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. 1987 Mar 11;15(5):2191–2201. doi: 10.1093/nar/15.5.2191

NMR and CD studies on an oligonucleotide containing N4-methylcytosine.

G V Fazakerley, A Kraszewski, R Téoule, W Guschlbauer
PMCID: PMC340626  PMID: 3562225

Abstract

The hexamer d(CGm4CGCG) exists predominantly as a right handed B form helix at 20 degrees C in 150 mM NaCl, as shown by 2D NOE spectra. Under these conditions a minor species is also observed which corresponds to the single strand in slow exchange on a proton NMR time scale with the double strand. This exchange is unusually slow and separate resonances for the two species are seen up to 65 degrees C. At 50 degrees C the lifetime of the single strand species is 0.85 s. Under high salt conditions the hexamer is partly converted into the Z form, but the complete transition is only observed at 5M NaCl at -6 degrees C.

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Selected References

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

  1. Behe M., Felsenfeld G. Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). Proc Natl Acad Sci U S A. 1981 Mar;78(3):1619–1623. doi: 10.1073/pnas.78.3.1619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Butkus V., Klimasauskas S., Kersulyte D., Vaitkevicius D., Lebionka A., Janulaitis A. Investigation of restriction-modification enzymes from M. varians RFL19 with a new type of specificity toward modification of substrate. Nucleic Acids Res. 1985 Aug 26;13(16):5727–5746. doi: 10.1093/nar/13.16.5727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ehrlich M., Gama-Sosa M. A., Carreira L. H., Ljungdahl L. G., Kuo K. C., Gehrke C. W. DNA methylation in thermophilic bacteria: N4-methylcytosine, 5-methylcytosine, and N6-methyladenine. Nucleic Acids Res. 1985 Feb 25;13(4):1399–1412. doi: 10.1093/nar/13.4.1399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Engel J. D., von Hippel P. H. Effects of methylation on the stability of nucleic acid conformations: studies at the monomer level. Biochemistry. 1974 Sep 24;13(20):4143–4158. doi: 10.1021/bi00717a013. [DOI] [PubMed] [Google Scholar]
  5. Fazakerley G. V., Téoule R., Guy A., Fritzsche H., Guschlbauer W. NMR studies on oligodeoxyribonucleotides containing the dam methylation site GATC. Comparison between d(GGATCC) and d(GGm6ATCC). Biochemistry. 1985 Aug 13;24(17):4540–4548. doi: 10.1021/bi00338a009. [DOI] [PubMed] [Google Scholar]
  6. Fazakerley G. V., van der Marel G. A., van Boom J. H., Guschlbauer W. Helix opening in deoxyribonucleic acid from a proton nuclear magnetic resonance study of imino and amino protons in d(CG)3. Nucleic Acids Res. 1984 Nov 12;12(21):8269–8279. doi: 10.1093/nar/12.21.8269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Feigon J., Leupin W., Denny W. A., Kearns D. R. Two-dimensional proton nuclear magnetic resonance investigation of the synthetic deoxyribonucleic acid decamer d(ATATCGATAT)2. Biochemistry. 1983 Dec 6;22(25):5943–5951. doi: 10.1021/bi00294a038. [DOI] [PubMed] [Google Scholar]
  8. Frechet D., Cheng D. M., Kan L. S., Ts'o P. O. Nuclear Overhauser effect as a tool for the complete assignment of nonexchangeable proton resonances in short deoxyribonucleic acid helices. Biochemistry. 1983 Oct 25;22(22):5194–5200. doi: 10.1021/bi00291a020. [DOI] [PubMed] [Google Scholar]
