplification oligonucleotide will have one of the following sequences: SEQ ID Nos: 85, 87, 91, 93, 95, 101, 103, 105, 107, 109, 111, 113, and 115. In an even more preferred embodiment, the amplification oligonucleotide will have one of the following sequences: SEQ ID Nos: 109 and 111.
The degree of amplification observed with a set of primers or promoter-primers depends on several factors, including the ability of the oligonucleotides to hybridize to their specific target sequences and their ability to be extended or recognized by an RNA polymerase. While oligonucleotides of different lengths and base composition may be used, more preferred amplification oligonucleotides have target binding regions of 30-60 bases and a predicted hybrid Tm of about 65° C.
A target nucleic acid sequence present on a nucleic acid molecule can be amplified using an amplification oligonucleotide 5′ of the target sequence and an amplification oligonucleotide 3′ of the target sequence. The preferred target sites for amplification oligonucleotides are regions greater than about 14 bases in length. The amplified region, defined by the amplification oligonucleotides, is preferably about 350 bases or less in length, and more preferably about 150 bases or less in length.
Parameters affecting probe hybridization such as Tm, complementarity and secondary structure also affect primer hybridization and therefore performance of the amplification oligonucleotides. These considerations, which were discussed above in the section concerning probe design, can be modified depending upon the amplification conditions. For example, amplification can be carried out under conditions of lower stringency than diagnostic hybridization assay conditions.
The degree of non-specific extension (primer-dimer or non-target copying) can affect amplification efficiency. Primers are preferably selected to have low self- or cross complementarity, particularly at the 3′ ends of the sequence. Long homopolymer tracts and high GC content are preferably avoided to reduce spurious primer extension. Computer programs are commercially available to aid in this aspect of the design.
The terms “E6”, “E6*” and “E6**” refer to the open reading frame of the HPV genome which encodes the number six “early” gene. This gene is designated by the prefix letter “E” for early, in conjunction with the arabic numeral “6” for the number six. The modifying terms designated by the characters “*” or “**” refer to alternatively spliced messenger RNAs which employ alternative acceptor splice sites within the E6 region of the HPV genome. Splicing at these sites during transcription of the E6 gene, results in the production of two different species of E6 mRNA's which differ in length from the canonical E6 mRNA. Therefore, three different E6 messenger RNA's may be generated depending upon which acceptor splice site is used within the E6 region of the genome. The HPV type 16 genome appears to express all three types of E6 mRNA while the HPV type 18 genome appears to express HPV type 18 E6 and E6* only.
In a particular embodiment of this invention primers and probes have been designed to amplify and detect each one of the heterogeneous E6 messenger RNA species. In a more preferred embodiment, two types of E6 messenger RNA may be amplified and detected by a set of primers and probes in the same reaction vessel. In the most preferred embodiment, all E6 messenger RNA species of a particular type may be simultaneously amplified and detected in the same reaction vessel by the primers and probes of this invention.
EXAMPLES
Described herein are preferred sequences for hybridization assay probes, helper probes, and amplification oligonucleotides designed to hybridize to target sequences in HPV Type 16 and/or Type 18 RNA or DNA. In addition, preferred embodiments of mixes of hybridization assay probes and helper probes useful for detecting HPV Type 16 and/or Type 18 are described. Also described are hybrids formed by a hybridization assay probe and a target sequence. Preferred methods for using the probes and amplification oligonucleotides to detect HPV Type 16 and/or Type 18 are included in this description.
The following examples illustrate several preferred embodiments of the present invention and should in no way be considered as limiting the scope of the invention which is defined in the appended claims. Various modifications of these examples could readily be performed by those skilled in the art without departing from the scope of the invention as defined in the claims.
Example 1
Probes Distinguishing HPV Type 16 from Type 18 and Vice Versa
This example illustrates the specificity of probes designed to be specific for HPV type 16 and 18. One hundred million copies of plasmid DNA containing a portion of the E6 gene from either HPV type 16 or type 18 were hybridized to a probe of SEQ ID NO. 5 or SEQ ID NO. 45.
To perform the hybridization, linearized plasmid contained HPV DNA sequences were heated to 95° C. for 5 minutes in 50 μl of a solution containing H2O and cooled 1-2 minutes in a room temperature water bath. Then, 0.025-0.05 pmol (=2.6×106 RLUs/assay) of either (SEQ ID NO. 5) probe or SEQ ID NO. 45 probe was added to a final volume of 100 μl of 0.05 M lithium succinate pH 5, 0.6 M LiCl, 1% (w/v) lithium lauryl sulfate, 10 mM EDTA, 10 mM EGTA.
Hybridization was conducted at 60° C. for 15 minutes. Following hybridization, 300 μl of 0.15 M sodium tetraborate pH 8.5, 1% TRITON X-100 at 60° C. was added for 5 minutes. Samples were subsequently read in a luminometer equipped with automatic injection of 0.1% hydrogen peroxide in 1 mM nitric acid, followed by injection of a 1 N sodium hydroxide solution. The results, given in Table 1, are reported in Relative Light Units (RLU), a measure of the photons detected by the luminometer from labeled hybrids formed between probes SEQ ID NO. 5 and SEQ ID NO. 45 and their target nucleotide sequence.







