Title
Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility
Date Issued
03 July 1998
Access level
metadata only access
Resource Type
journal article
Author(s)
University of Oregon
Publisher(s)
Academic Press
Abstract
The worm-like chain model has often been employed to describe the average conformation of long, intrinsically straight polymer molecules, including DNA. The present study extends the applicability of the wormlike chain model to polymers containing bends or sections of different flexibility. Several cases have been explicitly considered: (i) polymers with a single bend; (ii) polymers with multiple coplanar bends; (iii) polymers with two non-coplanar bends; and (iv) polymers comprised of sections with different persistence lengths. Expressions describing the average conformation of such polymers in terms of the mean-square end-to-end distance have been derived for each case. For cases (i) and (iv), expressions for the projection of the end-to-end vector onto the initial orientation of the chain are presented. The expressions derived here have been used to investigate DNA molecules with sequence-induced bending (A-tracts). Mean-square end-to-end distance values determined from a large number of A-tract containing DNA molecules visualized by scanning force microscopy resulted in an average bend angle of 13.5°per A-tract. A similar study was performed to characterize the flexibility of double-strandedDNA molecules containing a single-stranded region. Analysis of their mean-square end-to-end distance yielded a persistence length of 1.3 nm for single-stranded DNA.
Start page
41
End page
59
Volume
280
Issue
1
Language
English
OCDE Knowledge area
Bioquímica, Biología molecular
Subjects
Scopus EID
2-s2.0-0032479186
PubMed ID
Source
Journal of Molecular Biology
ISSN of the container
00222836
Sponsor(s)
We thank Professors Maxim Frank-Kamenetskii, Paul Hagerman, David Keller, Wilma Olson, Steve Smith and Victor Zhurkin for critical reading and comments on the manuscript. This work was supported by NSF grants MBC 9118482 and BIR 9318945 and NIH grant GM-32543. C.R. was supported by a Human Frontier Science Program (HFSP) long-term fellowship. C.W. was supported by NIH Training Grant GM 07759.
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