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In silico examination of the structure of closed naked DNA and protein/DNA complexes

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TitleInfo
Title
In silico examination of the structure of closed naked DNA and protein/DNA complexes
Name (type = personal)
NamePart (type = family)
Britton
NamePart (type = given)
Lauren Adrian
NamePart (type = date)
1976-
DisplayForm
Lauren Britton
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Olson
NamePart (type = given)
Wilma K
DisplayForm
Wilma K Olson
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = personal)
NamePart (type = family)
Pedersen
NamePart (type = given)
Henrik
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Henrik Pedersen
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Chiew
NamePart (type = given)
Yee
DisplayForm
Yee Chiew
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Tobias
NamePart (type = given)
Irwin
DisplayForm
Irwin Tobias
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
outside member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
Graduate School - New Brunswick
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school
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Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (qualifier = exact)
2012
DateOther (qualifier = exact); (type = degree)
2012-05
CopyrightDate (qualifier = exact)
2012
Place
PlaceTerm (type = code)
xx
Language
LanguageTerm (authority = ISO639-2b); (type = code)
eng
Abstract (type = abstract)
The focus of this thesis is to study the overall global shape of DNA and its dependence on various intrinsic parameters both when naked and bound to proteins. We developed a definition of the twist of DNA base-pair steps, TwSC, that can be related to the overall folding of the DNA molecule and is a new contribution to the field of DNA topology. We developed a software package, titled 3DNATwSC, to calculate TwSC. We established, by studying seven simplified ideal structures, the value of TwSC as an effective gauge for the topological landscape of DNA due to its sensitivity to changes in chirality. We constructed a web-based user-friendly database, named TwiDDL, to show the impact of protein binding on TwSC. TwiDDL makes it easy to look for unusual values of TwSC in biologically relevant structures. We identified a number of highly unusual over- and under-twisted molecules by comparing TwSC to the twist of ideal B-DNA. We developed 2D and 3D-plots to highlight patterns and unusual deformations in TwSC in a variety of structures. We examined the twisting of DNA in representative A, B, and Z-DNA structures as well as in a collection of 45 nucleosomes. We also studied the effects of shearing on TwSC. When shearing was removed from both a nucleosome and an HU-DNA structure, the value of TwSC approaches that of TwSP, the rigid-body step parameter twist. We created a user-friendly application, called 3DNAdesigner, that allows a user to construct minimum-energy configurations of open linear and spatially confined DNA molecules. We presented the software design, described its features, and gave three detailed examples. The software was used to create minimum-energy configurations of DNA mini-circles and DNA/protein complexes. The changes in Lk and energy introduced by binding protein to a mini-circle might be of interest to a lab performing in vitro studies. We also found numerous minimum-energy configurations of the Lac operon bound to the Lac repressor in the absence or presence the HU protein.
Subject (authority = RUETD)
Topic
Chemical and Biochemical Engineering
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_3896
PhysicalDescription
Form (authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
xxvi, 447 p. : ill.
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references
Note (type = statement of responsibility)
by Lauren Adrian Britton
Subject (authority = ETD-LCSH)
Topic
DNA-protein interactions
Subject (authority = ETD-LCSH)
Topic
Biological interfaces
Identifier (type = hdl)
http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000065097
RelatedItem (type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier (type = local)
rucore19991600001
Location
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NjNbRU
Identifier (type = doi)
doi:10.7282/T3K0736Z
Genre (authority = ExL-Esploro)
ETD doctoral
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Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Britton
GivenName
Lauren
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2012-04-10 13:38:46
AssociatedEntity
Name
Lauren Britton
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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