TABLE 1







SPECIFICITY OF PROBES SEQ ID NOs.


5 & 45 FOR HPV TYPE 16 AND 18.









PROBE












SEQ ID NO. 5
SEQ ID NO. 45



TARGET
RLU
RLU














HPV type 16 E6
226,896
1,048



cloned DNA





HPV type 18 E6
745
817,751



cloned DNA









The results (an average of two trial hybridization reactions) demonstrate that probe SEQ ID NO. 5 detects HPV type 16 E6 sequences in preference to those of HPV type 18. Similarly, the probe SEQ ID NO. 45 detects HPV type 18 E6 sequences in preference to those of HPV type 16.
This example illustrates that the designed oligonucleotides are capable of distinguishing target sequences from phylogenetically close species, since HPV type 16 and HPV type 18 are immediately related phylogenetically (see, Van Ranst et al., J. Gen. Vir., 73: 2653-60, 1992).
Example 2
Amplification and Detection of HPV Type 16 E6 DNA and RNA
This example illustrates the use of amplification oligonucleotides and hybridization assay probes targeted to HPV type 16 to facilitate amplification and detection of HPV type 16 nucleic acid. In this example, an assay probe for HPV type 16, of the same sense as E6 mRNA, was used to detect the products of a nucleic acid amplification method. (Kacian et al., supra).
Cloned DNA representing a portion of HPV type 16 E6 DNA was purified using a standard mini-prep procedure with reagents purchased from Qiagen®. Nucleic acid from cultured SiHa cells was prepared following trypsinization and centrifugation. The cell pellet was washed, resuspended and counted in phosphate buffered saline. Defined numbers of cells were pelleted and resuspended in Reagent I, a solution containing 3% (w/v) lithium lauryl sulfate, 30 mM sodium phosphate pH 6.8, 1.0 mM ethylene diamine tetra-acetic acid (EDTA), 1.0 mM ethylene glycol bis(beta-amino ethyl ether) N,N,N′,N′ tetra-acetic acid (EGTA). Detergent was removed from samples by precipitation following addition of potassium acetate to a final concentration of 0.6 M. The nucleic acid contained in the supernatant was amplified directly.
The target nucleic acid was heated to 95° C. for 5 minutes, cooled to 60° C. for 15 minutes in 90 μl of a solution containing 30 pmole of a promoter-primer synthesized with a promoter sequence 5′-AATTTAATACGACTCACTATAGGGAGA-3′ (SEQ ID NO. 97) at the 5′ end and a target hybridizing region 5′-CAGGACACAGTGGCTTTTGAC-3′ at the 3′ end (SEQ ID NO. 85), and 30 pmole of a primer synthesized with the sequence 5′-GACATTATTGTTATAGTTTGTATGGAAC-3′ (SEQ ID NO. 1). Following a 5 minute incubation at 37° C., 900 U Moloney Murine Leukemia Virus (MMLV) reverse transcriptase and 400 U T7 RNA polymerase were added. The reactions were performed in 50 mM Tris-HCl, pH 7.6, 100 mM potassium acetate, 17.5 mM MgCl2, 5.0 mM DTT, 2.0 mM spermidine, 6.2 mM rATP, 2.5 mM rCTP, 6.2 mM rGTP, 2.5 mM rUTP, 1 mM dATP, 1 mM dCTP, 1 mM dGTP, 1 mM dTTP, 7 mM N-Acetyl-L-cysteine, 0.03 mM EDTA, 3% glycerol, and 10% Tween.
Following a three hour incubation at 37° C., 10 μl of each reaction was assayed by hybridization using an acridinium ester labeled probe synthesized with sequence 5′-GAACAGCAAT ACAACAAACC GTTGTGTG-3′(SEQ ID NO. 5) in 100 μl of 0.05 M lithium succinate pH 5, 0.6 M LiCl, 1% (w/v) lithium lauryl sulfate, 10 mM EDTA, 10 mM EGTA at 60° C. for 15 minutes, followed by addition of 300 μl of 0.15 M sodium tetraborate pH 8.5, 1% TRITON X-100 at 60° C. for 5 minutes.
Samples were read in a luminometer equipped with automatic injection of 0.1% hydrogen peroxide in 1 mM nitric acid, followed by injection of a 1 N sodium hydroxide solution. Results are given in Relative Light Units (RLU), a measure of the photons detected by the luminometer. The results shown are the average of two reactions.







