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 usin g 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 obs erved. The positions of the phosphate and deoxyribose equilibria provide a quantitative measure of the ps to ns timescale dynamic exchange processes i n the DNA backbone. Linear correlations between %B-I, %S, and previously ca lculated model free C-13 order parameters (S-2) were observed. The %B-I of the phosphates were found to be correlated to the S' of the flanking C3' an d C4' atoms. The %B-I was also found to be correlated with the %S and C1' S -2 of the deoxyribose ring 5' of the phosphates. The %B-I of opposing phosp hates is correlated, while the %B-I of sequential phosphates is anti-correl ated. 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. (C) 2001 Aca demic Press.