Is DNA a Good Model Polymer?
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Doyle_Is DNA.pdf
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Author(s)
Tree, Douglas R.
Muralidhar, Abhiram
Doyle, Patrick S.
Dorfman, Kevin D.
Date Issued
October 2013
Journal
Macromolecules
Publisher
American Chemical Society (ACS)
Citation
Tree, Douglas R., Abhiram Muralidhar, Patrick S. Doyle, and Kevin D. Dorfman. “Is DNA a Good Model Polymer?” Macromolecules 46, no. 20 (October 22, 2013): 8369–8382.
Version
Author's final manuscript
Abstract
The details surrounding the crossover 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 nondraining 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.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
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DOI of Published Version
https://doi.org/10.1021/ma401507f
