Modeling single chain elasticity of single-stranded DNA: A comparison of three models

The dominant models of polymers, i.e., the freely jointed chain (FJC) model, the wormlike chain (WLC) model and the freely rotating chain (FRC) model are modified by integrating the inherent single-molecule elasticity obtained from quantum mechanics (QM) ab-initio calculations. The QM modified models have been utilized to generate fitting curves for single-stranded DNA obtained in organic solvent. The analyses on the deviation between the fitting curve and the experimental force curve demonstrate that the QM-FRC and QM-FJC model are suitable for ssDNA, but not the QM-WLC model. We also find that one repeating unit of ssDNA is corresponding to a Kuhn segment in QM-FJC model or two rotating units in QM-FRC. Having close correlation to the inherent elasticity and real molecular structure of the polymer, QM-FJC and QM-FRC are emerging as structure relevant models. (C) 2008 Elsevier Ltd. All rights reserved.