TABLE 2







AMPLIFICATION AND DETECTION OF


HPV type 16 E6 DNA AND RNA.


HPV type 16 E6 nucleic acid









RLU













copies cloned DNA




0
945



1,000
5,247



10,000
35,620



1,000,000
881,886



No. SiHa cells




100
1,335



1,000
2,182



10,000
428,602









These primers and probes were also able to amplify and detect DNA and RNA prepared from CaSki cells.

Example 3
Amplification and Detection of HPV Type 18 Sequences in HeLa Cell Extracts
This example illustrates the use of amplification oligonucleotides and hybridization assay probes targeted to HPV type 18 to amplify and detect HPV type 18 nucleic acid. In this example, an assay probe designed to HPV type 18, of the same sense as E6 mRNA, was used to detect the products of target nucleic acid amplification.
Cloned DNA representing a portion of the HPV type 18 E6 DNA, or nucleic acid prepared from HeLa cells (which contain HPV type 18 E6 nucleic acid sequences), was amplified with a primer synthesized with SEQ ID NO. 53 and a promoter primer containing the sequence (SEQ ID NO. 97) 5′-AATTTAATACGACTCACTATAGGGAGA-3′ at the 5′ end and a target hybridizing sequence (SEQ ID NO. 109) at the 3′ end.
Cultured HeLa cells were trypsinized and centrifuged, washed, resuspended and counted in phosphate buffered saline. Defined numbers of cells were pelleted and suspended in Reagent I. The detergent was precipitated with a 0.6 M final concentration of potassium acetate and the nucleic acid contained in the supernatant was amplified directly. Cloned DNA was placed into a mock specimen prepared by potassium acetate precipitation of detergent from Reagent I.
The target nucleic acid was heated to 95° C. for 5 minutes, cooled to 60° C. for 15 minutes, then cooled to 37° C. in 90 μl of a solution containing 30 pmole each of the primer and promoter-primer. Following 5 minutes at 37° C., 900 U MMLV reverse transcriptase and 400 U T7 RNA polymerase were added. The reaction conditions were as described in Example 1.
Following a three hour incubation at 37° C., 10 μl of the reaction were assayed by hybridization using an acridinium ester labeled probe synthesized with SEQ ID NO. 45 in 100 μl of 0.05 M lithium succinate pH 5, 0.6 M LiCl, 1% (w/v) lithium lauryl sulfate, 10 mM EDTA, 10 mM EGTA at 55° C. for 15 minutes, followed by addition of 300 μl of 0.15 M sodium tetraborate pH 8.5, 1% TRITON X-100 and incubation at 55° C. for 5 minutes. Luminescence values of the samples were determined as described in Example 1.







TABLE 3







AMPLIFICATION AND DETECTION OF HPV TYPE


18 SEQUENCES IN HELA CELL EXTRACTS.*









RLU













Copies cloned HPV type 18 E6 DNA




0
862



100
15,993



1,000
279,565



10,000
820,591



No. HeLa Cells




10,000
1,216,105



1,000
380,040



100
40,085





*Plasmid DNA was added following detergent precipitation. One HeLa cell contains approximately 10-50 copies of DNA. Therefore, 100 cells HeLa are equivalent to approximately 1,000-5,000 copies of DNA. HeLa number values which are lower than predicted from cloned DNA, are most likely the result of a loss of material during detergent precipitation.






