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. 1988 Aug 11;16(15):7685–7702. doi: 10.1093/nar/16.15.7685

Study of structure, base-pair opening kinetics and proton exchange mechanism of the d-(AATTGCAATT) self-complementary oligodeoxynucleotide in solution.

M Kochoyan 1, G Lancelot 1, J L Leroy 1
PMCID: PMC338435  PMID: 2842732

Abstract

Using proton magnetic resonance, we have investigated the structure and the base-pair opening kinetics of the d-(AATTGCAATT) self-complementary duplex. All the non-exchangeable (except H5',5") and most exchangeable proton resonances have been assigned. The structure belongs to the B family. Imino proton exchange, measured by line broadening, longitudinal relaxation and magnetization transfer from water, is catalyzed by proton acceptors. The base-pair lifetimes, obtained by extrapolation of the exchange times to infinite concentration of ammonia are 2 and 3 milliseconds for internal A.Ts and 18 ms for G.C at 15 degrees C. In the absence of added catalysts, the imino proton of the first A.T base pair exchanges faster than that of the unpaired thymidine of the duplex formed by the sequence d-(AATTGCAATTT). This gives strong evidence for intrinsic exchange catalysis. The exchange of adenine amino protons from the closed state has been observed. Hence amino proton exchange is ill-suited for the investigation of base-pair opening kinetics.

