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

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.

[1]  W. Gilbert,et al.  Sequencing end-labeled DNA with base-specific chemical cleavages. , 1980, Methods in enzymology.

[2]  A Klug,et al.  Sequence-dependent variation in the conformation of DNA. , 1981, Journal of molecular biology.

[3]  H. Drew,et al.  DNA structural variations in the E. coli tyrT promoter , 1984, Cell.

[4]  H R Drew,et al.  DNA bending and its relation to nucleosome positioning. , 1985, Journal of molecular biology.

[5]  H R Drew,et al.  Principles of sequence-dependent flexure of DNA. , 1986, Journal of molecular biology.

[6]  J M Rosenberg,et al.  Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution. , 1986, Science.

[7]  Homologous interactions of lambda repressor and lambda Cro with the lambda operator. , 1986, Cell.

[8]  H. Drew,et al.  Sequence periodicities in chicken nucleosome core DNA. , 1986, Journal of molecular biology.

[9]  S. Diekmann,et al.  Temperature and salt dependence of the gel migration anomaly of curved DNA fragments , 1987, Nucleic Acids Res..

[10]  D. Crothers,et al.  DNA bend direction by phase sensitive detection , 1987, Nature.

[11]  Donald M. Crothers,et al.  DNA sequence determinants of CAP-induced bending and protein binding affinity , 1988, Nature.

[12]  H R Drew,et al.  The intrinsic curvature of DNA in solution. , 1988, Journal of molecular biology.

[13]  A. Iserles.  Numerical recipes in C—the art of scientific computing , by W. H. Press, B. P. Flannery, S. A. Teukolsky and W. T. Vetterling. Pp 735. £27·50. 1988. ISBN 0-521-35465-X (Cambridge University Press) , 1989, The Mathematical Gazette.

[14]  R. Austin,et al.  DNA flexibility variation may dominate DNase I cleavage. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[15]  B. Matthews,et al.  Protein-DNA conformational changes in the crystal structure of a lambda Cro-operator complex. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[16]  A. Palleschi,et al.  Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. , 1990, Biochemistry.

[17]  I. Brukner,et al.  Sequence-dependent structural variations of DNA revealed by DNase I. , 1990, Nucleic acids research.

[18]  V. Zhurkin,et al.  CAP binding sites reveal pyrimidine-purine pattern characteristic of DNA bending. , 1990, Journal of biomolecular structure & dynamics.

[19]  R E Harrington,et al.  Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. Suck,et al.  DNase I-induced DNA conformation. 2 A structure of a DNase I-octamer complex. , 1991, Journal of molecular biology.

[21]  D. Suck,et al.  X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution. , 1992, Journal of molecular biology.

[22]  R Lavery,et al.  Conformational sub-states in B-DNA. , 1992, Journal of molecular biology.

[23]  S. Harrison,et al.  The phage 434 OR2/R1-69 complex at 2.5 A resolution. , 1993, Journal of molecular biology.

[24]  C. Hunter,et al.  Sequence-dependent DNA structure. The role of base stacking interactions. , 1993, Journal of molecular biology.

[25]  D. Goodsell,et al.  Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA. , 1993, Biochemistry.

[26]  K S Wilson,et al.  The crystal structure of EcoRV endonuclease and of its complexes with cognate and non‐cognate DNA fragments. , 1993, The EMBO journal.

[27]  D. Suck,et al.  DNA recognition by DNase I , 1994, Journal of molecular recognition : JMR.

[28]  I. Brukner,et al.  Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. , 1994, Journal of molecular biology.

[29]  A. Joachimiak,et al.  Determinants of repressor/operator recognition from the structure of the trp operator binding site , 1994, Nature.

[30]  E. Yeramian,et al.  CRP fixes the rotational orientation of covalently closed DNA molecules. , 1994, The EMBO journal.

[31]  Robert T. Sauer,et al.  DNA recognition by β-sheets in the Arc represser–operator crystal structure , 1994, Nature.

[32]  Stephen K. Burley,et al.  1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG , 1994, Nature Structural Biology.

[33]  Julio E. Herrera,et al.  Characterization of preferred deoxyribonuclease I cleavage sites. , 1994, Journal of molecular biology.