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Distribution Functions, Loop Formation Probabilities and Force-Extension Relations in a Model for Short Double-Stranded DNA Molecules | | P. Ranjith
; P. B. Sunil Kumar
; Gautam I. Menon
; | | Date: |
29 Nov 2004 | | Journal: | Phys. Rev. Lett. 94, 138102 (2005) | | Subject: | Soft Condensed Matter; Statistical Mechanics; Biomolecules | cond-mat.soft cond-mat.stat-mech q-bio.BM | | Affiliation: | IITM), P. B. Sunil Kumar (IITM), Gautam I. Menon (IMSc | | Abstract: | We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the appearance of ``bubbles’’, localized regions of enhanced flexibility associated with the opening of a few base pairs of double-stranded DNA in thermal equilibrium, leads to dramatic changes in $P(R)$ and unusual force-extension curves. An analytic formula for the loop formation probability in the presence of bubbles is proposed. For short {em heterogeneous} chains, we demonstrate a strong dependence of loop formation probabilities on sequence, as seen in recent experiments. | | Source: | arXiv, cond-mat/0411723 | | Other source: | [GID 813817] pmid15904042 | | Services: | Forum | Review | PDF | Favorites | |
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