Rapid and sensitive detection of Chlamydia trachomatis using a ligatable binary RNA probe and Qβ replicase

Molecular and Cellular Probes

Volumn 11, Issue 6, 1997, Pages 407-426

  Stefano, James E ^a,b   Genovese, Louis ^a   An, Qi ^a   Lu, Ling ^a   McCarty, Janice ^a   Du, Yan ^a   Stefano, Kyriaki ^a   Lawrence Burg, J ^a   King, Walter ^a   Lane, David J ^a  

^a GENE TRAK   (United States)

^b Genzyme Genetics   (United States)

Author keywords

C. trachomatis; Exponential amplification; Nucleic acid diagnostics; Q replicase; T4 DNA ligase

Indexed keywords

BACTERIAL RNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; Q BETA REPLICASE; RIBOSOME RNA;

ARTICLE; BACTERIUM DETECTION; CHLAMYDIA TRACHOMATIS; FLUORESCENCE; NONHUMAN; PRIORITY JOURNAL; RNA PROBE;

BACTERIA (MICROORGANISMS); CHLAMYDIA TRACHOMATIS; HYDRIDAE;

EID: 0031409426     PISSN: 08908508     EISSN: None     Source Type: Journal    
DOI: 10.1006/mcpr.1997.0135     Document Type: Article

References (36)

