Calculation of hydrodynamic properties of small nucleic acids from their atomic structure.

ABSTRACT: Hydrodynamic properties (translational diffusion, sedimentation coefficients and correlation times) of short B-DNA oligonucleotides are calculated from the atomic-level structure using a bead modeling procedure in which each non-hydrogen atom is represented by a bead. Using available experimental data of hydrodynamic properties for several oligonucleotides, the best fit for the hydrodynamic radius of the atoms is found to be approximately 2.8 A. Using this value, the predictions for the properties corresponding to translational motion and end-over-end rotation are accurate to within a few percent error. Analysis of NMR correlation times requires accounting for the internal flexibility of the double helix, and allows an estimation of approximately 0.85 for the Lipari-Szabo generalized order

SUBMITTER: Fernandes MX 

PROVIDER: S-EPMC113193 | biostudies-literature | 2002 Apr

REPOSITORIES: biostudies-literature