This paper reports a theoretical study of the free energy contributions to nucleic acid base stacking in aqueous solution. Electrostatic interactions are treated by using the finite difference Poisson-Boltzmann method and nonpolar effects are treated with explicit calculation of van der Waals interactions and/or free energy-surface area relationships. Although for some pairs of bases there is a favorable Coulombic interaction in the stacked conformation, generally the net effect of electrostatic interactions is to oppose stacking. This result is caused by the loss of favorable base-solvent electrostatic interactions, that accompany the partial removal of polar atoms from water in the stacked conformation. Nonpolar interactions, involving the hydrophobic effect and enhancement of van der Waals interactions caused by close-packing, drive stacking. The calculations qualitatively reproduce the experimental dependence of stacking free energy on purine-pyrimidine composition.
机构:
UNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
BASH, PA
;
SINGH, UC
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UNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
SINGH, UC
;
LANGRIDGE, R
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UNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
LANGRIDGE, R
;
KOLLMAN, PA
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UNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
机构:
UNIV CALIF SAN FRANCISCO, SCH PHARM, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, SCH PHARM, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
CIEPLAK, P
;
KOLLMAN, PA
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h-index: 0
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UNIV CALIF SAN FRANCISCO, SCH PHARM, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, SCH PHARM, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
机构:
UNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
BASH, PA
;
SINGH, UC
论文数: 0引用数: 0
h-index: 0
机构:
UNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
SINGH, UC
;
LANGRIDGE, R
论文数: 0引用数: 0
h-index: 0
机构:
UNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
LANGRIDGE, R
;
KOLLMAN, PA
论文数: 0引用数: 0
h-index: 0
机构:
UNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
机构:
UNIV CALIF SAN FRANCISCO, SCH PHARM, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, SCH PHARM, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA
CIEPLAK, P
;
KOLLMAN, PA
论文数: 0引用数: 0
h-index: 0
机构:
UNIV CALIF SAN FRANCISCO, SCH PHARM, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USAUNIV CALIF SAN FRANCISCO, SCH PHARM, DEPT PHARMACEUT CHEM, SAN FRANCISCO, CA 94143 USA