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

It has been noticed that converged conformations of B-DNA oligomers obtained in MD calculations often have very small atom position rmsd values from the canonical B-DNA and all helical parameters close to the standard values, but their minor grooves tend to be somewhat narrower. This apparent bias disappears, however, when C5' rather than phosphorus atoms are used for measuring the groove width. At the origin of this effect is the specific orientation of phosphate groups in the canonical B-DNA model which maximizes their separation across the minor groove. When measured by C5' traces, minor groove profiles of experimental structures available in the Nucleic Acids Database show much less tendency to narrow below the canonical width. Correlation analysis reveals a high degree of correspondence in shapes of minor grooves of calculated and experimental single-crystal structures of B-DNA oligomers.