Comparing the effects of Different Osmolytes in the B-To-Z DNA Transition

Abstract

In this study the effect of sequence context on the binding affinity and conformation of DNA dodecamers are explored. The Cre binding site (ACGT) was studied with a number of different flanking sequences. 31P-NMR was used to determine the conformational state (BI/BII ratio) of each step in the phosphate backbone. Importantly, the conformation of the binding site, the center tetrad which was not changed, varied significantly based on the sequence context. Fluorescence titration with the DNA intercalator 7-Aminoactinomycin D was performed to provide biological context to our conformation results. We found that the backbone conformation alone cannot explain the binding affinities in the dodecamers studied. Thus, we turned our attention to base pair dynamics. Preliminary results show that differences in binding affinities in sequences with similar backbone conformations can be explained by differential base pair opening rates.