An NMR study of A-T base pair opening rates in oligonucleotides. Influence of sequence and of adenine methytation

We report relaxation time measurements by semi-selective and totally selective NMR techniques on the thymidine imino protons of d(GGATATCC) and d(GGmsATATCC). For these oligonucleotides helix fraying, rather than single base pair opening, is the major exchange mechanism even 25° C below the Tm. We have therefore applied a new saturation transfer technique to measure exchange rates at temperatures where fraying has a very small or negligible contribution. Measurements of exchange rates as a function of temperature give significantly different activation energies for base pairs 3 and 4 in d(GGATATCC). Adenine methylation results in a slowing down of the opening rate for the m2A-T base pair but surprisingly has an even greater effect upon the adjacent non-methylated A-T base pair.