Sequence-dependent B-DNA conformation in crystals and in protein complexes

Nearly twenty years of single crystal x-ray analysis of DNA oligomers have led to a set of reasonably firm sequence/structure principles, involving sugar puckering, patterns of hydration, propeller twisting and groove width, mechanisms of local bending, and most especially the behavior of the local helix variables Roll, Slide and Twist. Local base sequence does not determine one fixed DNA structure, but places limits on the relative deformability of various regions of the helix. Differential deformability, most particularly stiffness vs. bendability, plays a significant role in the molecular recognition process. Y-R steps in protein/DNA complexes are frequently the loci of bends produced by large Roll angles, whereas A-A (especially in A-tracts) and other R-R steps tend not to bend significantly. Indeed, short A-tracts in protein-bound DNA appear to have been evolutionarily selected when helix bending is not desired. Observed sequence-dependent conformations are very similar in both protein/DNA complexes and in crystalline DNA, reflecting the fact that local DNA environments in these two situations are more like one another than either is to DNA in dilute aqueous solution.