This is a new proposal aimed at obtaining information on the structural, thermodynamic, and dynamic aspects of non-sequence specific modes of protein-nucleic acid recognition by the HMG-box motif. The objective will be to understand the recognition in terms of two limiting mechanisms: recognition of preformed structure (lock and key) vs induction of structure in inherently flexible DNA sequences (induced fit). A multifaceted approach is proposed in order to give the most complete picture: electrophoretic mobility shift assays and radical footprinting for characterizing binding of different DNA sequences, isothermal titration calorimetry for determining thermodynamic parameters, EPR for determining DNA dynamics, and NMR for structure analysis of the proteins and its complexes with DNA. The goal is to characterize the binding of nucleic acids containing one each of ~7 structural and/or dynamical features to a single HMG-box from the Xenopus Laevis Upstream Binding Factor (xUBFBox1).

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM055963-02
Application #
2771087
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Project Start
1997-09-30
Project End
2001-08-31
Budget Start
1998-09-01
Budget End
1999-08-31
Support Year
2
Fiscal Year
1998
Total Cost
Indirect Cost
Name
University of Washington
Department
Biochemistry
Type
Schools of Medicine
DUNS #
135646524
City
Seattle
State
WA
Country
United States
Zip Code
98195