Normal-mode analysis of circular DNA at the base-pair level, 1; Comparison of computed motions with the predicted behavior of an ideal elastic rod

Matsumoto, Atsushi; Tobias, I.*; Olson, W. K.*

We have extended a newly developed approach to study the low frequency normal modes of mesoscopic fragments of linear DNA in order to investigate the dynamics of closed circular molecules of comparable size, i.e., a few hundred base pairs. We have added restraint energy terms and a global minimization step to treat the more complicated, spatially constrained duplex in terms of the intrinsic conformation and flexibility of the constituent base-pair "step" parameters.

Language	:	English
Journal	:	Journal of Chemical Theory and Computation
Volume	:	1
Number	:	1
Pages	:	p.117 - 129
Publication Year/Month	:	2005/01
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Paper URL	:	https://doi.org/10.1021/ct049950r
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Keywords	:	Circular DNA; Ideal Elastic Rod; Normal-mode Analysis
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Registration No. : A20050354
JAEA Abstracts No. : 330927
Paper Submission No. : 12

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