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Computational modeling of DNA elastic energy to predict structure and topology of protein mediated DNA loops
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Perez, Pamela Joan. Computational modeling of DNA elastic energy to predict structure and topology of protein mediated DNA loops. Retrieved from https://doi.org/doi:10.7282/T3WH2T3C

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TitleComputational modeling of DNA elastic energy to predict structure and topology of protein mediated DNA loops
NamePerez, Pamela Joan (author); Olson, Wilma K (chair); Case, David (internal member); York, Darrin (internal member); Morozov, Alexandre (outside member); Rutgers University; School of Graduate Studies
Date Created2017
Other Date2017-10 (degree)
SubjectComputational Biology and Molecular Biophysics, Proteins--physiology
Extent1 online resource (ix, 138 p. : ill.)
DescriptionIn 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.
NotePh.D.
NoteIncludes bibliographical references
Noteby Pamela Joan Perez
Genretheses, ETD doctoral
Persistent URLhttps://doi.org/doi:10.7282/T3WH2T3C
Languageeng
CollectionSchool of Graduate Studies Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.
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