Sequence-dependent DNA structure.

The three-dimensional structure of DNA depends subtly on its sequence, and this property is used by the proteins that regulate gene expression to locate their target sequences. Despite the large body of experimental data that has been accumulated on the relationship between sequence and DNA structure, we still do not fully understand the molecular basis for these properties, nor can we predict a three-dimensional structure from a given sequence. We have been using computer modelling to tackle these problems. Some of our results and the implications for understanding the biological role of key sequences are discussed here.

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

[2]  A. Klug,et al.  The structure of an oligo(dA)·oligo(dT) tract and its biological implications , 1987, Nature.

[3]  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.

[4]  R. Dickerson,et al.  Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G. , 1992, Journal of molecular biology.

[5]  S. Diekmann,et al.  Definitions and nomenclature of nucleic acid structure parameters. , 1989, The EMBO journal.

[6]  Christopher A. Hunter,et al.  The nature of .pi.-.pi. interactions , 1990 .

[7]  D. Lilley,et al.  (A-T)n tracts embedded in random sequence DNA--formation of a structure which is chemically reactive and torsionally deformable. , 1986, Nucleic acids research.

[8]  A. R. Srinivasan,et al.  Nucleic acid model building: the multiple backbone solutions associated with a given base morphology. , 1987, Journal of biomolecular structure & dynamics.

[9]  H R Drew,et al.  A base-centred explanation of the B-to-A transition in DNA. , 1984, Journal of molecular biology.

[10]  R. Dickerson,et al.  Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. , 1991, Journal of molecular biology.

[11]  Jacques H. van Boom,et al.  Molecular structure of a left-handed double helical DNA fragment at atomic resolution , 1979, Nature.

[12]  C R Calladine,et al.  The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme. , 1995, Journal of molecular biology.

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

[14]  D. Lilley,et al.  The mechanism of cruciform formation in supercoiled DNA: initial opening of central basepairs in salt-dependent extrusion. , 1987, Nucleic acids research.

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

[16]  A Klug,et al.  A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. , 1979, Journal of molecular biology.

[17]  C. Calladine,et al.  Understanding DNA: The Molecule & How It Works , 1992 .

[18]  E. Pednault,et al.  Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. , 1994, Journal of molecular biology.

[19]  H. Drew,et al.  Negative supercoiling induces spontaneous unwinding of a bacterial promoter. , 1985, The EMBO journal.

[20]  O Kennard,et al.  The crystal structure of d(G-G-G-G-C-C-C-C). A model for poly(dG).poly(dC). , 1985, Journal of molecular biology.

[21]  R. Sauer.  Protein-DNA interactions , 1991 .

[22]  V. Zhurkin,et al.  B-DNA twisting correlates with base-pair morphology. , 1995, Journal of molecular biology.