HELIX BENDING AS A FACTOR IN PROTEIN DNA RECOGNITION/

Normal vectors perpendicular to individual base pairs are a powerful t ool for studying the bending behavior of B-DNA, both in the form of no rmal vector plots and in matrices that list angles between vectors for all possible base pair combinations. A new analysis program, FREEHELI X, has been written for this purpose, and applied to 86 examples of se quence-specific protein/DNA complexes whose coordinates are on deposit in the Nucleic Acid Data Base. Bends in this sample of 86 structures almost invariably follow Siam roll angles between adjacent base pairs; tilt makes no net contribution. Roll ill a direction compressing the broad major groove is much more common than that which compresses the minor groove. Three distinct types of B-DNA bending are observed, each with a different molecular origin. (1) Localized I;inking is produced by large roll at single steps or at two steps separated by one turn O f helix. (2) Smooth, planar curvature is produced by positive and nega tive loll angles spaced a half-turn apart, with random side-to-side zi gzag loll at intermediate points, rather than a tilt contribution that might have been expected theoretically. (3) Three-dimensional writhe results from significant roll angles at a continuous series of steps. Writhe need not change the overall direction of helix axis, if it is c ontinued indefinitely or for an integral number of helical tui ns. A-D NA itself can be formally considered as possessing uniform, continuous writhe that yields no net helix bending. Smooth curvature is the most intricate deformation of the three, and is least common. Writhe is th e simplest deformation and is most common; indeed a low level of conti nuous writhe is the normal condition of an otherwise unbent B-DNA heli x of general sequence. With one exception, every example of major kink ing in this sample of 86 structures involves a pyrimidine-purine step: C-A/T-G, T-A, or C-G. Purine-purine steps, especially A-A, show the l east tendency toward roll deformations. (C) John Wiley & Sons, Inc. Bi opoly 44, 361-403, 1997.