DIRECT ESTIMATION OF BASE-PAIR EXCHANGE KINETICS IN OLIGO-DNA BY A COMBINATION OF NOESY AND ROESY EXPERIMENTS

A new method for the determination of the kinetics of exchange of the imino protons of DNA duplex is reported using a combination NOESY and ROESY experiments at short mixing times (less-than-or-equal-to 20 ms). These results have been compared with the commonly used longitudinal relaxation approach through the T1 measurement. To calculate k(ex) and tau(ex) by ROESY-NOESY experiment, the volume of the cross-peaks betw een imino protons and water in the NOESY and ROESY spectra have been m easured separately from the magnetization term. This work shows that t he present approach for the measurement of the kinetics of slow exchan ging imino protons of DNA duplex is comparable to the saturation recov ery experiment in which the exchange rate can be accelerated by the ad dition of a base catalyst. The present ROESY-NOESY approach has been f ound to be particularly useful and reasonably accurate for the measure ment of exchange kinetics of both the fast- and slow-exchanging imino protons in DNA duplex both under non-physiological and physiological c ondition where the saturation recovery method can not be used.