Department of Chemistry, Yale University, New Haven, CT 06511.
J Mol Biol 244: 135-43 (1994)
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.
Mesh Headings
Unique Identifier: 95055751
Chemical Identifiers (Names)