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Selected References

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

  1. Bendel P. A proton NMR spin-lattice relaxation study of the imino proton exchange kinetics in calf-thymus DNA. Biopolymers. 1987 Apr;26(4):573–590. doi: 10.1002/bip.360260410. [DOI] [PubMed] [Google Scholar]
  2. Braunlin W. H., Bloomfield V. A. 1H NMR study of the base-pairing reactions of d(GGAATTCC): salt and polyamine effects on the imino proton exchange. Biochemistry. 1988 Feb 23;27(4):1184–1191. doi: 10.1021/bi00404a018. [DOI] [PubMed] [Google Scholar]
  3. Broido M. S., Zon G., James T. L. Complete assignment of the non-exchangeable proton nmr resonances of [d-(GGAATTCC)]2 using two-dimensional nuclear overhauser effect spectra. Biochem Biophys Res Commun. 1984 Mar 15;119(2):663–670. doi: 10.1016/s0006-291x(84)80301-0. [DOI] [PubMed] [Google Scholar]
  4. Crothers D. M., Cole P. E., Hilbers C. W., Shulman R. G. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol. 1974 Jul 25;87(1):63–88. doi: 10.1016/0022-2836(74)90560-9. [DOI] [PubMed] [Google Scholar]
  5. Early T. A., Kearns D. R., Hillen W., Wells R. D. A 300- and 600-MHz proton nuclear magnetic resonance investigation of a 12 base pair deoxyribonucleic acid restriction fragment: relaxation behavior of the low-field resonances in water. Biochemistry. 1981 Jun 23;20(13):3756–3764. doi: 10.1021/bi00516a014. [DOI] [PubMed] [Google Scholar]
  6. Fazakerley G. V., Guy A., Téoule R., Quignard E., Guschlbauer W. A proton 2D-NMR study of an oligodeoxyribonucleotide containing N6-methyladenine:d(GGm6ATATCC). Biochimie. 1985 Jul-Aug;67(7-8):819–822. doi: 10.1016/s0300-9084(85)80173-5. [DOI] [PubMed] [Google Scholar]
  7. Fazakerley G. V., Quignard E., Teoule R., Guy A., Guschlbauer W. A two-dimensional 1H-NMR study of the dam methylase site: comparison between the hemimethylated GATC sequence, its unmethylated analogue and a hemimethylated CATG sequence. The sequence dependence of methylation upon base-pair lifetimes. Eur J Biochem. 1987 Sep 15;167(3):397–404. doi: 10.1111/j.1432-1033.1987.tb13351.x. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. 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]
  10. Feigon J., Wang A. H., van der Marel G. A., Van Boom J. H., Rich A. A one- and two-dimensional NMR study of the B to Z transition of (m5dC-dG)3 in methanolic solution. Nucleic Acids Res. 1984 Jan 25;12(2):1243–1263. doi: 10.1093/nar/12.2.1243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Guittet E., Piveteau D., Lallemand J. Y., Huyn-Dinh T., Igolen J. Nuclear magnetic resonance study of d-TGGCCA in solution. Nucleic Acids Res. 1984 Jul 25;12(14):5927–5941. doi: 10.1093/nar/12.14.5927. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. Johnston P. D., Redfield A. G. Pulsed FT-NMR double resonance studies of yeast tRNAPhe: specific nuclear Overhauser effects and reinterpretation of low temperature relaxation data. Nucleic Acids Res. 1978 Oct;5(10):3913–3927. doi: 10.1093/nar/5.10.3913. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kochoyan M., Leroy J. L., Guéron M. Proton exchange and base-pair lifetimes in a deoxy-duplex containing a purine-pyrimidine step and in the duplex of inverse sequence. J Mol Biol. 1987 Aug 5;196(3):599–609. doi: 10.1016/0022-2836(87)90036-2. [DOI] [PubMed] [Google Scholar]
  15. Lancelot G., Mayer R., Thuong N. T., Chassignol M., Hélène C. Synthesis and structural studies of a self-complementary decadeoxynucleotide d(AATTGCAATT). II.-Proton magnetic resonance studies. Biochimie. 1981 Oct;63(10):785–790. doi: 10.1016/s0300-9084(81)80038-7. [DOI] [PubMed] [Google Scholar]
  16. Lancelot G., Thuong N. T. Nuclear magnetic resonance studies of complex formation between the oligonucleotide d(TATC) covalently linked to an acridine derivative and its complementary sequence d(GATA). Biochemistry. 1986 Sep 23;25(19):5357–5363. doi: 10.1021/bi00367a002. [DOI] [PubMed] [Google Scholar]
  17. Lefevre J. F., Lane A. N., Jardetzky O. Nuclear magnetic resonance study of the proton exchange rate in the operator-promoter DNA sequence of the trp operon of Escherichia coli. J Mol Biol. 1985 Oct 20;185(4):689–699. doi: 10.1016/0022-2836(85)90054-3. [DOI] [PubMed] [Google Scholar]
