TitleIn silico examination of the structure of closed naked DNA and protein/DNA complexes
NameBritton, Lauren Adrian (author), Olson, Wilma K (chair), Pedersen, Henrik (internal member), Chiew, Yee (internal member), Tobias, Irwin (outside member), Rutgers University, Graduate School - New Brunswick,
SubjectChemical and Biochemical Engineering,
DNA-protein interactions ,
DescriptionThe 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.
NoteIncludes bibliographical references
Noteby Lauren Adrian Britton
CollectionGraduate School - New Brunswick Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.