Proton NMR relaxation studies of the hydrogen-bonded imino protons of poly(dA-dT)

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Abstract
Measurements on the thymine imino proton relaxation rates have been used to study various structural and dynamic properties of 53 +/- 15 base pair long poly(dA-dT). Below 10 degrees C, the relaxation is dominated by dipolar magnetic interactions. At 1 degrees C the relaxation of the transverse magnetization is exponential (R2 = 124 s-1), but the relaxation of longitudinal magnetization is highly nonexponential due to spin-diffusion effects (initial decay rate constant of 28 s-1 and a slower rate of approximately 2.5 s-1 after equilibration of spin polarization). Neither a rigid-rod model nor simple wormlike motions can account for the observed low-temperature relaxation behavior. However, when localized internal motions of the base pairs (three-state jump model) are allowed for, a good fit of the experimental data is obtained by using a correlation time for internal motion of 7 X 10(-10) s and an angular displacement of the bases of +/- 32 degrees relative to the helix axis. The observed R2/R1 ratio for the thymine imino proton yields a value of 1.14 +/- 0.08 A for the imino proton nitrogen distance. Nuclear Overhauser effect (NOE) measurements establish that the base pairing in poly(dA-dT) is Watson-Crick in solution and not Hoogsteen. Exchange of the T-imino protons with H2O dominates the longitudinal relaxation above 28 degrees C (activation energy of 17 +/- 2 kcal and an exchange rate of 5 +/- 2 s-1 at 300 K). Similar values have been reported for the A X T base pairs in DNA restriction fragments and for A X U base pairs in poly(A) X poly(U). These observations can be explained by a model in which exchange of T-imino protons occurs as a result of a single base pair opening, with a rate that is approximately independent of nearest-neighbor sequences and DNA length. Our observations appear to be inconsistent with a soliton model of proton exchange.

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