SEQUENCE ELEMENTS RESPONSIBLE FOR DNA CURVATURE

Intrinsic DNA bending or curvature is a phenomenon that has been shown to play an important role in a variety of DNA transactions. Large cur vature occurs when short homopolymeric (dA.dT)(4-6) runs (A-tracts) ar e repeated in phase with the helical screw. We have used electrophoret ic 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 ( A(5-6)N(5))(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 hel ix 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 a nd all curvature results from positive roll in the B-DNA segments, the n this must be a general property of similar to 5 bp B-DNA sequences, not just special cases. This interpretation would require that the can onical structure of B-DNA be revised to include systematic roll betwee n the base-pairs of about 6 degrees. Alternatively, the data are also consistent with zero average roll in the B-DNA sequences, and wedge an gles dominated by negative roll in the A-tracts, or with an appropriat e mixture of the two models. It is not possible to resolve this ambigu ity using comparative electrophoresis or existing structural data. We show that published wedge angle parameters successfully predict the me asured direction and, with appropriate rescaling, the magnitude of cur vature due to a non-A-tract sequence containing the protein-free lac o perator CAP protein binding site.