Position-dependent internal motions and effective correlation times for magnetization transfer in DNA

Abstract

An effective correlation time that accounts for position dependence of the combined local angular motions and collective twisting and bending deformations, as well as for anisotropic uniform rotation, is defined in terms of the magnetization-transfer rate and expressed in terms of molecular parameters. Application to measured magnetization-transfer rates from H6 to H5 of cytosine in cases where all other relevant data, including the uniform rotational diffusion coefficients, are known, suggests that the amplitude of local angular motion, as well as that due to collective deformations, is significantly greater for a penultimate base pair than for base pairs near the center of the molecule, and that such amplitudes might be approximately transferable from one molecule to another. Protocols are suggested for using estimated ratios of effective correlation times in the initial calibrations of internuclear distances and in the subsequent structure-refinement process.