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Nucleic Acids Research, 1981, Vol. 9, No. 15 3765-3777
© 1981

CHEMISTRY

The molecular electrostatic potential, steric accessibility and hydration of Dickerson's B-DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG)

Richard Lavery and Bernard Pullman

Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique, associé au C.N.R.S. 13, rue Pierre et Marie Curie, 75005 Paris, France

Received June 15, 1981. The paper presents the results of computation of the electrostatic potential and steric accessibility of the B-DNA self-complementary dodecamer CGCGAATTCGCG following the geometry of the recent single crystal structure of Dickerson et al. This structure shows significant variations from classical B-DNA ; their influences on the calculated properties are discussed. The resultsare related to general features of hydration of the crystal. A particularly significant general finding concernsthe greater negative potential in the center of the oligonucleotide helix than at its extremities. This will be a general feature of such short helices, independant of their base sequence. It may have important implications for the reactivity of DNA oligomers.


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