1. Lizardi P. M., Guerra C. E., Lomelli H., Tussie-Luna I., Kramer F. R. Exponential amplification of recombinant RNA hybridization probes. Bio/Technology. 6:1988;1197-1202.
2. Burg J. L., Cahill P. B., Kutter M., Stefano J. E., Mahan D. E. Real time fluorescence detection of RNA amplified by Qβ replicase. Analytical Biochemistry. 230:1995;263-272.
3. Morrisey D. V., Lombardo M., Eldredge J. K., Kearney K. R., Groody E. P., Collins M. L. Nucleic acid hybridization assays employing dA-tailed capture probes. Analytical Biochemistry. 181:1989;345-359.
4. Lomeli H., Tyagi S., Pritchard C. G., Lizardi P. M., Kramer F. R. Quantitative assays based on the use of replicatable hybridization probes. Clinical Chemistry. 35:1989;1826-1831.
5. Prichard C. G., Stefano J. E. Amplified detection of viral nucleic acid at subattomole levels using Qβ replicase. Annales de Biologie Clinique. 48:1990;433-528.
6. Shah J., Buharin A., Williams C., Mahan D., Lane D., King W. European Patent Application. O 90/15159. 1990.
7. Nishihara T., Mills D. R., Kramer F. R. Localization of the Qβ replicase recognition site in MDV-1 RNA. Journal of Biochemistry (Tokyo). 93:1983;669-674.
8. Martinelli R. A., Donahue J. J., Unger T. Amplification of midivariant DNA templates. U.S. Patent No. 5:1995;407-798.
9. Dimond R. L., Ekenberg S. J., Hartnett J. R., Hudson G. R., Jones C. L., Maffitt M. A., Martinelli R. A, Mendoza L. G., Miller K. M., Monahan J. E., Pahuski E. E., Schumm J. W. Nucleic acid amplification with DNA-dependent RNA polymerase activity of RNA replicases. International Patent Application. 1991.
10. Moore M. J., Sharp P. A. Site-specific modification of pre-mRNA: the 2′ hydroxyl groups at the splice sites. Science. 256:1992;992-997.
11. Tyagi S., Landegren U., Tazi M., Lizard P. M., Kramer F. R. Extremely sensitive, background-free gene detection using binary probes and Qβ replicase. Proceedings of the National Academy of Science. 93:1996;5395-5400.
12. Burg J. L., DiFrancesco R., Lovern D., Stanick Lin-Goerke J., Mahdavi K., Wu Y., Farrell M. P. Evolution of host cell RNA into efficient template RNA by Qβ replicase: The origin of RNA in untemplated reactions. Biochemistry. 33:1994;13836-13847.
13. Dolganov G. M., Chestukhin A. V., Shemyakin M. F. A new procedure for the simultaneous large-scale purification of bacteriophage-T4-induced polynucleotide kinase, DNA ligase, RNA ligase and DNA polymerase. European Journal of Biochemistry. 114:1981;247-254.
14. Murray N. E, Bruce S. A, Murray K. Molecular cloning of the DNA ligase gene from bacteriophage T4. II. Amplification and preparation of the gene product. Journal of Molecular Biology. 132:1979;493-505.
15. Weisburg W. G., Hatch T. P., Woese C. R. Eubacterial origin of Chlamydiae. Journal of Bacteriology. 167:1986;570-574.
16. Stone B. B., Cohen S. P., Breton G. L., Nietupski R. M., Pelletier D. A., Fiandaca M. J., Moe J. G., Smith J. H., Shah J. S., Weisburg W. G. Detection of rRNA from four respiratory pathogens using an automated Qβ replicase assay. Molecular and Cellular Probes. 10:1996;359-370.
17. Shah J., Liu J., Smith J., Popoff S., Radcliffe G., O'Brien W. J., Serpe G., Olive D. M., King W. Novel, ultrasensitive, Q-beta replicase-amplified hybridization assay for detection ofChlamydia trachomatis. Journal of Clinical Microbiology. 32:1994;2718-2724.
18. Ranki M., Palva A., Vitranen M., Laaksonen M., Söderlund H. Sandwich hybridization as a convenient method for the detection of nucleic acids in crude samples. Gene. 21:1983;77-85.
19. Burg J. L., Juffras A. M., Wu Y., Blomquist C. L., Du Y. Single molecule detection of RNA reporter probes by amplification with Qβ replicase. Molecular and Cellular Probes. 10:1996;257-271.
20. Jaeger J. H., Turner D. H., Zuker M. Improved predictions of secondary structure for RNA. Proceedings of the National Academy of Science. 86:1989;7706-7710.
21. An Q., Liu J., O'Brien W. O., Radcliffe G., Buxton D., Popoff S., King W., Lu L, Vera-Garcia M., Shah J., Klinger J., Olive D. M. Comparison of characteristics of Qβ replicase-amplified assay with competitive PCR assay forChlamydia trachomatis. Journal of Clinical Microbiology. 33:1995;58-63.
22. Western L. M., Rose S. J. A novel joining activity catalyzed by T4 DNA ligase. Nucleic Acids Research. 19:1991;809-813.
23. Harada K., Orgel L. Unexpected substrate specificity of T4 DNA ligase revealed by in vitro selection. Nucleic Acids Research. 21:1993;2287-2291.
24. Biebricher C. K., Luce R. In vitro recombination and terminal elongation of RNA by Qβ replicase. The EMBO Journal. 11:1992;5129-5135.
25. Pheiffer B. H., Zimmerman S. B. Polymer-stimulated ligation: enhanced blunt- or cohesive-end ligation of DNA or deoxyribooligonucleotides by T4 DNA ligase in polymer solutions. Nucleic Acids Research. 11:1983;7853-7871.
26. Hayashi K., Nakazawa M., Ishizaki I., Hiraoka N., Obayashi A. Regulation of inter- and intramolecular ligation with T4 DNA ligase in the presence of polyethylene glycol. Nucleic Acids Research. 14:1986;7617-7631.
27. Doudna J. A., Szostak J. W. RNA-catalyzed synthesis of complementary-strand RNA. Nature. 339:1989;519-522.
28. Axelrod V. D., Brown E., Priano C., Mills D. R. Coliphage Qβ RNA replication: RNA catalytic for single-strand release. Virology. 184:1991;595-608.
29. Detmer J., Lagier R. L., Flynn J., Zayati C., Kolberg J., Collins M., Urdea M., Sanchez-Pescador R. Accurate quantification of hepatitis C virus (HCV) RNA from all HCV genotypes by using branched-DNA technology. Journal of Clinical Microbiology. 34:1996;901-907.
30. Kern K., Collins M., Fultz T., Detmer J., Hamren S., Peterkin J., Sheridan P., Urdea M., White R., Yeghiazarian T., Todd J. An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma. Journal of Clinical Microbiology. 34:1996;3196-3202.
31. Heid C. A., Stevens J., Livak K. J., Williams P. M. Real time quantitative PCR. Genome Research. 6:1996;986-994.
32. Gibson U. E. M., Heid C. A., Williams P. M. A novel method for real time quantitative RT-PCR. Genome Research. 6:1996;995-1001.
33. Ulrich P. P., Romeo J. M., Daniel L. J., Vyas G. N. An improved method for the detection of hepatitis C virus RNA in plasma utilizing heminested primers and internal control RNA. PCR Methods Applications. 2:1993;241-249.
34. Nakamura S., Katarnine S, Yamamoto T, Foung S. K, Kurata T, Hirabayashi Y, Shimada K, Hino S, Miyamoto T. Amplification and detection of a single molecule of human immunodeficiency virus RNA. Virus Genes. 7:1993;325-338.
35. Martinelli R. A., Donahue J. J., Unger T. Amplification of midivariant DNA templates. U.S. Patent No. 5:1995;407-798.
36. Morris T., Robertson B., Gallagher M. Rapid reverse transcription-PCR detection of hepatitis C virus RNA in serum by using the TaqMan Fluorogenic detection system. Journal of Clinical Microbiology. 34:1996;2933-2936.