Professor Department of Biochemistry, University of Kentucky (7/95-present) Joint appointment Graduate Center for Toxicology, University of Kentucky (7/96-present) Joint appointment Department of Chemistry, University of Kentucky (9/97-present) Director Biological NMR Facility, University of Kentucky (7/95-present)

NMR Evidence for Mechanical Coupling of Phosphate BI-BII Transitions With Deoxyribose Conformational Exchange in DNA

The conformational exchange of the phosphate and deoxyribose groups of the DNA oligomers d(GCGTACGC)2 and d(CGCTAGCG)2 have been investigated using a combination of homonuclear and heteronuclear NMR techniques. Two-state exchange between phosphate BI and BII conformations and deoxyribose N and S conformations was expressed as percent population of the major conformer, %BI or %S. Sequence context dependent variation in %BI and %S were observed. The positions of the phosphate and deoxyribose equilibria provide a quantitative measure of the ps to ns timescale dynamic exchange processes in the DNA backbone. Linear correlations between %BI, %S, and previously calculated model free 13C order parameters (S2) were observed. The %BI of the phosphates were found to be correlated to the S2 of the flanking C3' and C4' atoms. The %BI was also found to be correlated with the %S and C1' S2 of the deoxyribose ring 5' of the phosphates. The %BI of opposing phosphates is correlated, while the %BI of sequential phosphates is anti-correlated. These correlations suggest that conformational exchange processes in DNA are coupled to each other and are modulated by DNA base sequence, which may have important implications for DNA-protein interactions.