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

✍ Scribed by Simone Fausti; Giovanni La Penna; Carla Cuniberti; Angelo Perico

• Publisher: Wiley (John Wiley & Sons)
• Year: 1999
• Tongue: English
• Weight: 258 KB
• Volume: 50
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/(sici)1097-0282(199911)50:6<613::aid-bip6>3.0.co;2-g

✦ Synopsis

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