Example 4
Amplification and Detection of Both HPV Type 16 and Type 18 in the Same Reaction Vessel
Amplification oligonucleotides, as described herein, were designed to amplify both HPV type 16 and 18 DNA in the same reaction vessel, followed by detection with specific probes which can distinguish between the 16 and 18 variants. In this example, cloned target DNA from both HPV type 16 and 18 was amplified, followed by detection with the assay probes described.
Cloned DNA representing the HPV type 16 E6 DNA was amplified with a non-T7 primer consisting of SEQ ID NO. 1 and a promoter primer synthesized with a 3′ target hybridizing sequence, SEQ ID NO. 85. Cloned DNA representing HPV type 18 DNA was amplified with a primer consisting of SEQ ID NO. 53 and a promoter primer with a 3′ target hybridizing sequence SEQ ID NO. 109, both promoter primers containing the sequence 5′-AATTTAATACGACTCACTATAGGGAGA-3′ at their 5′ end.
The target nucleic acid in detergent precipitated Reagent I was heated to 95° C. for 5 minutes, cooled to 60° C. for 15 minutes, then cooled to 37° C. in 90 μl of a solution containing 30 picomoles of each primer and promoter primer. Following 5 minutes at 37° C., 900 U MMLV reverse transcriptase and 400 U T7 RNA polymerase were added. The reaction conditions are as described in Example 1.
Following a three hour incubation at 37° C., ten μl of the reaction was assayed by hybridization using an acridinium ester labeled probe synthesized SEQ ID NO. 45, in 100 μl of 0.05 M lithium succinate pH 5, 0.6 M LiCl, 1% (w/v) lithium lauryl sulfate, 10 mM EDTA, 10 mM EGTA at 55° C. for 15 minutes, followed by addition of 300 μl of 0.15 M sodium tetraborate pH 8.5, 1% TRITON X-100 and incubation at 55° C. for 5 minutes. Ten μl of each reaction was also analyzed with acridinium ester labeled probe SEQ ID NO. 5 in 100 μl as described for probe SEQ ID NO. 45 except that the incubations were performed at 60° C. Luminescence values of samples were determined as described in Example 1.
As can be determined from Table 4, the designed oligonucleotide primers work well in the same reaction vessel. The amplification of either HPV Type 16 and/or Type 18 does not hinder amplification of the other Papillomavirus and the presence of either HPV Type 16 and/or Type 18 hybridization probe does not interfere with the ability of the other probe to distinguish HPV type 16 from 18 or vice versa. In fact, the specificity of each probe is ten times greater for its target than for a non-target nucleotide sequence.







TABLE 4







CO-AMPLIFICATION OF HPV TYPE 16 AND 18.








PROBE










Copies HPV type
Copies HPV type
RLU










16 DNA
18 DNA
SEQ ID NO. 5
SEQ ID NO. 45













1,000,000
1,000,000
1,115,026
1,057,903


10,000
1,000,000
643,415
974,109


1,000
1,000,000
152,810
944,290


100
1,000,000
6,852
930,188


0
0
1,243
1,140


1,000,000
1,000,000
991,682
886,852


1,000,000
10,000
1,003,151
821,532


1,000,000
1,000
1,001,966
389,796


1,000,000
100
997,714
10,157









Example 5
Designed Mismatch Primer can Amplify HPV Type 16 and/or Type 18 Separately or Simultaneously
A promoter primer (SEQ ID NO. 113) was designed with mismatches to both HPV type 16 and 18 target nucleotide sequences. This promoter primer design has the ability to amplify both HPV type 16 and 18 DNA target sequences separately, or concurrently in the same reaction vessel.
Double stranded cloned targets were amplified with 30 pmole each of promoter primer synthesized with promoter SEQ ID NO. 97 at the 5′ end and a target hybridizing SEQ ID NO. 113 or SEQ ID NO. 93 at the 3′ end, in the presence of a primer synthesized with SEQ ID NO. 69 for HPV type 18 or a primer synthesized with SEQ ID NO. 37 for HPV type 16.
A 75 μl volume of the target nucleic acid was heated to 95° C. for 15 minutes and cooled to 42° C. Following 5 minutes at 42° C., 600 U MMLV reverse transcriptase and 300 U T7 RNA polymerase were added. Amplification reactions were performed in 50 mM Tris-HCl, pH 8.5, 5 mM potassium chloride, 20 mM MgCl2, 4 mM rATP, 4 mM rCTP, 4 mM rGTP, 4 mM rUTP, 1 mM dATP, 1 mM dCTP, 1 mM dGTP, 1 mM dTTP, 20 mM N-Acetyl-L-cysteine, and 5% glycerol.
Following a two hour incubation at 42° C., triplicate amplification reactions were pooled and 100 μl of each pool was hybridized with an acridinium ester labeled probe synthesized with SEQ ID NO. 73 for the detection of HPV type 18 or SEQ ID NO. 33 for the detection of HPV type 16.







TABLE 5







CO-AMPLIFICATION OF HPV TYPE 16 AND


18 USING A MISMATCH PROMOTER PRIMER.









RLU



Primers:











SEQ ID NO
SEQ ID No.
SEQ ID Nos.



No. 93/37
113/69
113/37 or 69



T7/Non-T7
T7/Non-T7
T7/Non-T7









Probe:













SEQ ID Nos.


Target
SEQ ID No. 33
SEQ ID No. 73
33 and 73













1,000 copies HPV type
251,581
6,495
158,771


16 DNA





1,000 copies HPV type
2,335
255,227
528,971


18 DNA





0 copies
4,509
3,379
6,105









As can be seen from an examination of Table 5, the single mismatch promoter primer of SEQ ID NO. 113, can amplify two HPV nucleic acids (16 & 18) differing in sequence by 3 bases in the primer binding site.

