NMR evidence for mechanical coupling of phosphate B_I-B_II 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 B_I and B_II conformations and deoxyribose N and S conformations was expressed as percent population of the major conformer, %B_I or %S. Sequence context-dependent variations in %B_I 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 %B_I, %S, and previously calculated model free ¹³C order parameters (S²) were observed. The %B_I of the phosphates were found to be correlated to the S² of the flanking C3′ and C4′ atoms. The %B_I was also found to be correlated with the %S and C1′ S² of the deoxyribose ring 5′ of the phosphates. The %B_I of opposing phosphates is correlated, while the %B_I 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.