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. 1993 May 25;21(10):2349–2353. doi: 10.1093/nar/21.10.2349

Cloning of RNA molecules in vitro.

H V Chetverina 1, A B Chetverin 1
PMCID: PMC309531  PMID: 7685078

Abstract

A method for RNA amplification in an immobilized medium is described. The medium contains a complete set of nucleotide substrates and purified Q beta replicase, an enzyme capable of exponentially amplifying RNAs under isothermal conditions. RNA amplification in the immobilized medium results in the formation of separate 'colonies', each comprising the progeny of a single RNA molecule (a clone). The colonies were visualized by staining with ethidium bromide, by utilizing radioactive substrates, and by hybridization with sequence-specific labeled probes. The number and identity of the RNA colonies corresponded to that of the RNAs seeded. When a mixture of different RNA species was seeded, these species were found in different colonies. Possible implementations of this technique include a search for recombinant RNAs, very sensitive nucleic acid diagnostics, and gene cloning in vitro.

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Selected References

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  1. Arnheim N., Erlich H. Polymerase chain reaction strategy. Annu Rev Biochem. 1992;61:131–156. doi: 10.1146/annurev.bi.61.070192.001023. [DOI] [PubMed] [Google Scholar]
  2. Biebricher C. K., Eigen M., Luce R. Kinetic analysis of template-instructed and de novo RNA synthesis by Q beta replicase. J Mol Biol. 1981 Jun 5;148(4):391–410. doi: 10.1016/0022-2836(81)90183-2. [DOI] [PubMed] [Google Scholar]
  3. Biebricher C. K., Luce R. In vitro recombination and terminal elongation of RNA by Q beta replicase. EMBO J. 1992 Dec;11(13):5129–5135. doi: 10.1002/j.1460-2075.1992.tb05620.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Biebricher C. K. Replication and evolution of short-chained RNA species replicated by Q beta replicase. Cold Spring Harb Symp Quant Biol. 1987;52:299–306. doi: 10.1101/sqb.1987.052.01.035. [DOI] [PubMed] [Google Scholar]
  5. Blumenthal T., Carmichael G. G. RNA replication: function and structure of Qbeta-replicase. Annu Rev Biochem. 1979;48:525–548. doi: 10.1146/annurev.bi.48.070179.002521. [DOI] [PubMed] [Google Scholar]
  6. Bodkin D. K., Knudson D. L. Sequence relatedness of Palyam virus genes to cognates of the Palyam serogroup viruses by RNA-RNA blot hybridization. Virology. 1985 May;143(1):55–62. doi: 10.1016/0042-6822(85)90096-0. [DOI] [PubMed] [Google Scholar]
  7. Chetverin A. B., Chetverina H. V., Munishkin A. V. On the nature of spontaneous RNA synthesis by Q beta replicase. J Mol Biol. 1991 Nov 5;222(1):3–9. doi: 10.1016/0022-2836(91)90729-p. [DOI] [PubMed] [Google Scholar]
  8. Christen A. A., Montalbano B. An ethidium bromide-agarose plate assay for the nonradioactive detection of cDNA synthesis. Anal Biochem. 1989 May 1;178(2):269–272. doi: 10.1016/0003-2697(89)90637-4. [DOI] [PubMed] [Google Scholar]
  9. Guatelli J. C., Whitfield K. M., Kwoh D. Y., Barringer K. J., Richman D. D., Gingeras T. R. Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc Natl Acad Sci U S A. 1990 Mar;87(5):1874–1878. doi: 10.1073/pnas.87.5.1874. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Haruna I., Spiegelman S. Autocatalytic synthesis of a viral RNA in vitro. Science. 1965 Nov 12;150(3698):884–886. doi: 10.1126/science.150.3698.884. [DOI] [PubMed] [Google Scholar]
