Difference FT-IR Studies on the Effects of Buffers on Nucleotide Binding to Reca

Abstract

The Escherichia coli protein RecA catalyzes DNA strand exchange and plays a role DNA repair and genetic recombination. Nucleotide binding influences RecA oligomerization and its affinity for DNA. Previous studies in our lab have shown buffer-specific changes in RecA stability and unfolding transitions. Past circular dichroism (CD), infrared (IR), and fluorescence studies suggest only minimal buffer dependent changes in nucleotide binding and secondary structure that did not explain the large buffer dependent differences in RecA stability and unfolding profiles. These observations led to further investigations of how the four common biological buffers Tris, HEPES, MES, and PO4 alter RecA structure and nucleotide binding. Here we have employed difference infrared spectroscopy utilized in conjunction with caged nucleotides to generate RecA-ADP minus RecA difference infrared spectra in each of the four buffers. These higher resolution studies are aimed at detecting if the buffers alter nucleotide binding to RecA. Preliminary results show that ADP binding results in perturbations in Gln, Glu, Asp, Asn, Tyr, and Lys residues and secondary structural changes. Initial comparisons of difference spectra obtained in the four buffers show some similar changes but also show some differences. These differences between RecA-ADP minus RecA difference spectra will be discussed.