Example 6
Amplification and Detection of Spliced E6* mRNA of HPV Type 16
This example illustrates the use of amplification oligonucleotides and hybridization assay probes for HPV type 16 to amplify and specifically detect E6* mRNA of HPV type 16. In this example, an assay probe of the same sense as the target E6* RNA nucleic acid was used to detect the products of a target nucleic acid amplification method.
Cultured SiHa cells were trypsinized, centrifuged, washed, resuspended and counted in phosphate buffered saline. Defined numbers of cells were pelleted and resuspended in Reagent I (i.e., Example 1). Detergent was removed from samples suspended in Reagent I by precipitation following addition of potassium acetate to a final concentration of 0.6 M. The nucleic acid contained in the supernatant was amplified directly.
The target nucleic acid was heated to 95° C. for 5 minutes, cooled to 60° C. for 15 minutes in 90 μl of a solution containing 30 pmole of each of the two primers. The promoter-primer had a target hybridizing region at the 3′ end (SEQ ID NO. 89), and the second primer had a target hybridizing region (SEQ ID NO. 21) at its 3′ end. Following 5 minutes at 37° C., 900 U MMLV reverse transcriptase and 400 U T7 RNA polymerase were added. The reaction conditions were as described in Example 1. [performed in 50 mM Tris-HCl, pH 7.6, 100 mM potassium acetate, 17.5 mM MgCl2, 5.0 mM DTT, 2.0 mM spermidine, 6.2 mM rATP, 2.5 mM rCTP, 6.2 mM rGTP, 2.5 mM rUTP, 1 mM dATP, 1 mM dCTP, 1 mM dGTP, 1 mM dTTP, 7 mM N-Acetyl-L-cysteine, 0.03 mM EDTA, 3% glycerol, Tween-20®]. Following a three hour incubation at 37° C., 10 μl of the reaction was assayed by hybridization using an acridinium ester labeled probe synthesized with SEQ ID NO. 9 in 100 μl of 0.05 M lithium succinate pH 5, 0.6 M LiCl, 1% (w/v) lithium lauryl sulfate, 10 mM EDTA, 10 mM EGTA at 60° C. for 15 minutes, followed by addition of 300 μl of 0.15 M sodium tetraborate pH 8.5, 1% TRITON X-100 and incubation at 60° C. for 5 minutes. Luminescence values of the samples were determined as described in Example 1. The results are the average of two reactions.







TABLE 6







AMPLIFICATION AND DETECTION


OF HPV TYPE 16 E6* mRNA.










No. SiHa cells
RLU













0
656



1,000
18,391



10,000
418,717









These primers and probes were also able to amplify and detect DNA and RNA prepared from CaSki cells.

Example 7
Hybridization Assay Probes Detect HPV Type 16 E6, E6* and E6** Nucleic Acid
Assay probes designed for HPV type 16 are able to detect products of the amplification of E6 nucleic acid, including un-spliced, E6, E6* and E6** mRNA targets. The primer and promoter primer were oriented in such a way that the predominant amplification product was the same sense as the messenger RNA. In this example, nucleic acid prepared from Caski cells was used. Defined numbers of cells were pelleted and suspended in Reagent I. Potassium acetate was added to a final concentration of 0.6 M to precipitate the detergent and the nucleic acid contained in the supernatant was amplified directly, Nucleic acid from 1.6×104 cells was amplified as described in Example 1 with a promoter primer synthesized with a 5′ T7 promoter and a 3′ target hybridizing SEQ ID NO. 21, and 30 pmole of a primer synthesized with SEQ ID NO. 13. Ten μl of each reaction was hybridized to probes synthesized with SEQ ID NO. 29, SEQ ID NO. 25, or SEQ ID NO 17.







TABLE 7







SPECIFIC DETECTION OF UN-SPLICED AND


SPLICED E6 MRNA PREPARED FROM CASKI CELLS.