  11. Haruna I., Spiegelman S. Recognition of size and sequence by an RNA replicase. Proc Natl Acad Sci U S A. 1965 Oct;54(4):1189–1193. doi: 10.1073/pnas.54.4.1189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Isaacs S. T., Tessman J. W., Metchette K. C., Hearst J. E., Cimino G. D. Post-PCR sterilization: development and application to an HIV-1 diagnostic assay. Nucleic Acids Res. 1991 Jan 11;19(1):109–116. doi: 10.1093/nar/19.1.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kramer F. R., Lizardi P. M. Replicatable RNA reporters. Nature. 1989 Jun 1;339(6223):401–402. doi: 10.1038/339401a0. [DOI] [PubMed] [Google Scholar]
  14. Landegren U., Kaiser R., Caskey C. T., Hood L. DNA diagnostics--molecular techniques and automation. Science. 1988 Oct 14;242(4876):229–237. doi: 10.1126/science.3051381. [DOI] [PubMed] [Google Scholar]
  15. Lomeli H., Tyagi S., Pritchard C. G., Lizardi P. M., Kramer F. R. Quantitative assays based on the use of replicatable hybridization probes. Clin Chem. 1989 Sep;35(9):1826–1831. [PubMed] [Google Scholar]
  16. Miele E. A., Mills D. R., Kramer F. R. Autocatalytic replication of a recombinant RNA. J Mol Biol. 1983 Dec 15;171(3):281–295. doi: 10.1016/0022-2836(83)90094-3. [DOI] [PubMed] [Google Scholar]
  17. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Milligan J. F., Uhlenbeck O. C. Determination of RNA-protein contacts using thiophosphate substitutions. Biochemistry. 1989 Apr 4;28(7):2849–2855. doi: 10.1021/bi00433a016. [DOI] [PubMed] [Google Scholar]
  19. Mills D. R. Engineered recombinant messenger RNA can be replicated and expressed inside bacterial cells by an RNA bacteriophage replicase. J Mol Biol. 1988 Apr 5;200(3):489–500. doi: 10.1016/0022-2836(88)90538-4. [DOI] [PubMed] [Google Scholar]
  20. Munishkin A. V., Voronin L. A., Chetverin A. B. An in vivo recombinant RNA capable of autocatalytic synthesis by Q beta replicase. Nature. 1988 Jun 2;333(6172):473–475. doi: 10.1038/333473a0. [DOI] [PubMed] [Google Scholar]
  21. Munishkin A. V., Voronin L. A., Ugarov V. I., Bondareva L. A., Chetverina H. V., Chetverin A. B. Efficient templates for Q beta replicase are formed by recombination from heterologous sequences. J Mol Biol. 1991 Sep 20;221(2):463–472. doi: 10.1016/0022-2836(91)80067-5. [DOI] [PubMed] [Google Scholar]
  22. Noren C. J., Anthony-Cahill S. J., Suich D. J., Noren K. A., Griffith M. C., Schultz P. G. In vitro suppression of an amber mutation by a chemically aminoacylated transfer RNA prepared by runoff transcription. Nucleic Acids Res. 1990 Jan 11;18(1):83–88. doi: 10.1093/nar/18.1.83. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Palasingam K., Shaklee P. N. Reversion of Q beta RNA phage mutants by homologous RNA recombination. J Virol. 1992 Apr;66(4):2435–2442. doi: 10.1128/jvi.66.4.2435-2442.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Saiki R. K., Scharf S., Faloona F., Mullis K. B., Horn G. T., Erlich H. A., Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985 Dec 20;230(4732):1350–1354. doi: 10.1126/science.2999980. [DOI] [PubMed] [Google Scholar]
  25. Virca G. D., Northemann W., Shiels B. R., Widera G., Broome S. Simplified northern blot hybridization using 5% sodium dodecyl sulfate. Biotechniques. 1990 Apr;8(4):370–371. [PubMed] [Google Scholar]
  26. Walker G. T., Fraiser M. S., Schram J. L., Little M. C., Nadeau J. G., Malinowski D. P. Strand displacement amplification--an isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 1992 Apr 11;20(7):1691–1696. doi: 10.1093/nar/20.7.1691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Wu Y., Zhang D. Y., Kramer F. R. Amplifiable messenger RNA. Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):11769–11773. doi: 10.1073/pnas.89.24.11769. [DOI] [PMC free article] [PubMed] [Google Scholar]

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