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. 1995 Apr 18;14(8):1812–1818. doi: 10.1002/j.1460-2075.1995.tb07169.x

Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.

I Brukner 1, R Sánchez 1, D Suck 1, S Pongor 1
PMCID: PMC398274  PMID: 7737131

Abstract

Structural parameters characterizing the bending propensity of trinucleotides were deduced from DNase I digestion data using simple probabilistic models. In contrast to dinucleotide-based models of DNA bending and/or bendability, the trinucleotide parameters are in good agreement with X-ray crystallographic data on bent DNA. This improvement may be due to the fact that the trinucleotide model incorporates more sequence context information than do dinucleotide-based descriptions.

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Selected References

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

  1. Barber A. M., Zhurkin V. B. CAP binding sites reveal pyrimidine-purine pattern characteristic of DNA bending. J Biomol Struct Dyn. 1990 Oct;8(2):213–232. doi: 10.1080/07391102.1990.10507803. [DOI] [PubMed] [Google Scholar]
  2. Bolshoy A., McNamara P., Harrington R. E., Trifonov E. N. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2312–2316. doi: 10.1073/pnas.88.6.2312. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brennan R. G., Roderick S. L., Takeda Y., Matthews B. W. Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex. Proc Natl Acad Sci U S A. 1990 Oct;87(20):8165–8169. doi: 10.1073/pnas.87.20.8165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brukner I., Dlakic M., Savic A., Susic S., Pongor S., Suck D. Evidence for opposite groove-directed curvature of GGGCCC and AAAAA sequence elements. Nucleic Acids Res. 1993 Feb 25;21(4):1025–1029. doi: 10.1093/nar/21.4.1025. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Brukner I., Jurukovski V., Savic A. Sequence-dependent structural variations of DNA revealed by DNase I. Nucleic Acids Res. 1990 Feb 25;18(4):891–894. doi: 10.1093/nar/18.4.891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brukner I., Susic S., Dlakic M., Savic A., Pongor S. Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. J Mol Biol. 1994 Feb 11;236(1):26–32. doi: 10.1006/jmbi.1994.1115. [DOI] [PubMed] [Google Scholar]
  7. Calladine C. R., Drew H. R., McCall M. J. The intrinsic curvature of DNA in solution. J Mol Biol. 1988 May 5;201(1):127–137. doi: 10.1016/0022-2836(88)90444-5. [DOI] [PubMed] [Google Scholar]
  8. Calladine C. R., Drew H. R. Principles of sequence-dependent flexure of DNA. J Mol Biol. 1986 Dec 20;192(4):907–918. doi: 10.1016/0022-2836(86)90036-7. [DOI] [PubMed] [Google Scholar]
  9. De Santis P., Palleschi A., Savino M., Scipioni A. Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. Biochemistry. 1990 Oct 2;29(39):9269–9273. doi: 10.1021/bi00491a023. [DOI] [PubMed] [Google Scholar]
  10. Diekmann S. Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucleic Acids Res. 1987 Jan 12;15(1):247–265. doi: 10.1093/nar/15.1.247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Drew H. R., Travers A. A. DNA bending and its relation to nucleosome positioning. J Mol Biol. 1985 Dec 20;186(4):773–790. doi: 10.1016/0022-2836(85)90396-1. [DOI] [PubMed] [Google Scholar]
  12. Drew H. R., Travers A. A. DNA structural variations in the E. coli tyrT promoter. Cell. 1984 Jun;37(2):491–502. doi: 10.1016/0092-8674(84)90379-9. [DOI] [PubMed] [Google Scholar]
  13. Gartenberg M. R., Crothers D. M. DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature. 1988 Jun 30;333(6176):824–829. doi: 10.1038/333824a0. [DOI] [PubMed] [Google Scholar]
  14. Grzeskowiak K., Goodsell D. S., Kaczor-Grzeskowiak M., Cascio D., Dickerson R. E. Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA. Biochemistry. 1993 Aug 31;32(34):8923–8931. doi: 10.1021/bi00085a025. [DOI] [PubMed] [Google Scholar]
  15. Herrera J. E., Chaires J. B. Characterization of preferred deoxyribonuclease I cleavage sites. J Mol Biol. 1994 Feb 18;236(2):405–411. doi: 10.1006/jmbi.1994.1152. [DOI] [PubMed] [Google Scholar]