RLU



Target: HPV16











E6 mRNA
E6* mRNA
E6** mRNA









Probe:










Sample
SEQ ID NO. 29
SEQ ID NO. 25
SEQ ID NO. 17














16,000
cells
551,715
38,908
236,324


0
cells
1,006
1,295
2,375









The results indicated in Table 7 support reports in the literature that the heterogeneous splice variations of E6 mRNA vary in quantity within the cell.
Example 8
Primers and Probes Detect HPV Type 18 E6* mRNA
Primers and probes capable of detecting the E6* mRN an HPV type 18 were designed. Defined numbers of HeLa cells were suspended in Reagent I and the nucleic acid was recovered following detergent precipitation, as in Example 7, and amplified directly. Amplification reactions were performed with a promoter primer synthesized with a 5′ promoter SEQ ID NO. 97 and a target hybridizing region SEQ ID NO. 101, and a primer consisting of SEQ ID NO. 49. Reaction conditions were as in Example 1. Ten μl of the amplification reaction was hybridized with an acridinium ester labeled probe synthesized with SEQ ID NO. 77 in 100 μl of 0.05 M lithium succinate pH 5, 0.6 M LiCl, 1% (w/v) lithium lauryl sulfate, 10 mM EDTA, 10 mM EGTA at 55° C. for 15 minutes, followed by addition of 300 μl of 0.15 M sodium tetraborate pH 8.5, 1% TRITON X-100 at 55° C. for 5 minutes. Luminescence values were determined as in Example 1.







TABLE 8







AMPLIFICATION AND DETECTION OF HPV TYPE 18 E6* mRNA


HPV type 18 E6*










No. HeLa cells
RLU













10,000
1,309,947



1,000
18,231



100
2,750



0
1,144









Example 9
Probes & Primers Amplify & Detect Both Spliced and Unspliced HPV Type 18 E6 mRNA
Primers and probes were designed to amplify and detect un-spliced and spliced E6 sequences of HPV type 18. A primer synthesized with SEQ ID NO. 41 and a promoter primer synthesized with a 5′ promoter sequence (SEQ ID NO. 97) 5′-AATTTAATACGACTCACTATAGGGAGA-3′ and a 3′ target hybridizing region SEQ ID NO. 109 were used to amplify cloned DNA representing HPV type 18 E6 sequences. The target nucleic acid was heated to 95° C. for 15 minutes, and cooled to 42° C. in 75 μl of a solution containing 25 picomoles of the primer and promoter primer. Following 5 minutes at 42° C., 600 U MMLV reverse transcriptase and 300 U T7 RNA polymerase were added. Amplification reactions were performed in 50 mM Tris-HCl, pH 8.5, 35 mM potassium acetate, 20 mM MgCl2, 4 mM rATP, 4 mM rCTP, 4 mM rGTP, 4 mM rUTP, 1 mM dATP, 1 mM dCTP, 1 mM dGTP, 1 mM dTTP, 20 mM N-Acetyl-L-cysteine, and 5% glycerol. Following a two hour incubation at 42° C., 20 μl of each reaction was assayed by hybridization using an acridinium ester labeled probe of SEQ ID NO. 81 for E6* detection, SEQ ID NO. 65 for E6 detection, or SEQ ID NO. 57 for both E6 and E6* detection, using conditions described in Example 1. An unlabeled helper probe consisting of sequence SEQ ID NO. 61 was used with probes 81 and 65, an unlabeled helper probe of sequence SEQ ID NO. 117 was used with probe SEQ ID NO. 57.







TABLE 9







AMPLIFICATION AND DETECTION OF HPV TYPE


18 SPLICED AND UNSPLICED E6 mRNA











RLU




Target: HPV18













E6*
E6
E6 and E6*











Probe:













SEQ ID
SEQ ID
SEQ ID




NO. 81
NO. 65
NO. 57











Helper:












E6 Target added
SEQ ID
SEQ ID
SEQ ID



to reaction:
NO. 61
NO. 61
NO. 117















106 unspliced
1,057
912,867
975,288



105 unspliced
703
343,900
406,958



104 unspliced
546
208,246
255,093



103 unspliced
582
58,946
90,836



106 spliced
1,387,098
5,709
1,499,335



105 spliced
704,412
3,430
807,331



104 spliced
184,847
1,446
300,340



103 spliced
27,907
936
46,798



Negative
564
1,542
619









Example 10
HPV Type 16 & 18 Detection from Clinical Samples
Endocervial swabs from patients attending a clinic were placed into a tube containing 5 ml of Reagent I. The swabs were expressed and discarded. Nucleic acid from Reagent I was extracted following addition of potassium acetate to 0.6 M and removal of the detergent pellet by centrifugation. A sample of the nucleic acid in the supernatant was analyzed for the presence of HPV by established procedures. In one test, a portion of the nucleic acid was phenol chloroform extracted and amplified by polymerase chain reaction using published primers targeting the L1 gene sequences. Samples were also assayed for amplification of L1 sequences by agarose gel analysis directly or following restriction endonuclease digestion. Alternatively, samples were analyzed by hybridization with acridinium ester labeled probes directed to published sequences of HPV type 16 and 18. Samples positive by gel for types other than HPV type 16 or HPV type 18 were assayed by with acridinium ester labeled L1 probes corresponding to the identified type (HPV 6, 11, 31, 33, 35, 39, 45, 51, 52 and 58) for confirmation. Samples characterized in this manner were then tested in the amplification format using the primers and promoter primers described herein. Amplified samples were assayed by HPA with detection probes directed to HPV type 16 (SEQ ID NO. 5) or HPV type 18 (SEQ ID NO. 45) sequences.







