DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotide x-ray crystal structures

Journal of Molecular Biology

Volumn 265, Issue 5, 1997, Pages 603-619

  Hunter, Christopher A ^a   Lu, Xiang Jun ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

Base stacking interactions; DNA; Sequence dependent structure energy calculation; X ray crystal structure

Indexed keywords

NUCLEIC ACID BASE; OLIGONUCLEOTIDE;

ARTICLE; CALCULATION; DNA BINDING; ENERGY; METHODOLOGY; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY;

EID: 0031556948     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0755     Document Type: Article

References (27)

1. Bhattacharyya D., Bansal M. Local variability and base sequence effects in DNA crystal structures. J. Biomol. Struct. Dynam. 8:1990;539-572.
2. Caillet J., Claverie P. Theoretical evaluation of the intermolecular interaction energy of a crystal: application to the analysis of crystal geometry. Acta Crystallog. sect. A. 31:1975;448-461.
3. Cornell W. D., Cieplak P., Bayly C. I., Gould I. R., Merz K. M., Ferguson D. M., Spellmeyer D. C., Fox T., Caldwell J. W., Kollman P. A. A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
4. Diekmann S. Definitions and nomenclature of nucleic acid structure parameters. J. Mol. Biol. 205:1989;787-791.
5. El Hassan, M. A. 1995, The Geometry and structure of DNA and its role in DNA/protein recognition. University of Cambridge.
6. El Hassan M. A., Calladine C. R. The assessment of the geometry of dinucleotide steps in double-helical DNA - a new local calculation scheme. J. Mol. Biol. 251:1995;648-664.
7. El Hassan M. A., Calladine C. R. Propeller-twisting of base-pairs and the confomational mobility of dinucleotide steps in DNA. J. Mol. Biol. 259:1996;95-103.
8. Gabb H. A., Harvey S. C. Conformational transitions in potential and free energy space for furanoses and 2′-deoxynucleosides. J. Am. Chem. Soc. 115:1993;4218-4227.
9. Gartenberg M. R., Crothers D. M. DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature. 333:1988;824-829.
10. Gorin A. A., Zhurkin V. B., Olson W. K. B -DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:1995;34-48.
11. Hunter C. A. Sequence-dependent DNA structure: the role of base-stacking interactions. J. Mol. Biol. 230:1993;1025-1054.
12. Hunter C. A., Sander J. K. M. The nature of π-π interactions. J. Am. Chem. Soc. 112:1990;5525-5534.
13. Hunter C. A., Lu X. J., Kapteijn G. M., Vankoten G. Influence of fluorine on aromatic interactions. J. Chem. Soc. Farad. Trans. 91:1995;2009-2015.
14. Koudelka G. B., Harrison S. C., Ptashne M. Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature. 326:1987;886-888.
15. Mohamadi F., Richards N. G. J., Guida W. C., Liskamp R., Lipton M., Caufield C., Chang G., Hendrickson T., Still W. C. MacroModel - an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J. Comput. Chem. 11:1990;440-467.
16. Sponer J., Kypr J. On the use of empirical potentials in studies of base-stacking in DNA. Theoretical Biochemistry and Molecular Biophysics. 1990;Adenine Press, New York.
17. Sponer J., Kypr J. Theoretical analysis of the base stacking in DNA - choice of the force-field and a comparison with the oligonucleotide crystal-structures. J. Biomol. Struct. Dynam. 11:1993;277-292.
18. Sun Y., Kollman P. A. Determination of solvent free energy using molecular dynamics with solute cartesian mapping: an application to the solvation of 18-crown-6. J. Chem. Phys. 97:1992;5108-5112.
19. Taylor R., Kennard O. Molecular structures of nucleosides and nucleotides. 2. Orthogonal coordinates for standard nucleic acid base residues. J. Am. Chem. Soc. 104:1982;3209-3212.
20. Travers A. A., Klug A. Bending of DNA in nucleoprotein complexes DNA Topology and Its Biological Effects. 1990;Cold Spring Harbour Laboratory Press, Cold Spring Harbor, NY.
21. Tung C. S., Harvey S. C. Base sequence, local helix structure and macroscopic curvature of A -DNA and B -DNA. J. Biol. Chem. 261:1986;3700-3709.
22. Vanopdenbosch N., Cramer R., Giarrusso F. F. SYBYL, the integrated molecular modeling system. J. Mol. Graph. 3:1985;110-111.
23. Vinter J. G. Extended electron distributions applied to the molecular mechanics of some inter-molecular interactions. J. Comput.-Aided Mol. Design, 8:1994;653-668.
24. Williams D. H. The molecular basis of biological order. Aldrichim. Acta. 24:1991;71-80.
25. Yanagi K., Prive G. G., Dickerson R. E. Analysis of local helix geometry in 3 B -DNA decamers and 8 dodecamers. J. Mol. Biol. 217:1991;201-214.
26. Young M. A., Ravishanker G., Beveridge D. L., Berman H. M. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys. J. 68:1995;2454-2468.
27. Zhurkin V. B. Local mobility in the DNA double helix: comparison of conformational calculations with experiment. J. Mol. Biol. 17:1983;495-509.