  16. Hochschild A., Ptashne M. Cooperative binding of lambda repressors to sites separated by integral turns of the DNA helix. Cell. 1986 Mar 14;44(5):681–687. doi: 10.1016/0092-8674(86)90833-0. [DOI] [PubMed] [Google Scholar]
  17. Hogan M. E., Roberson M. W., Austin R. H. DNA flexibility variation may dominate DNase I cleavage. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9273–9277. doi: 10.1073/pnas.86.23.9273. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hunter C. A. Sequence-dependent DNA structure. The role of base stacking interactions. J Mol Biol. 1993 Apr 5;230(3):1025–1054. doi: 10.1006/jmbi.1993.1217. [DOI] [PubMed] [Google Scholar]
  19. Kim J. L., Burley S. K. 1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nat Struct Biol. 1994 Sep;1(9):638–653. doi: 10.1038/nsb0994-638. [DOI] [PubMed] [Google Scholar]
  20. Lahm A., Suck D. DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex. J Mol Biol. 1991 Dec 5;222(3):645–667. doi: 10.1016/0022-2836(91)90502-w. [DOI] [PubMed] [Google Scholar]
  21. Lavigne M., Kolb A., Yeramian E., Buc H. CRP fixes the rotational orientation of covalently closed DNA molecules. EMBO J. 1994 Oct 17;13(20):4983–4990. doi: 10.1002/j.1460-2075.1994.tb06825.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lomonossoff G. P., Butler P. J., Klug A. Sequence-dependent variation in the conformation of DNA. J Mol Biol. 1981 Jul 15;149(4):745–760. doi: 10.1016/0022-2836(81)90356-9. [DOI] [PubMed] [Google Scholar]
  23. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Poncin M., Hartmann B., Lavery R. Conformational sub-states in B-DNA. J Mol Biol. 1992 Aug 5;226(3):775–794. doi: 10.1016/0022-2836(92)90632-t. [DOI] [PubMed] [Google Scholar]
  26. Quintana J. R., Grzeskowiak K., Yanagi K., Dickerson R. E. Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. J Mol Biol. 1992 May 20;225(2):379–395. doi: 10.1016/0022-2836(92)90928-d. [DOI] [PubMed] [Google Scholar]
  27. Raumann B. E., Rould M. A., Pabo C. O., Sauer R. T. DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. Nature. 1994 Feb 24;367(6465):754–757. doi: 10.1038/367754a0. [DOI] [PubMed] [Google Scholar]
  28. Satchwell S. C., Drew H. R., Travers A. A. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol. 1986 Oct 20;191(4):659–675. doi: 10.1016/0022-2836(86)90452-3. [DOI] [PubMed] [Google Scholar]
  29. Schultz S. C., Shields G. C., Steitz T. A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 1991 Aug 30;253(5023):1001–1007. doi: 10.1126/science.1653449. [DOI] [PubMed] [Google Scholar]
  30. Shakked Z., Guzikevich-Guerstein G., Frolow F., Rabinovich D., Joachimiak A., Sigler P. B. Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature. 1994 Mar 31;368(6470):469–473. doi: 10.1038/368469a0. [DOI] [PubMed] [Google Scholar]
  31. Shimon L. J., Harrison S. C. The phage 434 OR2/R1-69 complex at 2.5 A resolution. J Mol Biol. 1993 Aug 5;232(3):826–838. doi: 10.1006/jmbi.1993.1434. [DOI] [PubMed] [Google Scholar]
  32. Shliakhtenko L. S., Liubchenko Iu L., Chernov B. K., Zhurkin V. B. Vliianie temperatury i ionnoi sily na élektroforeticheskuiu podvizhnost' sinteticheskikh fragmentov DNK. Mol Biol (Mosk) 1990 Jan-Feb;24(1):79–95. [PubMed] [Google Scholar]
  33. Suck D. DNA recognition by DNase I. J Mol Recognit. 1994 Jun;7(2):65–70. doi: 10.1002/jmr.300070203. [DOI] [PubMed] [Google Scholar]
  34. Weston S. A., Lahm A., Suck D. X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution. J Mol Biol. 1992 Aug 20;226(4):1237–1256. doi: 10.1016/0022-2836(92)91064-v. [DOI] [PubMed] [Google Scholar]
  35. Winkler F. K., Banner D. W., Oefner C., Tsernoglou D., Brown R. S., Heathman S. P., Bryan R. K., Martin P. D., Petratos K., Wilson K. S. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 1993 May;12(5):1781–1795. doi: 10.2210/pdb4rve/pdb. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Zinkel S. S., Crothers D. M. DNA bend direction by phase sensitive detection. Nature. 1987 Jul 9;328(6126):178–181. doi: 10.1038/328178a0. [DOI] [PubMed] [Google Scholar]

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