Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility.

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 worm-like 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 degrees 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.

• Authors: C Rivetti, C Walker, C Bustamante
• Journal: Journal of molecular biology (J Mol Biol) Vol. 280 Issue 1 Pg. 41-59 (Jul 03 1998) ISSN: 0022-2836 [Print] Netherlands
• PMID: 9653030 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., Research Support, U.S. Gov't, P.H.S.)
• Copyright: Copyright 1998 Academic Press.

Chemical References

• DNA, Single-Stranded
• Polymers
• DNA

Topics

• DNA (chemistry)
• DNA, Single-Stranded
• Microscopy, Atomic Force (methods)
• Models, Molecular
• Models, Statistical
• Nucleic Acid Conformation
• Polymers