Skip to main content
NCBI home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1979 May;76(5):2232–2235. doi: 10.1073/pnas.76.5.2232

Structure-independent nucleotide sequence analysis.

D R Mills, F R Kramer
PMCID: PMC383572  PMID: 287063

Abstract

Substitution of inosine for granosine in the nucleic acid fragments synthesized for the sequencing of RNA effectively prevents the formation of secondary structures during electrophoretic analysis. Consequently, the mobility of each fragment in the sequencing gel is a strict function of its molecular weight. Inosine substitution should markedly improve the resolution that can be obtained in the sequencing of DNA as well as RNA.

Full text

PDF
2232

Images in this article

2233Image
on p.2233
2234Image
on p.2234

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Axelrod V. D., Vartikyan R. M., Aivazashvili V. A., Beabealashvili R. S. Specific termination of RNA polymerase synthesis as a method of RNA and DNA sequencing. Nucleic Acids Res. 1978 Oct;5(10):3549–3563. doi: 10.1093/nar/5.10.3549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Barnes W. M. DNA sequencing by partial ribosubstitution. J Mol Biol. 1978 Feb 15;119(1):83–99. doi: 10.1016/0022-2836(78)90271-1. [DOI] [PubMed] [Google Scholar]
  3. Bessman M. J., Lehman I. R., Adler J., Zimmerman S. B., Simms E. S., Kornberg A. ENZYMATIC SYNTHESIS OF DEOXYRIBONUCLEIC ACID. III. THE INCORPORATION OF PYRIMIDINE AND PURINE ANALOGUES INTO DEOXYRIBONUCLEIC ACID. Proc Natl Acad Sci U S A. 1958 Jul 15;44(7):633–640. doi: 10.1073/pnas.44.7.633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Billeter M. A., Dahlberg J. E., Goodman H. M., Hindley J., Weissmann C. Sequence of the first 175 nucleotides from the 5' terminus of Qbeta RNA synthesized in vitro. Nature. 1969 Dec 13;224(5224):1083–1086. doi: 10.1038/2241083a0. [DOI] [PubMed] [Google Scholar]
  5. Chamberlin M. J. Comparative properties of DNA, RNA, and hybrid homopolymer pairs. Fed Proc. 1965 Nov-Dec;24(6):1446–1457. [PubMed] [Google Scholar]
  6. Donis-Keller H., Maxam A. M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 1977 Aug;4(8):2527–2538. doi: 10.1093/nar/4.8.2527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Feix G., Hake H. Primer directed initiation of RNA synthesis catalysed by Qbeta replicase. Biochem Biophys Res Commun. 1975 Jul 22;65(2):503–509. doi: 10.1016/s0006-291x(75)80176-8. [DOI] [PubMed] [Google Scholar]
  8. Feix G. Primer-dependent copying of rabbit globin mRNA with Qbeta replicase. Nature. 1976 Feb 19;259(5544):593–594. doi: 10.1038/259593a0. [DOI] [PubMed] [Google Scholar]
  9. Feix G., Sano H. Initiation specificity of the poly(cytidylic acid)-dependent Qbeta replicase activity. Eur J Biochem. 1975 Oct 1;58(1):59–64. doi: 10.1111/j.1432-1033.1975.tb02348.x. [DOI] [PubMed] [Google Scholar]
  10. Feix G., Slor H., Weissmann C. Replication of viral RNA. 13. The early product of phage RNA synthesis in vitro. Proc Natl Acad Sci U S A. 1967 May;57(5):1401–1408. doi: 10.1073/pnas.57.5.1401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. HOARD D. E., OTT D. G. CONVERSION OF MONO- AND OLIGODEOXYRIBONUCLEOTIDES TO 5-TRIPHOSPHATES. J Am Chem Soc. 1965 Apr 20;87:1785–1788. doi: 10.1021/ja01086a031. [DOI] [PubMed] [Google Scholar]
  12. Haruna I., Spiegelman S. Specific template requirments of RNA replicases. Proc Natl Acad Sci U S A. 1965 Aug;54(2):579–587. doi: 10.1073/pnas.54.2.579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. INMAN R. B., BALDWIN R. L. HELIX--RANDOM COIL TRANSITIONS IN DNA HOMOPOLYMER PAIRS. J Mol Biol. 1964 Apr;8:452–469. doi: 10.1016/s0022-2836(64)80003-6. [DOI] [PubMed] [Google Scholar]
  14. KAHAN F. M., HURWITZ J. The role of deoxyribonucleic acid in ribonucleic acid synthesis. IV. The incorporation of pyrimidine and purine analogues into ribonucleic acid. J Biol Chem. 1962 Dec;237:3778–3785. [PubMed] [Google Scholar]
