DNA steric accessibility for water molecules and ions in the case of B–D transition

Beglov, D. B.; Lipanov, A. A.; Chuprina, V. P.

doi:10.7124/bc.0000D6

Biopolym. Cell. 1989; 5(4):66-70.

http://dx.doi.org/10.7124/bc.0000D6

Structure and Function of Biopolymers

DNA steric accessibility for water molecules and ions in the case of B–D transition

1Beglov D. B., 1Lipanov A. A., 2Chuprina V. P.

Institute of Molecular Genetics, Academy of Sciences of the USSR
Moscow, USSR
Research Computer Center, Academy of Sciences of USSR
Pushchino, Moscow Region, USSR

Abstract

Steric accessibility of DNA atoms in the B and D forms for water molecules has been calculated by the Lee and Richards method. It is shown that a decrease in the D-form nucleotide accessibility, reflecting more economic hydration of the D conformation as against the DNA B conformation is mainly induced by the narrowing of the double helix minor groove. D-form accessibility for sodium ions has been estimated as well. B-D transition mechanism in the AT-rich DNAs is discussed with allowance for the results of calculations.

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