Effect of base pair A/C and G/T mismatches on the thermal stabilities of DNA oligomers that form B-Z junctions

Biochemistry

Volumn 36, Issue 38, 1997, Pages 11419-11427

  Otokiti, Ebenezer O ^a   Sheardy, Richard D ^a  

^a SETON HALL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA B; DNA BASE; DNA Z; DOUBLE STRANDED DNA;

ARTICLE; BASE MISPAIRING; DNA CONFORMATION; GENE MUTATION; GENETIC STABILITY; HYDROGEN BOND; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; THERMODYNAMICS;

BASE COMPOSITION; CATIONS, MONOVALENT; CIRCULAR DICHROISM; DNA; HEAT; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; OLIGODEOXYRIBONUCLEOTIDES; SODIUM; THERMODYNAMICS;

EID: 0030885669     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi970972s     Document Type: Article

References (42)

1. Modrich, P. (1987) DNA mismatch correction. Annu. Rev. Biochem. 56, 435-466.
2. Lu, A.-L., and Chang, D.-Y. (1988) A novel nucleotide excision repair for the conversion of an A/G mismatch to C/G base pair in E. coli. Cell 54, 805-812.
3. Drew, H. R., and Dickerson, R. E. (1981) Conformation and dynamics in a Z-DNA tetramer. J. Mol. Biol. 152, 723-736.
4. Brown, T., Kennard, O., Kneale, G., and Rabinovich, D. (1985) High-resolution structure of a DNA helix containing mismatched base pairs. Nature 315, 604-606.
5. Ho, P. S., Fredrick, C. A., Quigly, G. J., van der Marel, G. A., van Boom, J. H., Wang, A. H. J., and Rich, A. (1985) G·T wobble base pairing in Z-DNA at 1 D atomic resolution: The crystal structure of d(CGCGTG). EMBO J. 4, 3617-3623.
6. Hunter, W. N., Brown, T., Anand, N. N., and Kennard, O. (1986) Structure of an adenine·cytosine base pair in DNA and its implications for mismatch repair. Nature 320, 552-555.
7. Hunter, W. N., Brown, T., Kneale, G., Anand, N. N., Rabinovich, D., and Kennard, O. (1987) The structure of guanosine·thymidine mismatches in B-DNA at 2.5 Å resolution. J. Biol. Chem. 262, 9962-9970.
8. Patel, D. J., Kozlowski, S. A., Ikuta, S., and Itakura, K. (1984) Deoxyadenosine-deoxycytidine pairing in the d(C-G-C-G-A-A-T-T-C-A-C-G) duplex: conformation and dynamics at and adjacent to the dACdC mismatch site. Biochemistry 23, 3218-3226.
9. 2. Biochemistry 31, 12087-12095.
10. Thomas, G. A., and Peticolas, W. L. (1984) Sequence dependence of conformations of self-complementary duplex tetradeoxynucleotides containing cytosine and guanine. Biochemistry 23, 3202-3207.
11. Benevides, J. M., Wang, A. H.-J., van der Marel, G. A., van Boom, J. H., and Thomas, G. J., Jr. (1989) Effect of the GCT mismatch on backbone and sugar conformations of Z-DNA and B-DNA: Analysis by Raman spectroscopy of crystal and solution structures of d(CGCGTG) and d(CGCGCG). Biochemistry 28, 304-310.
12. Gralla, J., and Crothers, D. M. (1973) Free energy of imperfect nucleic acid helices III. Small internal loops resulting from mismatches. J. Mol. Biol. 78, 301-319.
13. Tibanyenda, N., De Bruin, S. H., Haasnoot, C. A. G., van der Marel, G. A., van Boom, J. H., and Hilbers, C. W. (1984) The effects of single base pair mismatches on the duplex stability of d(T-A-T-T-A-A-T-A-T-C-A-A-G-T-T-G)·d(C-A-A-C-T-T-G-A-T-A-T-T-A-A-T-A). Eur. J. Biochem. 139, 19-27.
14. 3G (X, Y = A, C, G, T). Nucleic Acids Res. 13, 4811-4824.
15. Werntges, H., Steger, G., Riesner, D., and Fritz, H. J. (1986) Mismatches in DNA double strands: Thermodynamic parameters and their correlation to repair efficiencies. Nucleic Acids Res. 14, 3773-3790.
16. 6-methylguanine in reference both to Watson-Crick and to mismatched pairs. Biochemistry 28, 5881-5889.
17. Le Blanc, D. A., and Morden, K. M. (1991) Thermodynamic characterization of deoxyribonucleotide duplexes containing bulges. Biochemistry 30, 4042-4047.
18. Li, Y., Zon, G., and Wilson, W. D. (1991) Thermodynamics of DNA duplexes with adjacent GCA mismatches. Biochemistry 30, 7566-7572.
