ELECTROSTATIC FORCES IN DNA BENDING BY PROTEINS

Project: Research project

Project Details

Description

DNA is often bent when complexed with proteins. Understanding the forces
responsible for DNA bending in such complexes is of fundamental value in
exploring and predicting the interplay of these macromolecules. An
experimental approach has been devised to test the hypothesis that
proteins with cationic surfaces can induce substantial DNA bending simply
by neutralizing phosphates on one DNA face. Repulsions between phosphates
in the remaining anionic helix are predicted to result in an unbalanced
compression force acting to deform the DNA toward the protein. This
hypothesis is supported by the results of electrophoretic experiments in
which DNA spontaneously bends when one helical face is partially modified
by incorporation of neutral phosphate analogs. Phasing with respect to a
site of intrinsic DNA curvature (A6 tract) permits estimation of the
electrostatic bend angle, and demonstrates that such modified DNAs are
deformed toward the neutralized surface, as predicted&

It is proposed to extend these studies to (i) more fully characterize how
various arrangements of neutralized phosphates cause DNA bending, and (ii)
apply this model to real examples of DNA bending by proteins. Four
specific aims are described in this proposal:

l. Determine how the distribution and sequence of phosphate
neutralizations affect DNA bending;

2. Apply the bending model to specific DNA sequences known to be bent by
proteins;

3. Analyze zwitterionic nucleotides as an alternative to neutral phosphate
analogs,

4. Design and test two sequence-specific DNA bending proteins.

These studies seek to explore one of the general principles that may
explain DNA bending in nucleoprotein complexes.
StatusFinished
Effective start/end date9/1/9512/31/04

ASJC

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)