DOI: 10.1006/jmbi.1996.0755. DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures

DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures

10.1006/jmbi.1996.0755

Crossref journal-article

Elsevier BV

Journal of Molecular Biology (78)

Bibliography

Hunter, C. A., & Lu, X.-J. (1997). DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures. Journal of Molecular Biology, 265(5), 603â619.

Authors 2

Christopher A. Hunter (first)
Xiang-Jun Lu (additional)

References 27 Referenced 103

10.1080/07391102.1990.10507828 / J. Biomol. Struct. Dynam. / Local variability and base sequence effects in DNA crystal structures by Bhattacharyya (1990)
10.1107/S0567739475001015 / Acta Crystallog. sect. A / Theoretical evaluation of the intermolecular interaction energy of a crystal by Caillet (1975)
10.1021/ja00124a002 / J. Am. Chem. Soc. / A second generation force field for the simulation of proteins, nucleic acids and organic molecules by Cornell (1995)
10.1016/0022-2836(89)90324-0 / J. Mol. Biol. / Definitions and nomenclature of nucleic acid structure parameters by Diekmann (1989)
{'key': '10.1006/jmbi.1996.0755_BIB5', 'series-title': 'The Geometry and structure of DNA and its role in DNA/protein recognition', 'author': 'El Hassan', 'year': '1995'} / The Geometry and structure of DNA and its role in DNA/protein recognition by El Hassan (1995)
10.1006/jmbi.1995.0462 / J. Mol. Biol. / The assessment of the geometry of dinucleotide steps in double-helical DNA — a new local calculation scheme by El Hassan (1995)
10.1006/jmbi.1996.0304 / J. Mol. Biol. / Propeller-twisting of base-pairs and the confomational mobility of dinucleotide steps in DNA by El Hassan (1996)
10.1021/ja00063a045 / J. Am. Chem. Soc. / Conformational transitions in potential and free energy space for furanoses and 2′-deoxynucleosides by Gabb (1993)
10.1038/333824a0 / Nature / DNA sequence determinants of CAP-induced bending and protein binding affinity by Gartenberg (1988)
10.1006/jmbi.1994.0120 / J. Mol. Biol. / B-DNA twisting correlates with base-pair morphology by Gorin (1995)
10.1006/jmbi.1993.1217 / J. Mol. Biol. / Sequence-dependent DNA structure by Hunter (1993)
10.1021/ja00170a016 / J. Am. Chem. Soc. / The nature of π—π interactions by Hunter (1990)
10.1039/ft9959102009 / J. Chem. Soc. Farad. Trans. / Influence of fluorine on aromatic interactions by Hunter (1995)
10.1038/326886a0 / Nature / Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro by Koudelka (1987)
10.1002/jcc.540110405 / J. Comput. Chem. / MacroModel — an integrated software system for modeling organic and bioorganic molecules using molecular mechanics by Mohamadi (1990)
{'key': '10.1006/jmbi.1996.0755_BIB16', 'series-title': 'Theoretical Biochemistry and Molecular Biophysics', 'first-page': '271', 'article-title': 'On the use of empirical potentials in studies of base-stacking in DNA', 'author': 'Sponer', 'year': '1990'} / Theoretical Biochemistry and Molecular Biophysics / On the use of empirical potentials in studies of base-stacking in DNA by Sponer (1990)
10.1080/07391102.1993.10508726 / J. Biomol. Struct. Dynam. / Theoretical analysis of the base stacking in DNA — choice of the force-field and a comparison with the oligonucleotide crystal-structures by Sponer (1993)
10.1063/1.463832 / J. Chem. Phys. / Determination of solvent free energy using molecular dynamics with solute cartesian mapping by Sun (1992)
10.1021/ja00375a046 / J. Am. Chem. Soc. / Molecular structures of nucleosides and nucleotides. 2. Orthogonal coordinates for standard nucleic acid base residues by Taylor (1982)
{'key': '10.1006/jmbi.1996.0755_BIB20', 'series-title': 'Bending of DNA in nucleoprotein complexes DNA Topology and Its Biological Effects', 'first-page': '57', 'author': 'Travers', 'year': '1990'} / Bending of DNA in nucleoprotein complexes DNA Topology and Its Biological Effects by Travers (1990)
10.1016/S0021-9258(17)35704-6 / J. Biol. Chem. / Base sequence, local helix structure and macroscopic curvature of A -DNA and B -DNA by Tung (1986)
{'key': '10.1006/jmbi.1996.0755_BIB22', 'first-page': '110', 'article-title': 'SYBYL, the integrated molecular modeling system', 'volume': '3', 'author': 'Vanopdenbosch', 'year': '1985', 'journal-title': 'J. Mol. Graph'} / J. Mol. Graph / SYBYL, the integrated molecular modeling system by Vanopdenbosch (1985)
10.1007/BF00124013 / J. Comput.-Aided Mol. Design, / Extended electron distributions applied to the molecular mechanics of some inter-molecular interactions by Vinter (1994)
{'key': '10.1006/jmbi.1996.0755_BIB24', 'first-page': '71', 'article-title': 'The molecular basis of biological order', 'volume': '24', 'author': 'Williams', 'year': '1991', 'journal-title': 'Aldrichim. Acta'} / Aldrichim. Acta / The molecular basis of biological order by Williams (1991)
10.1016/0022-2836(91)90620-L / J. Mol. Biol. / Analysis of local helix geometry in 3 B -DNA decamers and 8 dodecamers by Yanagi (1991)
10.1016/S0006-3495(95)80427-3 / Biophys. J. / Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA—protein complexes by Young (1995)
{'key': '10.1006/jmbi.1996.0755_BIB27', 'first-page': '495', 'article-title': 'Local mobility in the DNA double helix', 'volume': '17', 'author': 'Zhurkin', 'year': '1983', 'journal-title': 'J. Mol. Biol.'} / J. Mol. Biol. / Local mobility in the DNA double helix by Zhurkin (1983)

Dates

Type	When
Created	22 years, 10 months ago (Oct. 7, 2002, 12:23 p.m.)
Deposited	2 years, 4 months ago (April 4, 2023, 10:16 a.m.)
Indexed	2 months, 3 weeks ago (June 11, 2025, 4:06 a.m.)
Issued	28 years, 8 months ago (Jan. 1, 1997)
Published	28 years, 8 months ago (Jan. 1, 1997)
Published Print	28 years, 8 months ago (Jan. 1, 1997)

Funders 0

None

BibTeX

@article{Hunter_1997, title={DNA base-stacking interactions: a comparison of theoretical calculations with oligonucleotide X-ray crystal structures}, volume={265}, ISSN={0022-2836}, url={http://dx.doi.org/10.1006/jmbi.1996.0755}, DOI={10.1006/jmbi.1996.0755}, number={5}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Hunter, Christopher A. and Lu, Xiang-Jun}, year={1997}, month=jan, pages={603–619} }

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