DNA BENDING - THE PREVALENCE OF KINKINESS AND THE VIRTUES OF NORMALITY

DNA bending in 86 complexes with sequence-specific proteins has been e xamined using normal vector plots, matrices of normal vector angles be tween all base pairs in the helix, and one-digit roll/slide/twist tabl es. FREEHELIX, a new program especially designed to analyze severely b ent and kinked duplexes, generates the foregoing quantities plus local roll, tilt, twist, slide, shift and rise parameters that are complete ly free of any assumptions about an overall helix axis. In nearly ever y case, bending results from positive roll at pyrimidine-purine base p air steps: C-A (= T-G), T-A, or less frequently C-G, in a direction th at compresses the major groove. Normal vector plots reveal three well- defined types of bending among the 86 examples: (i) localized kinks pr oduced by positive roll at one or two discrete base pairs steps, (ii) three-dimensional writhe resulting from positive roll at a series of a djacent base pairs steps, or (iii) continuous curvature produced by al ternations of positive and negative roll every 5 bp, with side-to-side zig-zag roll at intermediate position. In no case is tilt a significa nt component of the bending process. In sequences with two localized k inks, such as CAP and IHF, the dihedral angle formed by the three heli x segments is a linear function of the number of base pair steps betwe en kinks: dihedral angle = 36 degrees x kink separation. Twenty-eight of the 86 examples can be described as major bends, and significant el ements in the recognition of a given base sequence by protein. But eve n the minor bends play a role in fine-tuning protein/DNA interactions. Sequence dependent helix deformability is an important component of p rotein/DNA recognition, alongside the more generally recognized patter ns of hydrogen bonding. The combination of FREEHELIX, normal vector pl ots, full vector angle matrices, and one-digit roll/ slide/twist table s affords a rapid and convenient method for assessing bending in DNA.