Cations Mediate B-DNA Conformational Heterogeneity

Abstract

We demonstrate that DNA conformation is sensitive to cationic environment. We describe a high resolution (1.2 Å) potassium form of CGCGAATTCGCG, determined from crystals grown in the presence of spermine and magnesium, along with potassium. The structure was refined with anisotropic displacement-factors by SHELX-97 to an R-factor of 13.9%. A comparison of this structure with others, reveals that the conformation of CGCGAATTCGCG varies in direct response to cation type and position. The DNA conformation in the presence of excess magnesium differs from the conformation in the presence of excess spermine. Divalent cations near the minor groove sequester into the lip, which is the region between opposing phosphate groups. Minor groove width is sensitive to, and can be predicted by, cation positions. It appears that minor groove narrowing is facilitated by interactions of cations with opposing phosphate groups.