Content area

Abstract

Recent single molecule experiments have determined the probability of loop formation in DNA as a function of the DNA contour length for different types of looping proteins. The optimal contour length for loop formation as well as the probability density functions have been found to be strongly dependent on the type of looping protein used. We show, using Monte Carlo simulations and analytical calculations, that these observations can be replicated using the wormlike-chain model for double-stranded DNA if we account for the nonzero size of the looping protein. The simulations have been performed in two dimensions so that bending is the only mode of deformation available to the DNA while the geometry of the looping protein enters through a single variable which is representative of its size. We observe two important effects that seem to directly depend on the size of the enzyme: 1), the overall propensity of loop formation at any given value of the DNA contour length increases with the size of the enzyme; and 2), the contour length corresponding to the first peak as well as the first well in the probability density functions increases with the size of the enzyme. Additionally, the eigenmodes of the fluctuating shape of the looped DNA calculated from simulations and theory are in excellent agreement, and reveal that most of the fluctuations in the DNA occur in regions of low curvature. [PUBLICATION ABSTRACT]

Details

Title
Geometry of Mediating Protein Affects the Probability of Loop Formation in DNA
Publication title
Volume
94
Issue
8
Pages
3150-8
Number of pages
9
Publication year
2008
Publication date
Apr 15, 2008
Publisher
Biophysical Society
Place of publication
New York
Country of publication
United States
Publication subject
ISSN
00063495
e-ISSN
15420086
Source type
Scholarly Journal
Language of publication
English
Document type
Journal Article
Document feature
Equations; Graphs; References
Accession number
18192346
ProQuest document ID
215693856
Document URL
https://www.proquest.com/scholarly-journals/geometry-mediating-protein-affects-probability/docview/215693856/se-2?accountid=208611
Copyright
Copyright Biophysical Society Apr 15, 2008
Last updated
2024-10-04
Database
ProQuest One Academic