The molecular electrostatic potential, steric accessibility and hydration of Dickerson's B-DNA dodecamer...

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 results are related to general features of hydration of the crystal. A particularly significant general finding concerns the greater negative potential in the center of the oligonucleotide helix than at its extremities. This will be a general feature of such short helices, independent of their base sequence. It may have important implications for the reactivity of DNA oligomers.