Solution structure as a function of pH of two central mismatches, C·T and C·C, in the 29 to 39 K-ras gene sequence, by nuclear magnetic resonance and molecular dynamics

Journal of Molecular Biology

Volumn 268, Issue 2, 1997, Pages 331-347

  Boulard, Y ^a   Cognet, J A H ^b   Fazakerley, G V ^a  

^a DIF   (France)

^b INSTITUT GUSTAVE ROUSSY   (France)

Author keywords

Base protonation; DNA structure; Mismatches; NMR

Indexed keywords

CYTOSINE; DOUBLE STRANDED DNA; NITROGEN; OXYGEN; THYMINE;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; DNA SEQUENCE; DNA STRUCTURE; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; HYDROGEN BOND; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; ONCOGENE K RAS; PH; PRIORITY JOURNAL;

EID: 0031547972     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0975     Document Type: Article

References (45)

1. 2. Biochemistry. 26:1987;4068-4075.
2. Bodenhausen G., Kogler H., Ernst R. R. Selection of coherence-transfer pathways in NMR pulse experiments. J. Magn. Reson. 58:1984;370-388.
3. Boulard Y., Cognet J. A. H., Gabarro-Arpa J., Le Bret M., Sowers L. C., Fazakerley G. V. The pH dependent configuration of a C.A. mispair in DNA. Nucl. Acids Res. 20:1992;1933-1941.
4. Boulard Y., Cognet J. A. H., Gabarro-Arpa J., Le Bret M., Carbonnaux C., Fazakerley G. V. Solution structure of an oncogenic DNA duplex, the K- ras gene and the sequence containing a central C.A or A.G. mismatch as a function of pH: nuclear magnetic resonance and molecular dynamics studies. J. Mol. Biol. 246:1995;194-208.
5. Carbonnaux C., Fazakerley G. V., Sowers L. C. An NMR structural study of deaminated base-p[airs in DNA. Nucl. Acids Res. 18:1990;4075-4081.
6. Carbonnaux C., van der Marel G. A., van Boom J. H., Guschlbauer W., Fazakerley G. V. Solution structure of an oncogenic DNA duplex containing a G.A mismatch. Biochemistry. 30:1991;5449-5458.
7. Castati P., Gupta G., Garcia A. E., Radliff R., Hong L., Yau P., Moyzis R. K., Bradbury E. M. Unusual structures of the tandem repetitive DNA sequences located at human centromeres. Biochemistry. 33:1994;3819-3830.
8. Chuprina V. P., Poltev V. I. Possible conformations of double-helical polynucleotides containing incorrect base pairs. Nucl. Acids Res. 11:1983;5205-5222.
9. Chuprina V. P., Poltev V. I. Alteration of the DNA double helix conformation upon incorporation of mispairs as revealed by energy computations and pathways of point mutations. Nucl. Acids Res. 13:1985;141-154.
10. Cognet J. A. H., Gabarro-Arpa J., Le Bret M., van der Marel G. A., van Boom J. H., Fazakerley G. V. Solution conformation of an oligonucleotide containing a G.G mismatch determined by nuclear magnetic resonance and molecular mechanics. Nucl. Acids Res. 19:1991;6771-6779.
11. Cognet J. A. H., Boulard Y., Fazakerley G. V. Helical parameters, fluctuations, alternative hydrogen bonding, and bending in oligonucleotides containing a mismatched base-pair by NOESY distance restrained and distance free molecular dynamics. J. Mol. Biol. 246:1995;209-226.
12. Cornelis A. G., Haasnoot J. H. J., den Hartog J. F., de Rooij M., van Boom J. H., Cornelis A. Local destabilisation of a DNA double helix by a T.T wobble pair. Nature. 281:1979;235-236.
13. Cuniasse P., Sowers L. C., Eritja R., Kaplan B., Goodman M. F., Cognet J. A. H., Le Bret M., Guschlbauer W., Fazakerley G. V. An abasic site in DNA. Solution conformation determined by proton NMR and molecular mechanics calculations. Nucl. Acids Res. 15:1987;8003-8022.
14. 1H NMR spectra via two-dimensional homonuclear Hartmann-Hahn spectroscopy. J. Am. Chem. Soc. 107:1985;2820-2821.
15. Dohet C., Wagner R., Radman M. Repair of defined single base-pair mismatches in Escherichia coli. Proc. Natl Acad. Sci. USA. 82:1985;503-505.
16. Gao X., Patel D. J. G(syn).A(anti) mismatch formation in DNA dodecamers at acidic pH: pH-dependent conformational transition of G.A mispairs detected by proton NMR. J. Am. Chem. Soc. 110:1988;5178-5182.
17. Gervais V., Cognet J. A. H., Le Bret M., Sowers L. C., Fazakerley G. V. Solution structure of two mismatches A.A and T.T in the K- ras gene context by nuclear magnetic resonance and molecular dynamics. Eur. J. Biochem. 228:1995;279-290.
18. +base pairs can coexist with A.T base pairs between antiparallel strands of an oligodeoxynucleotide double-helix. Nucl. Acids Res. 12:1984;7565-7580.
19. 2, determined by 2D NMR and structural refinement methods. Biochemistry. 33:1994;1053-1062.