19. Ebel, S., Lane, A. N., and Brown, T. (1992) Very stable mismatch duplexes: structural and thermodynamic studies on tandem GCA mismatches in DNA Biochemistry 31, 12083-12086.
20. Sheardy, R. D., Levine, N., Marotta, S., Suh, D., and Chaires, J. B. (1994) A thermodynamic investigation of the melting of B-Z junction forming DNA oligomers. Biochemistry 33, 1385-1391.
21. Plum, E. G., Grollman, A. P., Johnson, F., and Breslauer, K. J. (1995) Influence of the oxidatively damaged adduct 8-oxodeoxyguanosine on the conformation, energetics, and thermodynamic stability of a DNA duplex. Biochemistry 34, 16148-16160.
22. Breslauer, K. J., Frank, R., Blocker, H., and Marky, L. A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750.
23. 4 endloops: Evaluation of nearest neighbor stacking interactions in DNA. Biopolymers 32, 849-864.
24. SantaLucia, J., Jr., Allawi, H. T., and Seneviratne, P. A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555-3562.
25. Fersht, A. R., Knill-Jones, J. W., and Tsui, W. C. (1982) Kinetic basis of spontaneous mutation: Misinsertion frequencies, proofreading specificities and cost of proofreading by DNA polymerases of Escherichia coli. J. Mol. Biol. 156, 37-51.
26. Watson, J. D., and Crick, F. H. C. (1953) Genetic implications of the structure of deoxyribonucleic acid. Nature 171, 964-967.
27. Crick, F. H. (1976) Codon-anticodon pairing: The wobble hypothesis. J. Mol. Biol. 19, 548-555.
28. Boulard, Y., Cognet, J. A. H., Gabarro-Apra, J., Le Bret, M., Carbonnaux, C., and Fazakerley, G. V. (1995) Solution structure of an oncogenic DNA duplex, the K-ras gene and the sequence containing a central C·A or G·A mismatch as a function of pH: NMR and MD studies. J. Mol. Biol. 246, 194-208.
29. 4-meT pairing in dodecanucleotide duplexes. Biochemistry 27, 100-108.
30. Boulard, Y., Cognet, J. A. H., Gabarro-Apra, J., Le Bret, M., Carbonnaux, C., and Fazakerley, G. V. (1992) The pH dependent configurations of the CCA mispair in DNA. Nucleic Acids Res. 20, 1933-1941.
31. 31P NMR spectra. Biochemistry 29, 5245-5251.
32. Sheardy, R. D. (1988) Preliminary spectroscopic characterization of a synthetic DNA oligomer containing a B-Z junction at high salt. Nucleic Acids Res. 16, 1153-1167.
33. Sheardy, R. D., and Winkle, S. A. (1989) Temperature dependent CD and NMR studies on a synthetic DNA oligomer containing a B-Z junction at high salt. Biochemistry 28, 720-725.
34. Winkle, S. A., Aloyo, M. C., Morales, N., Zambrano, T. Y., and Sheardy, R. D. (1991) Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme Mbo I. Biochemistry 30, 10601-10606.
35. Guo, Q., Lu, M., Sharestanifar, M., Sheardy, R. D., and Kallenbach, N. R. (1991) Drug binding to a B-Z molecule: Analysis by chemical footprinting. Biochemistry 30, 11735-11741.
36. Suh, D., Sheardy, R. D., and Chaires, J. B. (1991) Unusual binding of ethidium to a deoxyoligonucleotide containing a B-Z Junction. Biochemistry 30, 8722-8726.
37. Lu, M., Guo, Q., Kallenbach, N. R., and Sheardy, R. D. (1992) Conformational properties of B-Z junctions in DNA. Biochemistry 31, 4712-4719.
38. Sheardy, R. D., Suh, D., Kurzinsky, R., Doktycz, M. J., Benight, A. S., and Chaires, J. B. (1993) Sequence dependence of the free energy of B-Z junction formation in deoxyoligonucleotides. J. Mol. Biol. 231, 475-488.
39. Otokiti, E. O., and Sheardy, R. D. (1997) Sequence effects on the relative thermodynamic stabilities of B-Z junction forming DNA oligomers Biophys. J. (in press).
40. Caruthers, M. H. (1991) Chemical synthesis of DNA and DNA analogues. Acc. Chem. Res. 24, 274-284.
41. 5C). Proc. Natl. Acad. Sci. U.S.A. 78, 1619-1623.
42. Marky, L. A., and Breslauer, K. J. (1987) Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 26, 1601-1620.