Abstract:
:A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Hückel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Sambriski EJ,Schwartz DC,de Pablo JJdoi
10.1016/j.bpj.2008.09.061subject
Has Abstractpub_date
2009-03-04 00:00:00pages
1675-90issue
5eissn
0006-3495issn
1542-0086pii
S0006-3495(08)04006-Xjournal_volume
96pub_type
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