Is DNA a Good Model Polymer?

• Published in: Macromolecules Vol. 46; no. 20; pp. 8369 - 8382
• Main Authors: Tree, Douglas R, Muralidhar, Abhiram, Doyle, Patrick S, Dorfman, Kevin D
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 22.10.2013
• Subjects: algorithms; Analytical, structural and metabolic biochemistry; Applied sciences; Biological and medical sciences; diffusivity; DNA; Dna, deoxyribonucleoproteins; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; Gibbs free energy; ionic strength; Miscellaneous; molecular weight; Natural polymers; Nucleic acids; Physicochemistry of polymers; polymers; Molecular rigidity; Monte Carlo method; Double stranded DNA; Hydrodynamic radius; Computer simulation; Theoretical study; Persistence length; Single stranded DNA; Aqueous solution; Diffusion coefficient; Form factor; Conformation
• ISSN: 0024-9297; 1520-5835; 1520-5835
• DOI: 10.1021/ma401507f

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.