PROTEIN-DNA INTERACTIONS

Project: Research project

Description

The major goals of the proposed research are (1) a better understanding of
the relationship between base sequence and DNA structure and (2)
elucidation of the means by which specific DNA-binding proteins induce
alterations in DNA structure. Alteration in helix structure, as a
consequence of specific protein-DNA interactions, are generally believed to
play a major, albeit undefined, role in a wide variety of processes,
including DNA processing, the regulation of transcription, and DNA
packaging. A knowledge of the molecular mechanisms of such processes is of
fundamental importance to our general understanding of gene expression. In studying the sequence-dependence of helix structure, advantage will be
taken of the observation that certain sequences give rise to curvature of
the helix axis. A number of models have been proposed to explain the
observed curvature; however, these models have not been directly testable
due to the paucity of quantitative experimental data regarding curvature.
One of the primary aims of this proposal is to establish a quantitative
relationship between helix curvature and base sequence. The technique of
differential decay of birefringence (DDB) will be utilized thoughout the
proposed investigations. The DDB measurements (sensitive to differences in
DNA length as small as one-percent) will be used in conjunction with DNA
ring-closure measurements and oligodeoxynucleotide synthesis to carry out
essentially all of the studies comprising this proposal. Three specific protein-DNA complexes will be used as paradigms for the
investigation of protein-induced structural alterations of the helix axis.
The first protein, EcoRI endonuclease, is an example of a DNA processing
enzyme, and its complex with DNA is the first to have been visualized by
X-ray diffraction methods. The second protein, the catabolite gene
activator protein, is of major importance in the regulation of
transcription in E coli. The third protein, HU of E coli, is involved in
DNA organization and/or packaging. For each of these three systems,
protein-induced curvature has been proposed on the basis of X-ray
diffraction studies, changes in linking number, and/or behavior on gels.
Using DDB and ring-closure measurements, protein-induced alterations in
helix structure will be evaluated for each of the systems, as will the
relationship between curvature, if present, and base sequence. This study
will therefore provide an important link between structures deduced from
diffraction studies and those existing in solution.
StatusFinished
Effective start/end date7/1/856/30/04

Funding

  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health: $264,728.00
  • National Institutes of Health
  • National Institutes of Health: $57,838.00
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health: $191,108.00
  • National Institutes of Health: $256,312.00
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health
  • National Institutes of Health

Fingerprint

Nucleic Acids
DNA
RNA
Proteins
Birefringence
Leucine Zippers
Energy transfer
Conformations
Luminescence
Molecules
DNA Ligases
Histones
TATA Box
Viral RNA
Capsid Proteins
Viruses
Rigidity
Machinery
Geometry
Carrier Proteins

ASJC

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