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Association, intrinsic shape, and mo...

Freeman, Gordon Samuel.

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Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation./
Author:	Freeman, Gordon Samuel.
Description:	190 p.
Notes:	Source: Dissertation Abstracts International, Volume: 74-12(E), Section: B.
Contained By:	Dissertation Abstracts International74-12B(E).
Subject:	Engineering, Chemical. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3592113
ISBN:	9781303329760

Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation.
Freeman, Gordon Samuel.

Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation. - 190 p.

Source: Dissertation Abstracts International, Volume: 74-12(E), Section: B.

Thesis (Ph.D.)--The University of Wisconsin - Madison, 2013.

This item must not be sold to any third party vendors.

DNA is of central importance in biology as it is responsible for carrying, copying, and translating the genetic code into the building blocks that comprise life. In order to accomplish these tasks, the DNA molecule must be versatile and robust. Indeed, the underlying molecular interactions that allow DNA to execute these tasks are complex and their origins are only beginning to be understood. While experiments are able to elucidate many key biophysical phenomena, there remain many unanswered questions. Molecular simulation is able to shed light on phenomena at the molecular scale and provide information that is missing from experimental views of DNA behavior. In this dissertation I use state-of-the-art coarse-grained DNA models to address two key problems.

ISBN: 9781303329760Subjects--Topical Terms:

1018531
Engineering, Chemical.

Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation.
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100 1 $a Freeman, Gordon Samuel. $3 3170778
245 1 0 $a Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation.
300 $a 190 p.
500 $a Source: Dissertation Abstracts International, Volume: 74-12(E), Section: B.
500 $a Adviser: Juan J. de Pablo.
502 $a Thesis (Ph.D.)--The University of Wisconsin - Madison, 2013.
506 $a This item must not be sold to any third party vendors.
520 $a DNA is of central importance in biology as it is responsible for carrying, copying, and translating the genetic code into the building blocks that comprise life. In order to accomplish these tasks, the DNA molecule must be versatile and robust. Indeed, the underlying molecular interactions that allow DNA to execute these tasks are complex and their origins are only beginning to be understood. While experiments are able to elucidate many key biophysical phenomena, there remain many unanswered questions. Molecular simulation is able to shed light on phenomena at the molecular scale and provide information that is missing from experimental views of DNA behavior. In this dissertation I use state-of-the-art coarse-grained DNA models to address two key problems.
520 $a In the first, metadynamics calculations are employed to uncover the free energy surface of two complimentary DNA strands. This free energy surface takes on the appearance of a hybridization funnel and reveals candidates for intermediate states in the hybridization of short DNA oligomers. Such short oligomers are important building blocks for DNA-driven self-assembly and the mechanism of hybridization in this regime is not well understood.
520 $a The second problem is that of nucleosome formation. Nucleosomes are the fundamental subunit of genome compaction in the nucleus of a cell. As such, nucleosomes are a key epigenetic factor and affect gene expression and the ability of DNA-binding proteins to locate and bind to the appropriate position in the genome. However, the factors that drive nucleosome positioning are not well understood. While DNA sequence is known to affect nucleosome formation, the mechanism by which it does so has not been established and a number of hypotheses explaining this sequence-dependence exist in the literature. I demonstrate that DNA shape dominates this process with contributions arising from both intrinsic DNA curvature as well as DNA-protein interactions driven by sequence-dependent variations in minor groove dimensions.
590 $a School code: 0262.
650 4 $a Engineering, Chemical. $3 1018531
650 4 $a Biophysics, General. $3 1019105
650 4 $a Physics, Molecular. $3 1018648
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710 2 $a The University of Wisconsin - Madison. $b Chemical Engineering. $3 2094015
773 0 $t Dissertation Abstracts International $g 74-12B(E).
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791 $a Ph.D.
792 $a 2013
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3592113