A proton NMR spin-lattice relaxation study of the imino proton exchange kinetics in calf-thymus DNA.

Abstract

AbstractThe results of semiselective 1H‐nmr inversion recovery experiments on sonicated calf thymus DNA fragments are reported. The measurements were conducted in aqueous solutions containing 85% D2O, in order to reduce the dipolar contribution to the observed relaxation rates. In solutions containing 0.2M NaCl, 0.4 mM EDTA, and 10 mM cacodylate at pH = 7.0, the exchange rates of the imino protons in A‐T base pairs confirm values published earlier in the literature, extrapolating to 0.25 s−1 at 25°C. Corresponding values for the G‐C base pairs are published for the first time, and are about sixfold slower. The addition of up to 0.1M Tris buffer (pH = 7.3 at 25°C), caused a striking increase in the measured exchange rates for both the A‐T and G‐C imino protons, resembling the effect recently observed for poly(rA)‐poly(rU) and poly(rI)‐poly(rC), and suggesting that the exchange rates measured for nucleic acid duplexes in low buffer concentrations at neutral pH do not reflect base‐pair opening rates as assumed in the past. Lower limits to the base‐pair opening rates could be estimated from extrapolation of the experimental data to infinite buffer concentration, and are 1 × 103 s−1 for the A‐T, and 50 s−1 for the G‐C, base paris at 62°C.