Internal correlations in minor groove profiles of experimental and computed B-DNA conformations

It has been noticed that converged conformations of B-DNA oligomers obtaine d in MD calculations often have very small atom position rmsd values from t he canonical B-DNA and all helical parameters close to the standard values, but their minor grooves tend to be somewhat narrower. This apparent bias d isappears, however, when C5' rather than phosphorus atoms are used for meas uring the groove width. At the origin of this effect is the specific orient ation of phosphate groups in the canonical B-DNA model which maximizes thei r separation across the minor groove. When measured by C5' traces, minor gr oove profiles of experimental structures available in the Nucleic Acids Dat abase show much less tendency to narrow below the canonical width. Correlat ion analysis re reveals a high degree of correspondence in shapes of minor grooves of calculated and experimental single-crystal structures of B-DNA o ligomers. (C) 1999 Academic Press.