Sequence elements responsible for DNA curvature

Abstract

Intrinsic DNA bending or curvature is a phenomenon that has been shown to play an important role in a variety of DNA transactions. Large curvature occurs when short homopolymeric (dA.dT)4-6 runs (A-tracts) are repeated in phase with the helical screw. We have used electrophoretic mobility modulation to examine how bending depends on the nature of the 5 bp DNA sequence between the A tracts in molecules of the form (A5-6N5)n. We show that A-tract-induced DNA curvature can indeed be affected by other sequence elements, although by only about +/- 10%. The small observed curvature modulation implies that the overall helix axis deflection contributed by 5-bp B-DNA segments between A-tracts varies little from one sequence to another. This result validates, to first order, the assumption that DNA curvature results from inserting A-tracts at integral turn phasing into generic B-DNA. Therefore, if, as has been proposed, A-tracts have zero roll between the base-pairs and all curvature results from positive roll in the B-DNA segments, then this must be a general property of approximately 5 bp B-DNA sequences, not just special cases. This interpretation would require that the canonical structure of B-DNA be revised to include systematic roll between the base-pairs of about 6 degrees. Alternatively, the data are also consistent with zero average roll in the B-DNA sequences, and wedge angles dominated by negative roll in the A-tracts, or with an appropriate mixture of the two models. It is not possible to resolve this ambiguity using comparative electrophoresis or existing structural data. We show that published wedge angle parameters successfully predict the measured direction and, with appropriate rescaling, the magnitude of curvature due to a non-A-tract sequence containing the protein-free lac operator CAP protein binding site.