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Computational modeling of DNA elastic energy to predict structure and topology of protein mediated DNA loops
Descriptive
TitleInfo
Title
Computational modeling of DNA elastic energy to predict structure and topology of protein mediated DNA loops
Name
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Perez
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Pamela Joan
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Pamela Joan Perez
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author
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Olson
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Wilma K
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Wilma K Olson
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Advisory Committee
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chair
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David
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David Case
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Advisory Committee
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internal member
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(type = family)
York
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(type = given)
Darrin
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Darrin York
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Advisory Committee
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internal member
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(type = family)
Morozov
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Alexandre
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Alexandre Morozov
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Advisory Committee
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outside member
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Rutgers University
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degree grantor
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School of Graduate Studies
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theses
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2017
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2017-10
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2017
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xx
Language
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eng
Abstract
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In addition to the genetic message, DNA base sequence carries a multitude of structural and energetic signals important to the packaging and processing of the genetic material. One way in which these signals enter is through the looping of DNA, mediated by proteins that attach to specific, widely separated base-pair elements along the chain molecule. Here I explore the influence of local sequence-dependent features of DNA on the ease of looping between the binding headpieces of the Lac repressor protein. I then consider the role that conformational flexibility of the Lac repressor plays on the conformation of the intervening DNA. I also provide insight into genome architecture by modeling nucleoprotein systems of protein partitioned-minicircles with two topologically independent domains. I identify the energetically preferred spatial pathways of short, protein-anchored fragments of ideal DNA and show that the energies capture the looping propensities and modes of chain attachment found by direct computer sampling. I examine the effects of the helical repeat, mode/range of local deformations, and intrinsic curvature on overall energy and chain configuration. I discuss the findings in the context of the effects of nucleotide sequence seen in recent studies of Lac repressor-mediated loops, including the looping topologies dictated by the settings of a naturally curved DNA insert and the looping propensities of A·T- vs. G·C-rich DNA. I describe the effects of fluctuations in protein conformation on looping likelihood.
Subject
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Topic
Computational Biology and Molecular Biophysics
Subject
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Topic
Proteins--physiology
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Rutgers University Electronic Theses and Dissertations
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ETD_8517
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electronic resource
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application/pdf
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Extent
1 online resource (ix, 138 p. : ill.)
Note
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Ph.D.
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Includes bibliographical references
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by Pamela Joan Perez
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School of Graduate Studies Electronic Theses and Dissertations
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rucore10001600001
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Identifier
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doi:10.7282/T3WH2T3C
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ETD doctoral
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Rights
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The author owns the copyright to this work.
RightsHolder
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Name
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Perez
GivenName
Pamela
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Joan
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Permission or license
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2017-10-03 16:37:24
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Pamela Perez
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Rutgers University. School of Graduate Studies
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Author Agreement License
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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.
RightsEvent
DateTime
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2017-10-31
DateTime
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2019-10-31
Type
Embargo
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after October 31st, 2019.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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