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Journal of Physical Chemistry B, Vol.103, No.45, 10065-10074, 1999
Optimization of the hydrodynamic bead model for the analysis of DNA conformations in solution
The construction of detailed bead models with atomic resolution has been proposed to identify DNA and RNA conformations by hydrodynamic methods in solution. Comparison of model predictions with experimental values for the translational and rotational diffusion coefficients of a homologous series of double-helical B-DNA oligonucleotides has demonstrated the validity and consistency of this strategy when hydration of the molecules is properly accounted for. Further investigations of "hairpin" and quadruplex; model oligonucleotides reveal the potential of this technique to differentiate between DNA conformations. This combination of model calculations with experimental hydrodynamic methods provides a powerful means to identify DNA or RNA conformations in solution, follow conformational changes under a wide variety of solvent conditions, or characterize intermolecular associations with other components of (bio)molecular importance.