TABLE 10







DETECTION OF HPV TYPE 16 &


18 FROM CLINICAL SAMPLES












HPV type by



Clinical isolate
HPV type by L1
AE probe
Amplification


number
PCR RFLP
hybridization
result













16
6
6
16−


25
6
6
16−


28
6
6
16−


797
6
6 + 11 + 33
16−


3
16
16
16+


29
16
16
16+


41
16
16
16+


72
16 + 6
16+6
16+


133
16
16
16+


146
16
16
16+


173
16 + 33
16 + 33
16+


185
16 + G × 3(*)
16
16+


190
16
16
16+


204
16
16
16+


216
16
16
16+


224
16 + G × 3(*)
16
16+


234
16
16
16+


293
16 + 35
16 + 35
16+


341
16
16
16+


364
16
16
16+


368
16 + 58
16
16+


369
16 + 58
16
16+


370
16 + 58
16
16+


789
16
16
16+


796
16
16
16+


96
18
18
18+


114
18
18
18+


177
18 + G × 9(*)
18
16 − 18+


290
18
18 + 16
18


297
18
18
18


798
11 + 18
18
18


101
31
31
16−


118
31
31
16−


115
33
33
16−


166
33
33
16−


791
33
33
16−


192
39
N.D.
16−


109
58
N.D.
16−


175
58
N.D.
16−


176
58
N.D.
16−


182
58
N.D.
16−


779
58
N.D.
16−









The data in this table are reported as positive if the RLU value was over the value of the negative control by a factor of 1.5-2.0× for the luminometer employed in this example. Acridinium ester labeled probe SEQ ID NO. 5 was used for detection of HPV type 16 and acridinium labeled probe SEQ ID NO. 45 was used with unlabeled helper probe SEQ ID NOs. 121, 123, 127, or 125 for detection of HPV type 18.
The data shown in the various examples described above confirm that the novel probes herein described and claimed are capable of distinguishing HPV from their known nearest phylogenetic neighbors. Furthermore, complementary oligonucleotide probes, i.e., those having the same sense as the target, are utilized to detect the products of target amplification procedures now being utilized to increase the detection sensitivity of assays for organisms.
Sequence information was obtained experimentally and from published information. (See Weisburg, et al., J. Bacteriol 171:6455 (1989).) Experimental information was obtained by isolating and sequencing RNA or DNA from various organisms using standard techniques known in the art. More specifically, RNA sequence information was obtained by first using oligonucleotide primers complementary to conserved regions which vary little between prokaryotic organisms. The oligonucleotide primers were hybridized to the conserved regions in purified RNA and extended with the enzyme reverse transcriptase and deoxyribonucleotides to produce cDNA. E.g., Lane et al., Proc. Nat'l Acad. Sci. USA 82:6955 (1985).
The invention illustratively described herein suitably may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims.
Those references not previously incorporated herein by reference, including both patent and non-patent references, are expressly incorporated herein by reference for all purposes. Other embodiments are within the following claims.

## Claims

1. A composition for amplification and detection of mRNA of HPV type 16 comprising:
amplification oligonucleotides selected from the group consisting of
a promoter-primer made up of a 5′ promoter sequence covalently linked to a 3′ target hybridizing region consisting of SEQ ID NO:89 and a primer consisting of SEQ ID NO:21 , and
a promoter-primer made up of a 5′ promoter sequence covalently linked to a 3′ target hybridizing region consisting of SEQ ID NO:21 and a primer consisting of SEQ ID NO:13, and

a detection probe oligonucleotide consisting of the sequence of SEQ ID NO:25 or the completely complementary sequence of SEQ ID NO:25.

2. A kit comprising the composition of claim 1.

3. The kit of claim 2 further comprising a detection probe consisting of SEQ ID NO:29.

4. The kit of claim 2 further comprising a detection probe oligonucleotide consisting of SEQ ID NO:17.

5. The composition of claim 1 wherein the promoter-primer is made up of a 5′ promoter consisting of SEQ ID NO:97 covalently linked to the 3′ target hybridizing region consisting of SEQ ID NO:89, the primer consists of SEQ ID NO:21, and the detection probe is labeled with an acridinium ester label.

