Mode-coupling smoluchowski dynamics of a double-stranded DNA oligomer

摘要: The local dynamics of a double-stranded DNA d(TpCpGpCpG)(2) is obtained to second order in the mode-coupling expansion Smoluchowski diffusion theory. time correlation functions bond variables are derived and (13)C-nmr spin-lattice relaxation times T(1) different (13)C along chains calculated compared experimental data from literature at three frequencies. considered as fluctuating three-dimensional structure undergoing rotational diffusion. fluctuations evaluated using molecular simulations, with ensemble averages approximated by trajectory length 1 ns. Any technique for sampling configurational space can be used an alternative. For (3D) first-order vector modes lower rates, higher basis sets second-rank tensor built give required mode coupling dynamics. Second- even theories found close agreement results, especially high frequency, where differences base pairs, sugar, backbone well described. These atomistic calculations general application studying, on basis, 3D structures such double-helix fragments, proteins, protein-DNA complexes. Copyright 1999 John Wiley & Sons, Inc.