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Arginine-rich motif peptides as tools for understanding single-stranded DNA recognition /Landt, Stephen George. January 2004 (has links)
Thesis (Ph.D.)--University of California, San Francisco, 2004. / Includes bibliographical references. Also available online.
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Studies on the sequence-selective nuclease, bovine pancreatic DNase IDoherty, Aidan Joseph January 1992 (has links)
No description available.
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Studies on the active site mutants of bovine panreatic DNase 1Jones, Stephen Jeffrey January 1994 (has links)
No description available.
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The mechanism of interaction of the linker histone with DNA and nucleosomesEllen, Thomas Patrick 27 June 2003 (has links)
This dissertation examines the interaction of the linker histone with DNA and with
nucleosomes. The first goal of the project was to characterize the interaction of the
linker histone with DNA. Three factors previously reported to influence the linker
histone's interaction with DNA were examined: ratio of linker histone to DNA sites
of binding, monovalent ions in the local environment, and conformation of the DNA
molecules. Evidence obtained through gel mobility shift assays demonstrates the
strong preference by the linker histone for DNA with superhelical torsion, i.e.,
supercoiling, and the negative cooperative mode of binding that the linker histone
exhibits in association with supercoiled DNA.
The second part of the dissertation examines the location of linker histone binding
on the nucleosome, and documents the pronounced tendency of the linker histone to
bind to two DNA duplex strands. A preparation of homogeneous nucleosome core
particles, consisting of a defined 238 base pair DNA fragment and the core histone
octamer positioned precisely on this DNA, was used as a substrate for the UV-induced
crosslinking of the linker histone to the DNA of this nucleosome. By site-specific
labeling of a single site on the DNA of the nucleosome, the linker histone was
observed crosslinked at that labeled site, confirming that the linker histone binds at the
pseudo-dyad axis of the nucleosome. This evidence was used to support a model of
linker histone binding to the nucleosome that invokes the association of the linker
histone with no fewer than two duplex strands of DNA of the nucleosome. / Graduation date: 2004
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Binding and assembly of H5 (and the globular domain of H5) onto DNACarter, George John 07 January 1998 (has links)
In order to better characterize linker histone interactions with DNA, avian erythrocyte-specific linker H5 and the trypsin-resistant globular domain of H5 (GH5) were used in DNA binding studies. To begin, H5 displayed a considerably higher binding
affinity for DNA than the isolated globular domain (GH5), supporting the importance of the terminal tail domains in binding. This conclusion is based upon binding curves conducted in low-salt solution, and on the considerably-higher salt concentration required
to prevent protein-DNA contact. Linker histones also induce DNA-protein aggregation in a process that was found to result in protein insolubility in 2% SDS, and included protein-protein interactions that did not require the terminal tail domains. In addition, DNA supercoiling appeared to impede the aggregation process; this that may be attributable to binding of linker histones in isolated clusters, as gauged by a limit in the number of observed dithiobis (succinimidyl) propionate (DSP)-crosslinkable contacts. In a related study, the property of GH5 to bind, then organize onto DNA was investigated. GH5 crosslinked onto DNA with dithiobis (succinimidyl propionate), then cleaved with chymotrypsin, displayed highly uniform contacts that appeared to involve the C-terminal four amino acids, and suggests protein-protein interactions are important for binding. This finding may be relevant since GH5 (and H5) were observed to self-associate free in solution in an arguably specific manner. Finally, the exposure of Phe 93 to chymotrypsin was used to identify the surface of the globular domain that contacts DNA for the binding
of intact H5. Results suggests that the side of the protein opposite to the recognition helix preferentially binds to DNA, supporting a novel winged-helix protein DNA-binding mechanism.
Furthermore, parallel studies with octamers reconstituted onto a DNA fragment with twelve copies of the 208 b.p. rDNA 5s gene from Lytechinus variegatus, shows that H5 had a high binding affinity with all detectable protein binding to the reconstituted complex. H5 binding conferred protection to a site located near the dyad axis from endonuclease digestion, supporting the contention that H5 binds near or at the nucleosome dyad axis. H5 binding also was observed to condense fibers as observed from agarose gel electrophoresis, although velocity analytical sedimentation studies indicate that H5 in itself was not sufficient to fully compact chromatin fibers; rather H5 and 30 mM NaCl, in combination, were required. Results indicate that the chromatin-reconstituted "208-12 DNA" makes an excellent model for analyzing the effect of linker proteins on chromatin morphology. / Graduation date: 1998
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Protein-DNA interactions molecular modeling and energetics /Plaxco, Kevin W., Goddard, William A., January 1994 (has links)
Thesis (Ph. D.)--California Institute of Technology, 1994. UM #94-06,216. / Advisor names found in the Acknowledgements pages of the thesis. Title from home page. Viewed 01/15/2010. Includes bibliographical references.
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The topology and geometry of DNA and DNA-protein interactions /Buck, Dorothy E. January 2001 (has links)
Thesis (Ph. D.)--University of Texas at Austin, 2001. / Vita. Includes bibliographical references (leaves 110-115). Available also in a digital version from Dissertation Abstracts.
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Interactions of the parA protein in the partition of DNA during bacterial cell division /Zong, Qiuling. January 1997 (has links)
Thesis (M.A.)--Central Connecticut State University, 1997. / Thesis advisor: Kathy A. Martin-Troy, Ph. D. "... in partial fulfillment of the requirements for the degree of Master of Arts in Biology." Includes bibliographical references (leaves 23-24).
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DNA sequence selectivity and kinetic properties of de novo designed metalloprotein dimersWong-Deyrup, Siu Wah. January 2007 (has links)
Thesis (Ph. D.)--University of Iowa, 2007. / Supervisor: Sonya J. Franklin Includes bibliographical references (leaves 161-168).
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Structure and assembly of filamentous bacteriophagesRowitch, David Henry January 1987 (has links)
No description available.
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