6. The composition of claim 1, wherein the promoter-primer is made up of a 5′ promoter sequence consisting of SEQ ID NO:97 covalently linked to the 3′ target hybridizing region consisting of SEQ ID NO:21, the primer consists of SEQ ID NO:13, and the detection probe consists of SEQ ID NO:25 labeled with an acridinium ester.

7. The composition of claim 1, wherein the detection probe oligonucleotide is labeled with a non-isotopic label selected from the group consisting of fluorescent molecules, chemiluminescent molecules, enzymes, co-factors, enzyme substrates, haptens or other ligands.

8. The composition of claim 1, wherein the detection probe oligonucleotide is labeled with a chemiluminescent molecule.

9. A method of detecting a HPV Type 16 nucleic acid in a sample comprising the steps of:
a) contacting a sample containing HPV type 16 nucleic acid with a mixture of amplification oligonucleotides consisting of a promoter-primer made up of a 5′ promoter sequence covalently linked to a 3′ target hybridizing region consisting of SEQ ID NO:21and a primer consisting of SEQ ID NO:13;
b) amplifying the HPV type 16 nucleic acid in an in vitro amplification reaction that includes at lease one polymerase that acts with an amplification oligonucleotide in the mixture to produce one or more HPV type 16 amplification products by using the HPV type 16 nucleic acid as a template;
c) contacting the HPV type 16 amplification products with at least one hybridization assay probe consisting of SEQ ID NO:25 that forms a detectable SEQ ID NO:25 probe: HPV type 16 target hybrid under stringent hybridization conditions; and
d) detecting a signal from the SEQ ID NO:25 probe: MN type 16 target hybrid, thereby indicating the presence of HPV type 16 in the sample.

10. The method of claim 9, further comprising additional steps after the amplifying step that include a contacting step wherein the HPV type 16 amplification products are contacted with a hybridization assay probe consisting of SEQ ID NO:29 to form a detectable SEQ ID NO:29 probe: HPV type 16 target hybrid under stringent hybridization conditions, and a detecting step that detects a signal from the SEQ ID NO:29 probe: HPV type 16 target hybrid, thereby indicating the presence of an amplification product made from an HPV type 16 E6 mRNA.

11. The method of claim 10, wherein the detecting step detects a signal from a chemiluminescent label attached to the probe in the SEQ ID NO:29probe:
HPV type 16 target hybrid.

12. The method of claim 9, further comprising additional steps after the amplifying step that include a contacting step wherein the HPV type 16 amplification products are contacted with a hybridization assay probe consisting of SEQ ID NO:17 to form a SEQ ID NO:17 detectable probe: HPV type 16 target hybrid under stringent hybridization conditions, and a detecting step that detects a signal from the SEQ ID NO:17 probe: HPV type 16 target hybrid, thereby indicating the presence of an amplification product made from an HPV type 16 E6** mRNA.

13. The method of claim 12, wherein the detecting step detects a signal from a chemiluminescent label attached to the probe in the SEQ ID NO:17probe:
HPV type 16 target hybrid.

14. The method of claim 9, wherein the promoter-primer is made up of a 5′ promoter sequence consisting of SEQ ID NO:97 covalently linked to the 3′ target hybridizing region.

15. The method of claim 9, wherein the detecting step detects a signal from a chemiluminescent label attached to the probe in the SEQ ID NO:25 probe: HPV type 16 target hybrid.

16. A method of detecting a HPV Type 16 nucleic acid in a sample comprising the steps of:
a) contacting a sample containing HPV type 16 nucleic acid with a mixture of amplification oligonucleotides consisting of a promoter-primer made up of a 5′ promoter sequence covalently linked to a 3′ target hybridizing region consisting of SEQ ID NO:89and a primer consisting of SEQ ID NO:21;
b) amplifying the HPV type 16 nucleic acid in an in vitro amplification reaction that includes at lease one polymerase that acts with an oligonucleotide in the mixture to produce one or more HPV type 16 amplification products by using the HPV type 16 nucleic acid as a template;
c) contacting the HPV type 16 amplification products with at least one hybridization assay probe consisting of a completely complementary sequence of SEQ ID NO:25 that binds to an amplification product and forms a detectable probe: HPV type 16 target hybrid under stringent hybridization conditions; and
d) detecting a signal from the probe: HPV type 16 target hybrid, thereby indicating the presence of HPV type 16 in the sample.

17. The method of claim 16, wherein the detecting step detects a signal from a non-isotopic label attached to the probe in the probe: HPV type 16 target hybrid.

18. The method of claim 17, wherein the detecting step detects a signal from a chemiluminescent label attached to the probe in the probe: HPV type 16 target hybrid.