Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1987 Nov 11;15(21):9011–9025. doi: 10.1093/nar/15.21.9011

Base pair opening dynamics of a 2-aminopurine substituted Eco RI restriction sequence and its unsubstituted counterpart in oligonucleotides.

P O Lycksell 1, A Gräslund 1, F Claesens 1, L W McLaughlin 1, U Larsson 1, R Rigler 1
PMCID: PMC306419  PMID: 2825124

Abstract

Studies of 1H NMR selective saturation recovery were performed to determine the imino proton exchange with solvent water of the base pairs in the Eco RI endonuclease recognition sequence GAATTC, placed at the center of self-complementary decamer and dodecamer oligonucleotides. In one oligonucleotide the innermost adenine was replaced by the fluorescent base analogue 2-aminopurine (2AP). From the measurements at different concentrations of TRIS buffer acting as proton exchange catalyst, base pair lifetimes were evaluated. The results at 25 degrees show that the AT base pairs have lifetimes of the order of a few ms, whereas the surrounding GC base pairs in a dodecamer have lifetimes of about 100 ms. The (2AP)T base pair has a shorter lifetime than the corresponding AT base pair. The temperature dependent optical absorption, and for the 2AP containing oligonucleotide fluorescence, were used to study the single strand-duplex equilibrium of the decamers. The results indicate that NMR and the optical techniques, although applied at very different concentrations, monitor the same conformational transition of the oligonucleotide.

Full text

PDF
9011

Selected References

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

  1. Brennan C. A., Van Cleve M. D., Gumport R. I. The effects of base analogue substitutions on the cleavage by the EcoRI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J Biol Chem. 1986 Jun 5;261(16):7270–7278. [PubMed] [Google Scholar]
  2. Freier S. M., Albergo D. D., Turner D. H. Solvent effects on the dynamics of (dG-dC)3. Biopolymers. 1983 Apr;22(4):1107–1131. doi: 10.1002/bip.360220408. [DOI] [PubMed] [Google Scholar]
  3. Guéron M., Kochoyan M., Leroy J. L. A single mode of DNA base-pair opening drives imino proton exchange. Nature. 1987 Jul 2;328(6125):89–92. doi: 10.1038/328089a0. [DOI] [PubMed] [Google Scholar]
  4. Halford S. E., Johnson N. P. The EcoRI restriction endonuclease with bacteriophage lambda DNA. Equilibrium binding studies. Biochem J. 1980 Nov 1;191(2):593–604. doi: 10.1042/bj1910593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Jack W. E., Terry B. J., Modrich P. Involvement of outside DNA sequences in the major kinetic path by which EcoRI endonuclease locates and leaves its recognition sequence. Proc Natl Acad Sci U S A. 1982 Jul;79(13):4010–4014. doi: 10.1073/pnas.79.13.4010. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Johnston P. D., Redfield A. G. An NMR study of the exchange rates for protons involved in the secondary and tertiary structure of yeast tRNA Phe. Nucleic Acids Res. 1977 Oct;4(10):3599–3615. doi: 10.1093/nar/4.10.3599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Johnston P. D., Redfield A. G. Study of transfer ribonucleic acid unfolding by dynamic nuclear magnetic resonance. Biochemistry. 1981 Jul 7;20(14):3996–4006. doi: 10.1021/bi00517a008. [DOI] [PubMed] [Google Scholar]
  8. Kyogoku Y., Lord R. C., Rich A. The effect of substituents on the hydrogen bonding of adenine and uracil derivatives. Proc Natl Acad Sci U S A. 1967 Feb;57(2):250–257. doi: 10.1073/pnas.57.2.250. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Leroy J. L., Broseta D., Guéron M. Proton exchange and base-pair kinetics of poly(rA).poly(rU) and poly(rI).poly(rC). J Mol Biol. 1985 Jul 5;184(1):165–178. doi: 10.1016/0022-2836(85)90050-6. [DOI] [PubMed] [Google Scholar]
  10. McClarin J. A., Frederick C. A., Wang B. C., Greene P., Boyer H. W., Grable J., Rosenberg J. M. Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution. Science. 1986 Dec 19;234(4783):1526–1541. doi: 10.1126/science.3024321. [DOI] [PubMed] [Google Scholar]
  11. Patel D. J., Pardi A., Itakura K. DNA conformation, dynamics, and interactions in solution. Science. 1982 May 7;216(4546):581–590. doi: 10.1126/science.6280281. [DOI] [PubMed] [Google Scholar]
  12. Ronen A. 2-Aminopurine. Mutat Res. 1980 Jan;75(1):1–47. doi: 10.1016/0165-1110(80)90026-3. [DOI] [PubMed] [Google Scholar]
  13. Sowers L. C., Fazakerley G. V., Eritja R., Kaplan B. E., Goodman M. F. Base pairing and mutagenesis: observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR. Proc Natl Acad Sci U S A. 1986 Aug;83(15):5434–5438. doi: 10.1073/pnas.83.15.5434. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Teitelbaum H., Englander S. W. Open states in native polynucleotides. I. Hydrogen-exchange study of adenine-containing double helices. J Mol Biol. 1975 Feb 15;92(1):55–78. doi: 10.1016/0022-2836(75)90091-1. [DOI] [PubMed] [Google Scholar]
  15. Terry B. J., Jack W. E., Rubin R. A., Modrich P. Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences. J Biol Chem. 1983 Aug 25;258(16):9820–9825. [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES