MPD AND DNA BENDING IN CRYSTALS AND IN SOLUTION

Bending of 15 to 24 degrees is observed within crystal structures of B -DNA duplexes, is strongly sequence-dependent, and exhibits no correla tion with the concentration of MPD (2-methyl-2,4-pentanediol) in the c rystallizing solution. Two types of bends are observed: facultative be nds or flexible hinges at junctions between regions of G . C and A . T base-pairs, and a persistent and almost obligatory bend at the center of the sequence R-G-C-Y. Only A-tracts are characteristically straigh t and unbent in every crystal structure examined to date. A detailed e xamination of normal vector plots for individual strands of a double h elix provides an explanation, in terms of the stacking properties of g uanine and adenine bases. The effect of high MPD concentrations, in bo th solution and crystal, is to decrease local bending somewhat without removing it altogether. MPD gel retardation experiments provide no ba sis for choosing among the three models that seek to explain macroscop ic curvature of DNA by means of microscopic bending: junction bending, bent A-tracts, or bent general-sequence DNA. Crystallographic data on the straightness of A-tracts, the bendability of non-A sequences, and the identity of inclination angles in A-tract and non-A-tract B-DNA s upport only the general-sequence bending model. The pre-melting transi tion observed in A-tract DNA probably represents a relaxation of stiff adenine stacks to a flexible conformation more typical of general-seq uence DNA. (C) 1996 Academic Press Limited.