An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data

Nucleic Acids Research

Volumn 31, Issue 10, 2003, Pages 2647-2658

  Kanhere, Aditi ^a   Bansal, Manju ^a,b  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b ITPL   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CURVED DNA; CYTOSINE; DINUCLEOTIDE; DNA FRAGMENT; GUANINE; TRINUCLEOTIDE; DNA; OLIGONUCLEOTIDE;

ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; CRYSTAL STRUCTURE; DNA CONFORMATION; DNA DETERMINATION; DNA SEQUENCE; GC RICH SEQUENCE; GEL MOBILITY SHIFT ASSAY; INTERMETHOD COMPARISON; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE REPEAT;

BASE SEQUENCE; DNA; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; REPETITIVE SEQUENCES, NUCLEIC ACID; SOFTWARE;

EID: 0038381548     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg362     Document Type: Article

References (58)

1. Hagerman,P.J. (1990) Sequence-directed curvature of DNA. Annu. Rev. Biochem., 59, 755-781.
2. McFall,S.M., Chugani,S.A. and Chakrabarty,M.A. (1998) Transcriptional activation of the catechol and chlorocatechol operons: variations on a theme. Gene, 223, 257-267.
3. McGill,G. and Fisher,D.E. (1998) DNA bending and the curious case of Fos/Jun. Chem. Biol., 5, R29-R38.
4. Perez-Martin,J., Rojo,F. and de Lorenzo,V. (1994) Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol. Rev., 58, 268-290.
5. Polaczek,P., Kwan,K., Liberies,D.A. and Campbell,J.L. (1997) Role of architectural elements in combinatorial regulation of initiation of DNA replication in Escherichia coli. Mol. Microbiol., 26, 261-275.
6. Henriquez.V., Milisavljevic,V., Kahn,J.D. and Gennaro,M.L. (1993) Sequence and structure of cmp, the replication enhancer of the Staphylococcus aureus plasmid pT181. Gene, 134, 93-98.
7. Widlund,H.R., Kuduvalli,P.N., Bengtsson,M., Cao,H., Tullius,T.D, and Kubista,M. (1999) Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence. J. Biol. Chem., 274, 31847-31852.
8. Muller,H.P. and Varmus,H.E. (1994) DNA bending creates favored sites for retroviral integration: an explanation for preferred insertion sites in nucleosomes. EMBO J., 13, 4704-4714.
9. Fitzgerald,D.J., Dryden,G.L., Bronson,E.C., Williams,J.S. and Anderson,J.N. (1994) Conserved patterns of bending in satellite and nucleosome positioning DNA. J. Biol. Chem., 269, 21303-21314.
10. Zahn,K. and Blattner,F.R. (1985) Sequence-induced DNA curvature at the bacteriophage lambda origin of replication. Nature, 317, 451-453.
11. Nelson,H.C., Finch,J.T., Luisi,B.F. and Klug,A. (1987) The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature, 330, 221-226.
12. Goodsell,D.S., Kaczor-Grzeskowiak,M. and Dickerson,R.E. (1994) The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps. J. Mol. Biol., 239, 79-96.
13. Goodsell,D.S., Kopka,M.L., Cascio,D. and Dickerson,R.E. (1993) Crystal structure of CATGGCCATG and its implications for A-tract bending models. Proc. Natl Acad. Sci. USA, 90, 2930-2934.
14. DiGabriele,A.D. and Steitz,T.A. (1993) A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend. J. Mol. Biol., 231, 1024-1039.
15. DiGabriele,A.D., Sanderson,M.R. and Steitz,T.A. (1989) Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natl Acad. Sci. USA, 86, 1816-1820.
16. Shatzky-Schwartz,M., Arbuckle,N.D., Eisenstein,M., Rabinovich,D., Bareket-Samish,A., Haran,T.E., Luisi,B.F. and Shakked,Z. (1997) X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature. J. Mol. Biol., 267, 595-623.
