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Description
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
ContributorsChang, Ruihong (Performer) / ASU Library. Music Library (Publisher)
Created2018-03-29
Description
Filtration for microfluidic sample-collection devices is desirable for sample selection, concentration, preprocessing, and downstream manipulation, but microfabricating the required sub-micrometer filtration structure is an elaborate process. This thesis presents a simple method to fabricate polydimethylsiloxane (PDMS) devices with an integrated membrane filter that will sample, lyse, and extract the DNA from microorganisms in aqueous environments. An off-the-shelf membrane filter disc was embedded in a PDMS layer and sequentially bound with other PDMS channel layers. No leakage was observed during filtration. This device was validated by concentrating a large amount of cyanobacterium Synechocystis in simulated sample water with consistent performance across devices. After accumulating sufficient biomass on the filter, a sequential electrochemical lysing process was performed by applying 5VDC across the filter. This device was further evaluated by delivering several samples of differing concentrations of cyanobacterium Synechocystis then quantifying the DNA using real-time PCR. Lastly, an environmental sample was run through the device and the amount of photosynthetic microorganisms present in the water was determined. The major breakthroughs in this design are low energy demand, cheap materials, simple design, straightforward fabrication, and robust performance, together enabling wide-utility of similar chip-based devices for field-deployable operations in environmental micro-biotechnology.
ContributorsLecluse, Aurelie (Author) / Meldrum, Deirdre (Thesis advisor) / Chao, Joseph (Thesis advisor) / Westerhoff, Paul (Committee member) / Arizona State University (Publisher)
Created2011
Description
Four Souvenirs for Violin and Piano was composed by Paul Schoenfeld (b.1947) in 1990 as a showpiece, spotlighting the virtuosity of both the violin and piano in equal measure. Each movement is a modern interpretation of a folk or popular genre, re- envisioned over intricate jazz harmonies and rhythms. The work was commissioned by violinist Lev Polyakin, who specifically requested some short pieces that could be performed in a local jazz establishment named Night Town in Cleveland, Ohio. The result is a work that is approximately fifteen minutes in length. Schoenfeld is a respected composer in the contemporary classical music community, whose Café Music (1986) for piano trio has recently become a staple of the standard chamber music repertoire. Many of his other works, however, remain in relative obscurity. It is the focus of this document to shed light on at least one other notable composition; Four Souvenirs for Violin and Piano. Among the topics to be discussed regarding this piece are a brief history behind the genesis of this composition, a structural summary of the entire work and each of its movements, and an appended practice guide based on interview and coaching sessions with the composer himself. With this project, I hope to provide a better understanding and appreciation of this work.
ContributorsJanczyk, Kristie Annette (Author) / Ryan, Russell (Thesis advisor) / Campbell, Andrew (Committee member) / Norton, Kay (Committee member) / Arizona State University (Publisher)
Created2015
ContributorsWhite, Aaron (Performer) / Kim, Olga (Performer) / Hammond, Marinne (Performer) / Shaner, Hayden (Performer) / Yoo, Katie (Performer) / Shoemake, Crista (Performer) / Gebe, Vladimir, 1987- (Performer) / Wills, Grace (Performer) / McKinch, Riley (Performer) / Freshmen Four (Performer) / ASU Library. Music Library (Publisher)
Created2018-04-27
ContributorsRosenfeld, Albor (Performer) / Pagano, Caio, 1940- (Performer) / ASU Library. Music Library (Publisher)
Created2018-10-03
ContributorsCao, Yuchen (Performer) / Chen, Sicong (Performer) / Soberano, Chino (Performer) / Nam, Michelle (Performer) / Collins, Clarice (Performer) / Witt, Juliana (Performer) / Liu, Jingting (Performer) / Chen, Neilson (Performer) / Zhang, Aihua (Performer) / Jiang, Zhou (Performer) / ASU Library. Music Library (Publisher)
Created2018-04-25
ContributorsMcLin, Katherine (Performer) / Campbell, Andrew (Pianist) (Performer) / Ericson, John Q. (John Quincy), 1962- (Performer) / McLin/Campbell Duo (Performer) / ASU Library. Music Library (Publisher)
Created2018-09-23