title: Is DNA a Good Model Polymer?
abstract: The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48,500 base pairs) does not exhibit "ideal" scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior.
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Tree
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota.
authors.forename: Abhiram
authors.initials: A
authors.lastname: Muralidhar
authors.affiliation: Department of Chemical Engineering, Massachusetts Institute of Technology.
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Doyle
authors.affiliation: Department of Chemical Engineering and Materials Science, University of Minnesota.
authors.forename: Kevin D
authors.initials: KD
authors.lastname: Dorfman