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.
  1. Institute of Molecular Genetics, Academy of Sciences of the USSR
    Moscow, USSR
  2. 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.
Full text: (PDF, in Russian)

References

[1] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[2] Saenger W, Hunter WN, Kennard O. DNA conformation is determined by economics in the hydration of phosphate groups. Nature. 1986 Nov 27-Dec 3;324(6095):385-8.
[3] Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol. 1971;55(3):379-400.
[4] Arnott S, Chandrasekaran R, Hall IH, Puigjaner LC. Heteronomous DNA. Nucleic Acids Res. 1983;11(12):4141-55.
[5] Arnott S, Chandrasekaran R, Puigjaner LC, Walker JK, Hall IH, Birdsall DL, Ratliff RL. Wrinkled DNA. Nucleic Acids Res. 1983;11(5):1457-74.
[6] Arnott S, Chandrasekaran R, Hukins DW, Smith PJ, Watts L. Structural details of double-helix observed for DNAs containing alternating purine and pyrimidine sequences. J Mol Biol. 1974;88(2):523-33.
[7] Arnott S, Hukins DW. Optimised parameters for A-DNA and B-DNA. Biochem Biophys Res Commun. 1972;47(6):1504-9.
[8] Alden CJ, Kim SH. Solvent-accessible surfaces of nucleic acids. J Mol Biol. 1979;132(3):411-34.
[9] Bartenev VN, Golovamov EuI, Kapitonova KA, Mokulskii MA, Volkova LI, Skuratovskii IYa. Structure of the B DNA cationic shell as revealed by an X-ray diffraction study of CsDNA. Sequence-specific cationic stabilization of B form DNA. J Mol Biol. 1983;169(1):217-34.
[10] Chuprina V. P., Khutorsky V. E., Poltev V. Theoretical refinement of A- and B-conformation models of regular polynucleotides. Stud biophys. 1981; 85(2):81-8.
[11] Suzuki E, Pattabiraman N, Zon G, James TL. Solution structure of [d(A-T)5]2 via complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect spectra and molecular mechanics calculations: evidence for a hydration tunnel. Biochemistry. 1986;25(22):6854-65.
[12] Mahendrasingam A, Forsyth VT, Hussain R, Greenall RJ, Pigram WJ, Fuller W. Time-resolved X-ray diffraction studies of the B in equilibrium D structural transition in the DNA double helix. Science. 1986;233(4760):195-7.
[13] Drew HR, Dickerson RE. Structure of a B-DNA dodecamer. III. Geometry of hydration. J Mol Biol. 1981;151(3):535-56.
[14] Alexeev DG, Lipanov AA, Skuratovskii IYa. Poly(dA).poly(dT) is a B-type double helix with a distinctively narrow minor groove. Nature. 1987 Feb 26-Mar 4;325(6107):821-3.
[15] Chuprina VP. Anomalous structure and properties of poly (dA).poly(dT). Computer simulation of the polynucleotide structure with the spine of hydration in the minor groove. Nucleic Acids Res. 1987;15(1):293-311.
[16] Lipanov AA, Beglov DB, Alexeev DG, Skuratovsky IYa. Buckle of the A-T Pair in the Bh-form of poly(dA):poly(dT). Biopolym Cell. 1989; 5(1):16-22.