20. Hare D., Shapiro L., Patel D. J. Wobble dG.dT pairing in right-handed DNA: solution conformation of the d(CGTGAATTCGCG) duplex deduced from distance geometry analysis of NOE spectra. Biochemistry. 25:1986;7445-7456.
21. Holbrook S. R., Cheong C., Tinoco I., Kim S.-H. Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature. 353:1991;579-581.
22. Jordan F., Sostman H. D. Molecular orbital (CNDO/2 and MINDO) calculations on protonated deoxyribonucleic acid bases. The effects of base protonation on intermolecular interactions. J. Am. Chem. Soc. 95:1973;6544-6554.
23. Kalnik M. W., Chang C.-N., Grollman A. P., Patel D. J. NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite the cyclic analogue of 2-deoxyribose. Biochemistry. 27:1988;924-931.
24. 2, and d(CGCAGAATTCGCG).d(CGCGAATTCGCG). Biopolymers. 23:1984;2901-2929.
25. Kouchakdjian M., Li B. F. L., Swann P. F., Patel D. J. Pyrimidine.pyrimidine base-pair mismatches in DNA. A nuclear magnetic resonance study of T.T pairing at neutral pH and C.C pairing at acidic pH in dodecanucleotide duplexes. J. Mol. Biol. 202:1988;139-155.
26. Kramer B., Kramer W., Fritz H. J. Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli. Cell. 38:1984;879-887.
27. Lane A. N., Peck B. Conformational flexibility in DNA duplexes containing G.G mismatches. Eur. J. Biochem. 230:1995;1073-1087.
28. Leroy J., Guéron M. Solution structure of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons. Structure. 3:1995;101-120.
29. Leroy J., Gehring K., Kettani A., Guéron M. Acid multimers of oligodeoxycytidine strands: stoichiometry, base-pair characterization, and proton exchange properties. Biochemistry. 32:1993;6019-6031.
30. Li Y., Zon G., Wilson W. D. NMR and molecular modeling evidence for a G.A mismatch base pair in a purine-rich DNA duplex. Proc. Natl Acad. Sci. USA. 88:1991;26-30.
31. Marugg J. E., Tromp M., Jhuranci P., Hoyng C. F., van der Marel G. A., van Boom J. H. Synthesis of DNA fragments by the hydroxybenzotriazole phosphotriester approach. Tetrahedron Letters. 40:1984;73-78.
32. 2. Biochemistry. 32:193;3583-3595.
33. McConnell B., Seawell P. C. Amino protons of cytosine. Chemical exchange, rotational exchange, and salt-induced proton magnetic resonance chemical shifts of aqueous 2′,3′-cyclic cytidine monophosphate. Biochemistry. 12:1973;4426-4434.
34. Patel D. J., Kozlowski S. A., Marky L. A., Rice J. A., Broka C., Dallas J., Itakura K. A., Breslauer K. J. Structure, dynamics, and energetics of deoxyguanosine.thymidine wobble base pair formation in the self complementary d(CGTGAATTCGCG) duplex in solution. Biochemistry. 21:1982;437-444.
35. Patel D. J., Kozlowski S. A., Ikuta S., Itakura K. Dynamics of DNA duplexes containing internal G.T, G.A, A.C, and T.C pairs: hydrogen exchange at and adjacent to mismatch sites. Fed. Proc. Am. Soc. Exp. Biol. 43:1984;2663-2670.
36. Plateau P., Guéron M. Exchangeable proton NMR without base-line distortion, using new strong-pulse sequences. J. Am. Chem. Soc. 104:1982;7310-7311.
37. Radhakrishnan I., Patel D. J. Solution structure and hydration patterns of a pyrimidine.purine.pyrimidine DNA triplex containing a novel T.CG base-triple. J. Mol. Biol. 241:1994;600-619.
38. n(Y-) DNA triplexes in solution: imino and amino proton and nitrogen markers of G.TA base triple formation. Biochemistry. 30:1991;9022-9030.
39. 4. Nature. 339:1989;637-640.
40. SantaLucia J., Jr, Kierzek R., Turner D. H. Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U.U and C.C+ pairs. Biochemistry. 30:1991;8242-8251.
41. Sowers L. C., Fazakerley G. V., Kim H., Dalton L., Goodman M. F. Variation of nonexchangeable proton resonance chemical shifts as a probe of aberrant base pair formation in DNA. Biochemistry. 25:1986;3983-3988.
42. Su S. S., Lahue R. S., Au K. O., Modrich P. Mispair specificity of methyl-directed DNA mismatch correction. J. Biol. Chem. 263:1988;6829-6835.
43. van der Marel G., van Boeckel C. A. A., Wille G., van Boom J. H. A new approach to the synthesis of phosphotriester intermediates of nucleosides and nucleic acids. Tetrahedron Letters. 22:1981;3887-3890.
44. Wagner R., Debbie P., Radman M. Mutation detection using immobilized mismatch binding protein (MutS). Nucl. Acids Res. 23:1995;3944-3948.
45. Woodson S. A., Crothers D. M. Preferential location of bulged guanosine internal to a GC tract by a 1H NMR. Biochemistry. 27:1988;445-455.