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The statistical mechanics of free and protein-bound DNA by Monte Carlo simulation

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TypeOfResource
Text
TitleInfo (ID = T-1)
Title
The statistical mechanics of free and protein-bound DNA by Monte Carlo simulation
Identifier
ETD_1535
Identifier (type = hdl)
http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000051086
Language
LanguageTerm (authority = ISO639-2); (type = code)
eng
Genre (authority = marcgt)
theses
Subject (ID = SBJ-1); (authority = RUETD)
Topic
Chemistry and Chemical Biology
Subject (ID = SBJ-1); (authority = ETD-LCSH)
Topic
DNA-protein interactions
Abstract
There are many challenges involved in the simulation of DNA. In this work, novel Monte Carlo techniques are developed and applied to understanding the biophysical properties of DNA. A coarse-grained model is applied to feasibly simulate long DNA chains of
hundreds to thousands of base pairs, using a reduced base-pair step representation of the DNA. Using this model, a canonical Monte Carlo simulation of DNA is developed to characterize the structure and flexibility of double-helical DNA. By applying a unique algorithm for generating uncorrelated DNA conformations a priori, limitations of the original Metropolis Monte Carlo algorithm are avoided.
Furthermore, there is developing experimental evidence that non-specifically associating proteins that induce DNA bending modulate the in-vivo flexibility of DNA. To investigate the effect of these proteins, a grand canonical Monte Carlo simulation technique is developed, extending the model of free DNA to incorporate non-specific protein-DNA interactions. In this technique, DNA chains are simulated with varying numbers of bound proteins. Ubiquitous DNA architectural proteins such as the prokaroytic nucleoid protein HU and the eukaryotic HMG-box proteins are investigated with this technique. By incorporating structural information from the protein-DNA complexes
currently available in the Nucleic Acid Database, models of these DNA-binding proteins are constructed and used in this method.
The results predict an enhancement of DNA flexibility due to non-specific binding of these proteins, and calculations of the cyclization (ring-closure) properties and force-extension responses of protein-bound DNA chains compared to free DNA chains are presented. In addition, the effects of these proteins on the topological properties of closed circular DNA and on the looping properties of DNA constrained by binding to the Lac repressor protein assembly are characterized in large-scale parallel simulations. Coordination of protein binding on circular and looped DNA and induction of negative supercoiling of DNA by DNA architectural proteins is predicted, with important
biological implications for chromosome organization and transcription regulation.
PhysicalDescription
Form (authority = gmd)
electronic resource
Extent
xvi, 126 p. : ill.
InternetMediaType
application/pdf
InternetMediaType
text/xml
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references (p. 119-125)
Note (type = statement of responsibility)
by Luke Czapla
Name (ID = NAME-1); (type = personal)
NamePart (type = family)
Czapla
NamePart (type = given)
Luke
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author
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Luke Czapla
Name (ID = NAME-2); (type = personal)
NamePart (type = family)
Olson
NamePart (type = given)
Wilma
Role
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chair
Affiliation
Advisory Committee
DisplayForm
Wilma K Olson
Name (ID = NAME-3); (type = personal)
NamePart (type = family)
Talaga
NamePart (type = given)
David
Role
RoleTerm (authority = RULIB); (type = )
internal member
Affiliation
Advisory Committee
DisplayForm
David S Talaga
Name (ID = NAME-4); (type = personal)
NamePart (type = family)
Castner
NamePart (type = given)
Edward
Role
RoleTerm (authority = RULIB); (type = )
internal member
Affiliation
Advisory Committee
DisplayForm
Edward W Castner
Name (ID = NAME-5); (type = personal)
NamePart (type = family)
Morozov
NamePart (type = given)
Alexandre
Role
RoleTerm (authority = RULIB); (type = )
outside member
Affiliation
Advisory Committee
DisplayForm
Alexandre V Morozov
Name (ID = NAME-1); (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB); (type = )
degree grantor
Name (ID = NAME-2); (type = corporate)
NamePart
Graduate School - New Brunswick
Role
RoleTerm (authority = RULIB); (type = )
school
OriginInfo
DateCreated (point = ); (qualifier = exact)
2009
DateOther (qualifier = exact); (type = degree)
2009-01
Place
PlaceTerm (type = code)
xx
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
RelatedItem (type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier (type = local)
rucore19991600001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/T3TH8MZR
Genre (authority = ExL-Esploro)
ETD doctoral
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The author owns the copyright to this work.
Copyright
Status
Copyright protected
Availability
Status
Open
RightsEvent (AUTHORITY = rulib); (ID = 1)
Type
Permission or license
Detail
Non-exclusive ETD license
AssociatedObject (AUTHORITY = rulib); (ID = 1)
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.
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Technical

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ETD
MimeType (TYPE = file)
application/pdf
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application/x-tar
FileSize (UNIT = bytes)
5836800
Checksum (METHOD = SHA1)
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