  18. Leontis N. B., Moore P. B. Imino proton exchange in the 5S RNA of Escherichia coli and its complex with protein L25 at 490 MHz. Biochemistry. 1986 Sep 23;25(19):5736–5744. doi: 10.1021/bi00367a058. [DOI] [PubMed] [Google Scholar]
  19. Leroy J. L., Bolo N., Figueroa N., Plateau P., Guérón M. Internal motions of transfer RNA: a study of exchanging protons by magnetic resonance. J Biomol Struct Dyn. 1985 Feb;2(5):915–939. doi: 10.1080/07391102.1985.10507609. [DOI] [PubMed] [Google Scholar]
  20. 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]
  21. Leroy J. L., Kochoyan M., Huynh-Dinh T., Guéron M. Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton. J Mol Biol. 1988 Mar 20;200(2):223–238. doi: 10.1016/0022-2836(88)90236-7. [DOI] [PubMed] [Google Scholar]
  22. Lycksell P. O., Gräslund A., Claesens F., McLaughlin L. W., Larsson U., Rigler R. Base pair opening dynamics of a 2-aminopurine substituted Eco RI restriction sequence and its unsubstituted counterpart in oligonucleotides. Nucleic Acids Res. 1987 Nov 11;15(21):9011–9025. doi: 10.1093/nar/15.21.9011. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Mandal C., Kallenbach N. R., Englander S. W. Base-pair opening and closing reactions in the double helix. A stopped-flow hydrogen exchange study in poly(rA).poly(rU). J Mol Biol. 1979 Dec 5;135(2):391–411. doi: 10.1016/0022-2836(79)90443-1. [DOI] [PubMed] [Google Scholar]
  24. Marion D., Lancelot G. Sequential assignment of the 1H and 31P resonances of the double stranded deoxynucleotide d (ATGCAT)2 by 2D-NMR correlation spectroscopy. Biochem Biophys Res Commun. 1984 Nov 14;124(3):774–783. doi: 10.1016/0006-291x(84)91025-8. [DOI] [PubMed] [Google Scholar]
  25. McConnell B. General acid-base catalysis in nucleobase amino proton exchange: cytidine. J Biomol Struct Dyn. 1986 Dec;4(3):419–436. doi: 10.1080/07391102.1986.10506359. [DOI] [PubMed] [Google Scholar]
  26. Nakanishi M., Mitane Y., Tsuboi M. A hydrogen exchange study of the open segment in a DNA double helix. Biochim Biophys Acta. 1984 Mar 22;798(1):46–52. doi: 10.1016/0304-4165(84)90008-4. [DOI] [PubMed] [Google Scholar]
  27. Patel D. J., Hilbers C. W. Proton nuclear magnetic resonance investigations of fraying in double-stranded d-ApTpGpCpApT in H2O solution. Biochemistry. 1975 Jun 17;14(12):2651–2656. doi: 10.1021/bi00683a014. [DOI] [PubMed] [Google Scholar]
  28. Patel D. J., Kozlowski S. A., Weiss M., Bhatt R. Conformation and dynamics of the Pribnow box region of the self-complementary d(C-G-A-T-T-A-T-A-A-T-C-G) duplex in solution. Biochemistry. 1985 Feb 12;24(4):936–944. doi: 10.1021/bi00325a019. [DOI] [PubMed] [Google Scholar]
  29. Premilat S., Albiser G. Conformations of A-DNA and B-DNA in agreement with fiber X-ray and infrared dichroism. Nucleic Acids Res. 1983 Mar 25;11(6):1897–1908. doi: 10.1093/nar/11.6.1897. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. 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]
  31. Sklenár V., Brooks B. R., Zon G., Bax A. Absorption mode two-dimensional NOE spectroscopy of exchangeable protons in oligonucleotides. FEBS Lett. 1987 Jun 1;216(2):249–252. doi: 10.1016/0014-5793(87)80699-3. [DOI] [PubMed] [Google Scholar]
  32. Thuong N. T., Chassignol M., Lancelot G., Mayer R., Hartmann B., Leng M., Hélène C. Synthesis and structural studies of a self-complementary decadeoxynucleotide d(AATTGCAATT). I.-Synthesis and chemical characterization of the decanucleotide. Biochimie. 1981 Oct;63(10):775–784. doi: 10.1016/s0300-9084(81)80037-5. [DOI] [PubMed] [Google Scholar]
  33. Weiss M. A., Patel D. J., Sauer R. T., Karplus M. Two-dimensional 1H NMR study of the lambda operator site OL1: a sequential assignment strategy and its application. Proc Natl Acad Sci U S A. 1984 Jan;81(1):130–134. doi: 10.1073/pnas.81.1.130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Wemmer D. E., Chou S. H., Hare D. R., Reid B. R. Duplex-hairpin transitions in DNA: NMR studies on CGCGTATACGCG. Nucleic Acids Res. 1985 May 24;13(10):3755–3772. doi: 10.1093/nar/13.10.3755. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Wemmer D. E., Chou S. H., Hare D. R., Reid B. R. Sequence-specific recognition of DNA: assignment of nonexchangeable proton resonances in the consensus Pribnow promoter DNA sequence by two-dimensional NMR. Biochemistry. 1984 May 8;23(10):2262–2268. doi: 10.1021/bi00305a027. [DOI] [PubMed] [Google Scholar]

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