  9. Fujii S., Wang A. H., van der Marel G., van Boom J. H., Rich A. Molecular structure of (m5 dC-dG)3: the role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA. Nucleic Acids Res. 1982 Dec 11;10(23):7879–7892. doi: 10.1093/nar/10.23.7879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hare D. R., Wemmer D. E., Chou S. H., Drobny G., Reid B. R. Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods. J Mol Biol. 1983 Dec 15;171(3):319–336. doi: 10.1016/0022-2836(83)90096-7. [DOI] [PubMed] [Google Scholar]
  11. Janulaitis A., Klimasauskas S., Petrusyte M., Butkus V. Cytosine modification in DNA by BcnI methylase yields N4-methylcytosine. FEBS Lett. 1983 Sep 5;161(1):131–134. doi: 10.1016/0014-5793(83)80745-5. [DOI] [PubMed] [Google Scholar]
  12. McConnell B. The amino 1H resonances of oligonucleotide helices: d(CGCG). J Biomol Struct Dyn. 1984 Jun;1(6):1407–1421. doi: 10.1080/07391102.1984.10507528. [DOI] [PubMed] [Google Scholar]
  13. Orbons L. P., Altona C. Conformational analysis of the B and Z forms of the d(m5C-G)3 and d(br5C-G)3 hexamers in solution. A 300-MHz and 500-MHz NMR study. Eur J Biochem. 1986 Oct 1;160(1):141–148. doi: 10.1111/j.1432-1033.1986.tb09950.x. [DOI] [PubMed] [Google Scholar]
  14. Orbons L. P., van der Marel G. A., van Boom J. H., Altona C. The B and Z forms of the d(m5C-G)3 and d(br5C-G)3 hexamers in solution. A 300-MHz and 500-MHz two-dimensional NMR study. Eur J Biochem. 1986 Oct 1;160(1):131–139. doi: 10.1111/j.1432-1033.1986.tb09949.x. [DOI] [PubMed] [Google Scholar]
  15. Pohl F. M., Jovin T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). J Mol Biol. 1972 Jun 28;67(3):375–396. doi: 10.1016/0022-2836(72)90457-3. [DOI] [PubMed] [Google Scholar]
  16. Quadrifoglio F., Manzini G., Vasser M., Dinkelspiel K., Crea R. Conformational stability of alternating d (CG) oligomers in high salt solution. Nucleic Acids Res. 1981 May 11;9(9):2195–2206. doi: 10.1093/nar/9.9.2195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Quignard E., Fazakerley G. V., Teoule R., Guy A., Guschlbauer W. Consequences of methylation on the amino group of adenine. A proton two-dimensional NMR study of d(GGATATCC) and d(GGm6ATATCC). Eur J Biochem. 1985 Oct 1;152(1):99–105. doi: 10.1111/j.1432-1033.1985.tb09168.x. [DOI] [PubMed] [Google Scholar]
  18. Raszka M., Kaplan N. O. Association by hydrogen bonding of mononucleotides in aqueous solution. Proc Natl Acad Sci U S A. 1972 Aug;69(8):2025–2029. doi: 10.1073/pnas.69.8.2025. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Roy K. B., Miles H. T. A thermally driven interconversion of B and Z-dna. Biochem Biophys Res Commun. 1983 Aug 30;115(1):100–105. doi: 10.1016/0006-291x(83)90974-9. [DOI] [PubMed] [Google Scholar]
  20. Scheek R. M., Boelens R., Russo N., van Boom J. H., Kaptein R. Sequential resonance assignments in 1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy. Biochemistry. 1984 Mar 27;23(7):1371–1376. doi: 10.1021/bi00302a006. [DOI] [PubMed] [Google Scholar]
  21. Shoup R. R., Miles H. T., Becker E. D. Restricted rotation about the exocyclic carbon-nitrogen bond in cytosine derivatives. J Phys Chem. 1972 Jan 6;76(1):64–70. doi: 10.1021/j100645a012. [DOI] [PubMed] [Google Scholar]
  22. Wang A. H., Quigley G. J., Kolpak F. J., Crawford J. L., van Boom J. H., van der Marel G., Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680–686. doi: 10.1038/282680a0. [DOI] [PubMed] [Google Scholar]
  23. Woisard A., Fazakerley G. V., Guschlbauer W. Z-DNA is formed by poly (dC-dG) and poly (dm5C-dG) at micro or nanomolar concentrations of some zinc(II) and copper(II) complexes. J Biomol Struct Dyn. 1985 Jun;2(6):1205–1220. doi: 10.1080/07391102.1985.10507633. [DOI] [PubMed] [Google Scholar]

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