  15. Kacian D. L., Mills D. R., Kramer F. R., Spiegelman S. A replicating RNA molecule suitable for a detailed analysis of extracellular evolution and replication. Proc Natl Acad Sci U S A. 1972 Oct;69(10):3038–3042. doi: 10.1073/pnas.69.10.3038. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kramer F. R., Mills D. R., Cole P. E., Nishihara T., Spiegelman S. Evolution in vitro: sequence and phenotype of a mutant RNA resistant to ethidium bromide. J Mol Biol. 1974 Nov 15;89(4):719–736. doi: 10.1016/0022-2836(74)90047-3. [DOI] [PubMed] [Google Scholar]
  17. Kramer F. R., Mills D. R. RNA sequencing with radioactive chain-terminating ribonucleotides. Proc Natl Acad Sci U S A. 1978 Nov;75(11):5334–5338. doi: 10.1073/pnas.75.11.5334. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lehrach H., Diamond D., Wozney J. M., Boedtker H. RNA molecular weight determinations by gel electrophoresis under denaturing conditions, a critical reexamination. Biochemistry. 1977 Oct 18;16(21):4743–4751. doi: 10.1021/bi00640a033. [DOI] [PubMed] [Google Scholar]
  19. MILES H. T. Tautomeric forms in a polynucleotide helix and their bearing on the structure of DNA. Proc Natl Acad Sci U S A. 1961 Jun 15;47:791–802. doi: 10.1073/pnas.47.6.791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Maat J., Smith A. J. A method for sequencing restriction fragments with dideoxynucleoside triphosphates. Nucleic Acids Res. 1978 Dec;5(12):4537–4545. doi: 10.1093/nar/5.12.4537. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Maniatis T., Jeffrey A., van deSande H. Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry. 1975 Aug 26;14(17):3787–3794. doi: 10.1021/bi00688a010. [DOI] [PubMed] [Google Scholar]
  22. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Mills D. R., Dobkin C., Kramer F. R. Template-determined, variable rate of RNA chain elongation. Cell. 1978 Oct;15(2):541–550. doi: 10.1016/0092-8674(78)90022-3. [DOI] [PubMed] [Google Scholar]
  24. Mills D. R., Kramer F. R., Spiegelman S. Complete nucleotide sequence of a replicating RNA molecule. Science. 1973 Jun 1;180(4089):916–927. doi: 10.1126/science.180.4089.916. [DOI] [PubMed] [Google Scholar]
  25. Reijnders L., Sloof P., Sival J., Borst P. Gel electrophoresis of RNA under denaturing conditions. Biochim Biophys Acta. 1973 Oct 26;324(3):320–333. doi: 10.1016/0005-2787(73)90278-5. [DOI] [PubMed] [Google Scholar]
  26. Sanger F., Brownlee G. G., Barrell B. G. A two-dimensional fractionation procedure for radioactive nucleotides. J Mol Biol. 1965 Sep;13(2):373–398. doi: 10.1016/s0022-2836(65)80104-8. [DOI] [PubMed] [Google Scholar]
  27. Sanger F., Coulson A. R. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975 May 25;94(3):441–448. doi: 10.1016/0022-2836(75)90213-2. [DOI] [PubMed] [Google Scholar]
  28. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [DOI] [PubMed] [Google Scholar]
  29. Sanger F., Donelson J. E., Coulson A. R., Kössel H., Fischer D. Use of DNA polymerase I primed by a synthetic oligonucleotide to determine a nucleotide sequence in phage fl DNA. Proc Natl Acad Sci U S A. 1973 Apr;70(4):1209–1213. doi: 10.1073/pnas.70.4.1209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Shapiro L., August J. T. Replication of RNA viruses. 3. Utilization of ribonucleotide analogs in the reaction catalyzed by a RNA virus RNA polymerase. J Mol Biol. 1965 Nov;14(1):214–220. doi: 10.1016/s0022-2836(65)80241-8. [DOI] [PubMed] [Google Scholar]
  32. Simoncsits A., Brownlee G. G., Brown R. S., Rubin J. R., Guilley H. New rapid gel sequencing method for RNA. Nature. 1977 Oct 27;269(5631):833–836. doi: 10.1038/269833a0. [DOI] [PubMed] [Google Scholar]
  33. Yoshikawa M., Kato T., Takenishi T. A novel method for phosphorylation of nucleosides to 5'-nucleotides. Tetrahedron Lett. 1967 Dec;50:5065–5068. doi: 10.1016/s0040-4039(01)89915-9. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES