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The twists & turns of DNA: the importance of DNA deformability and local features that influence genomic structure and function
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Young, Robert T.. The twists & turns of DNA: the importance of DNA deformability and local features that influence genomic structure and function. Retrieved from https://doi.org/doi:10.7282/t3-c1ng-tc42

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TitleThe twists & turns of DNA: the importance of DNA deformability and local features that influence genomic structure and function
NameYoung, Robert T. (author); Olson, Wilma (chair); Case, David (member); York, Darrin (member); Khare, Sagar (member); Nanda, Vikas (member); Rutgers University; School of Graduate Studies
Date Created2022
Other Date2022-10 (degree)
SubjectChemistry, Biophysics, Computational chemistry, DNA loops, DNA minicircles, Lac operon, Molecular modeling, Nucleosome, Protein-DNA interactions
Extent1 online resource (159 pages) : illustrations
DescriptionThe organization of DNA is essential to genetic protection and access and is highly dependent on factors that can cause bending, stretching, and torsional changes along the double-helical chain. Interactions with small molecules lead to localized distortions of DNA whose strain is taken up by neighboring naked regions with its length and sequence composition influencing compensatory efforts. Advancements in biophysical experimentation have provided new insights in the role of DNA structure versus function and an increase in high-resolution structures of protein-bound DNA. Computational modeling tools have also improved, including the ability to incorporate constraints in the design of energetically optimized models, such as regions of undertwisting or extreme bending of DNA at a protein-binding site. The research presented here shows how variables at the DNA base-pair step level can influence the organization of DNA on the mesoscale level, examining first the development of DNA models as a collection of rigid-body base-pair steps. The first application highlights the loss and subsequent reemergence of DNA looping propensity from a well-studied regulatory loop system after first incorporating a linearizing protein and then addition of a kinking protein situated upstream in artificial architectural protein design. The second study is a survey of various supercoiled topoisomers bearing a superhelical DNA pathway characteristic of the chromosome architectural subunit known as the nucleosome. The collection of 164 nucleosome core particles is organized into seven groups that vary due to the uptake of twist along the DNA path and optimization of the circular minichromosomes shows how these local variations in twist affect the configuration of the free loop. Finally, the focus shifts to the role of sequence on DNA configuration by updating a knowledge-based potential from over 3000 high-resolution protein-DNA structures in the Protein Data Bank and expanding the base-pair step to include tetrameric sequence context. This update and expansion were applied to a series of 150-bp and 336-bp sequences, leading to new insights in the role sequence plays in both structural curvature and protein signaling.
NotePh.D.
NoteIncludes bibliographical references
Genretheses
Persistent URLhttps://doi.org/doi:10.7282/t3-c1ng-tc42
LanguageEnglish
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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