Abstract:
:A new Fourier series representation of supercoiled DNA is employed in Langevin dynamics simulations to study large-scale configurational motions of intermediate-length chains. The polymer is modeled as an ideal elastic rod subject to long-range van der Waals' interactions. The van der Waals' term prevents the self-contact of distant chain segments and also mimics attractive forces thought to stabilize the association of closely spaced charged rods. The finite Fourier series-derived polymer formulation is an alternative to the piecewise B-spline curves used in past work to describe the motion of smoothly deformed supercoiled DNA in terms of a limited number of independent variables. This study focuses on two large-scale configurational events: the interconversion between circular and figure-8 forms at a relatively low level of supercoiling, and the transformation between branched and interwound structures at a higher superhelical density.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Liu G,Schlick T,Olson AJ,Olson WKdoi
10.1016/S0006-3495(97)78205-5subject
Has Abstractpub_date
1997-10-01 00:00:00pages
1742-62issue
4eissn
0006-3495issn
1542-0086pii
S0006-3495(97)78205-5journal_volume
73pub_type
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