17. Umemoto,K., Sarma,M.H., Gupta,G. and Sarma,R.H. (1990) Effect of the methyl group on DNA bending and curvature: structure of d(GA4U4C)2 in solution. Biochemistry, 29, 4714-4722.
18. 2. Biochemistry, 27, 3423-3432.
19. MacDonald,D., Herbert,K., Zhang,X., Pologruto,T., Lu,P. and Polgruto,T. (2001) Solution structure of an A-tract DNA bend. J. Mol. Biol., 306, 1081-1098.
20. Marini,J.C., Effron,P.N., Goodman,T.C., Singleton,C.K., Wells,R.D., Wartell,R.M. and Englund,P.T. (1984) Physical characterization of a kinetoplast DNA fragment with unusual properties. J. Biol. Chem., 259, 8974-8979.
21. Wu,H.M. and Crothers,D.M. (1984) The locus of sequence-directed and protein-induced DNA bending. Nature, 308, 509-513.
22. Kahn,J.D. and Crothers,D.M. (1992) Protein-induced bending and DNA cyclization. Proc. Natl Acad. Sci. USA, 89, 6343-6347.
23. Ulanovsky,L.E. and Trifonov,E.N. (1987) Estimation of wedge components in curved DNA. Nature, 326, 720-722.
24. Koo,H.S. and Crothers,D.M. (1988) Calibration of DNA curvature and a unified description of sequence-directed bending. Proc. Natl Acad. Sci. USA, 85, 1763-1767.
25. Bolshoy,A., McNamara,P., Harrington,R.E. and Trifonov,E.N. (1991) Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Natl Acad. Sci. USA, 88, 2312-2316.
26. Bansal,M. (1996) Structural variations observed in DNA crystal structures and their implications for protein-DNA interaction. In Sarma,R.H. and Sarma,M.H. (eds), Biological Structure and Dynamics, Proceedings of the Ninth Convention. Adenine Press, New York, NY, Vol. 1, pp. 121-134.
27. Liu,Y. and Beveridge,D.L. (2001) A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data. J. Biomol. Struct. Dyn., 18, 505-526.
28. Ulyanov,N.B. and James,T.L. (1995) Statistical analysis of DNA duplex structural features. Methods Enzymol., 261, 90-120.
29. Jernigan,R.L., Sarai,A., Ting,K.L. and Nussinov,R. (1986) Hydrophobic interactions in the major groove can influence DNA local structure. J. Biomol. Struct. Dyn., 4, 41-48.
30. Calladine,C.R., Drew,H.R. and McCall,M.J. (1988) The intrinsic curvature of DNA in solution. J. Mol. Biol., 201, 127-137.
31. Cacchione,S., De Santis,P., Foti,D., Palleschi,A. and Savino,M. (1989) Periodical polydeoxynucleotides and DNA curvature. Biochemistry, 28, 8706-8713.
32. DeSantis,P., Palleschi,A., Savino,M. and Scipioni,A. (1990) Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. Biochemistry, 29, 9269-9273.
33. Gorin,A.A., Zhurkin,V.B. and Olson,W.K. (1995) B-DNA twisting correlates with base-pair morphology. J. Mol. Biol., 247, 34-48.
34. Tung,C.S. and Harvey,S.C. (1986) Base sequence, local helix structure and macroscopic curvature of A-DNA and B-DNA. J. Biol. Chem., 261, 3700-3709.
35. Brukner,I., Sanchez,R., Suck,D. and Pongor,S. (1995) Sequence dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J., 14, 1812-1818.
36. Goodsell,D.S. and Dickerson,R.E. (1994) Bending and curvature calculations in B-DNA. Nucleic Acids Res., 22, 5497-5503.
37. Satchwell,S.C.. Drew,H.R. and Travers,A.A. (1986) Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol., 191, 659-675.
38. Kabsch,W., Sander,C. and Trifonov,F.N. (1982) The ten helical twist angles of B-DNA. Nucleic Acids Res., 10, 1097-1104.
