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Global solution structure of IHF-induced DNA bend using cyclization kinetics and Monte Carlo simulation

Record Type:	Electronic resources : Monograph/item
Title/Author:	Global solution structure of IHF-induced DNA bend using cyclization kinetics and Monte Carlo simulation
Author:	Yang, Seung-Min.
Description:	113 p.
Notes:	Director: Donald M. Crothers.
Notes:	Source: Dissertation Abstracts International, Volume: 65-03, Section: B, page: 1314.
Contained By:	Dissertation Abstracts International65-03B.
Subject:	Chemistry, Biochemistry.
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3125335
ISBN:	0496726250

Global solution structure of IHF-induced DNA bend using cyclization kinetics and Monte Carlo simulation
Yang, Seung-Min.

Global solution structure of IHF-induced DNA bend using cyclization kinetics and Monte Carlo simulation [electronic resource] - 113 p.

Director: Donald M. Crothers.

Thesis (Ph.D.)--Yale University, 2004.

In chapter 3, DNA parameters, such as bending and flexibilities, of the H' site were estimated using the combined methods. The results show that the site bends toward the minor groove with an overall bend of &sim;20°. Slightly increased bending flexibility is also detected, which may facilitate the bend formation upon IHF binding.

ISBN: 0496726250Subjects--Topical Terms:

226900
Chemistry, Biochemistry.

Global solution structure of IHF-induced DNA bend using cyclization kinetics and Monte Carlo simulation
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500 $a Source: Dissertation Abstracts International, Volume: 65-03, Section: B, page: 1314.
502 $a Thesis (Ph.D.)--Yale University, 2004.
520 # $a In chapter 3, DNA parameters, such as bending and flexibilities, of the H' site were estimated using the combined methods. The results show that the site bends toward the minor groove with an overall bend of &sim;20°. Slightly increased bending flexibility is also detected, which may facilitate the bend formation upon IHF binding.
520 # $a In chapter 4 we show that IHF induces a large DNA bend which is toward the minor groove. The bend angle is more than 160°, which is consistent with the crystal structure. The lack of any outstanding structural distortions of the IHF-bound DNA other than the bending implies that the versatile role of IHF in cellular processes is caused mainly by the capacity of the protein to induce a large bend. Our results extend the application of cyclization kinetics experiments coupled with computer simulations to an extreme case of DNA bending induced by proteins.
520 # $a Integration host factor (IHF) is an architectural protein that can bind to DNA at a specific site and bend the DNA to participate in recombination, gene regulation and DNA packaging. Using cyclization kinetics experiments combined with Monte Carlo simulations we elucidated the global solution structures of its target DNA, H', both when the DNA was in protein-free state and protein-bound state. Both the biological function and the crystal structure of IHF are explained in chapter 1. Chapter 2 describes the thermodynamic properties of IHF binding to the H'. Pre-bent DNA, such as closed circles and supercoils, lowers free binding energies of IHF more than one hundred fold compared to linear DNA, which implicates an existence of an IHF-induced large bend.
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