39. Dlakic,M. and Harrington,R.E. (1998) Unconventional helical phasing of repetitive DNA motifs reveals their relative bending contributions, Nucleic Acids Res., 26, 4274-4279.
40. Nagaich,A.K., Bhattacharyya,D., Brahmachari,S.K. and Bansal,M. (1994) CA/TG sequence at the 5′ end of oligo(A)-tracts strongly modulates DNA curvature. J. Biol. Chem., 269, 7824-7833.
41. Brukner,I., Susic,S., Dlakic,M., Savic,A. and Pongor,S. (1994) Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. J. Mol. Biol., 236, 26-32.
42. Bansal,M., Bhattacharyya,D. and Ravi,B. (1995) NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. CABIOS, 11, 281-287.
43. Trifonov,E.N. and Ulanovasky,L.E. (1987) Inherently curved DNA and its structural elements. In Wells,R.D. and Harvey,S.C. (eds) Unusual DNA Structures. Springer-Verlag, Berlin, Germany, pp. 173-187.
44. Srinivasan,A.R., Torres,R., Clark,W. and Olson,W.K. (1987) Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology. J. Biomol. Struct. Dyn., 5, 459-496.
45. Tung,C.S., Garcia,A.E., Marr,T.G., Mitra,S.K. and Burks,C. (1988) Measures of DNA curvature. In Olson,W.K., Sarma,M.H., Sarma,R.H. and Sundaralingam,M. (eds), DNA Bending and Curvature. Adenine Press, New York, NY, Vol. 3, pp. 265-278.
46. Bansal,M., Bhattacharya,D. and Mohanty,D. (1991) DNA bending: a natural consequence of base sequence dependent variability. In Balaram,P. and Ramaseshan,S. (eds), Molecular Conformation and Biological Interactions. Indian Academy of Sciences, Bangalore, India, pp. 347-362.
47. Jernigan,R.L., Sarai,A., Shapiro,B. and Nussinov,R. (1987) Relationship between curved DNA conformations and slow gel migration. J. Biomol. Struct. Dyn., 4, 561-567.
48. Olson,W.K., Marky,N.L., Jernigan,R.L. and Zhurkin,V.B. (1993) Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. J. Mol. Biol., 232, 530-554.
49. Haran,T.E., Kahn,J.D. and Crothers,D.M. (1994) Sequence elements responsible for DNA curvature. J. Mol. Biol., 244, 135-143.
50. Hagerman,P.J. (1986) Sequence-directed curvature of DNA. Nature, 321, 449-450.
51. Hagerman,P.J. (1985) Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry, 24, 7033-7037.
52. Brukner,I., Jurukovski,V., Konstantinovic,M. and Savic,A. (1991) Curved DNA without AA/TT dinucleotide step. Nucleic Acids Res., 19, 3549-3551.
53. Brukner,I., Dlakic,M., Savic,A., Susic,S., Pongor,S. and Suck,D. (1993) Evidence for opposite groove-directed curvature of GGGCCC and AAAAA sequence elements. Nucleic Acids Res., 21, 1025-1029.
54. Ussery,D.W., Higgins,C.F. and Bolshoy,A. (1999) Environmental influences on DNA curvature. J. Biomol. Struct. Dyn., 16, 811-823.
55. Tanaka,K., Muramatsu,S., Yamada,H. and Mizuno,T. (1991) Systematic characterization of curved DNA segments randomly cloned from Escherichia coli and their functional significance. Mol. Gen. Genet., 226, 367-376.
56. McAllister,C.F. and Achberger,E.C. (1988) Effect of polyadenine-containing curved DNA on promoter utilization in Bacillus subtilis J. Biol. Chem., 263, 11743-11749.
57. McAllister,C.F. and Achberger,E.C. (1989) Rotational orientation of upstream curved DNA affects promoter function in Bacillus subtilis. J. Biol. Chem., 264, 10451-10456.
58. Brukner,I., Sanchez,R., Suck,D. and Pongor,S. (1995) Trinucleotide models for DNA bending propensity: comparison of models based on DNase I digestion and nucleosome packaging data. J. Biomol. Struct. Dyn., 13, 309-317.