Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 31 for “"smFRET"”.
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Navigating exponentially large spaces in biology : methods for directed evolution and smFRET time series analysis
The recent explosion of high throughput technologies in many fields of biology has necessitated the use of sophisticated algorithms to guide experimental design and analyze results. This thesis explores two such fields: directed protein evolution and single molecule fluorescence resonance energy …
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Single-molecule FRET analysis of the dynamics of AMPA receptor
… fluorescence resonance energy transfer (smFRET) spectroscopy has advanced to become a powerful tool in characterizing biomolecules to the molecular level. In this thesis, the smFRET technique was utilized for the first time to analyze the dynamics of the conformational changes of the …
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Single-molecule visualization of conformational changes in the SecA ATPase
… Fbrster resonance energy transfer (smFRET). Directly measuring conformational changes in an ATPase will also provide further insight into the guiding principles of ATPase function. First, we will build a smFRET microscope and assemble a software package to analyze the data it …
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Single-Stranded Dna Scanning And Deamination With Single-Molecule Resolution
… Förster resonance energy transfer (smFRET) to study ssDNA scanning and deamination by Apo3G and AID. Consistent with previous ensemble measurements, single-molecule trajectories exhibit short binders (<25 s) and long binders (25 s - 10 min), which are heterogeneously distributed for …
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Unveiling Dna Polymerase Synthesis And Proofreading Activities - One Molecule At A Time
… molecule Förster resonance energy transfer (smFRET) approach to monitor the polymerase position on the DNA with single base pair resolution. </p> <p> We have worked to optimize nearly every aspect of that approach and to apply the technique to characterize DNA polymerase dynamics on the DNA …
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The Molecular Mechanism of the Escherichia Coli vitamin B12 Transporter BtuCD-F: Real-time Observation of the Transporter in Motion
… molecule fluorescence resonance energy transfer (smFRET) measurements. Fluorescent probes have been introduced at a variety of diagnostic sites, enabling smFRET to be used to measure distance changes in different conformational states as well as to observe the transitions between these states in …
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Single molecule fluorescence studies of replicative helicases
… molecule Förster Resonance Energy Transfer (smFRET) methods on the Bacteriophage T7 replisome (helicase/primase and polymerase). Our results suggest a model whereby the primase loop allows the coordination of leading and lagging strand DNA synthesis by enabling the newly synthesized RNA …
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Engineering Fluorescently Labeled Human Fibroblast Growth Factor One Mutants and Characterizing Their Photophysics Properties Towards Designing FRET Assays
… which can lead to a myriad of cancers. smFRET is an ultrasensitive distant dependent (1-10 nm) technique capable of resolving such heterogeneity in structural dynamics and binding affinities (Kd). Therefore, we successfully designed and characterized fluorescently labeled hFGF1 tracers …
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Study Of Protein-Rna Interactions Using Fluorescence Resonance Energy Transfer (fret) And Single-Molecule Fret
… Fluorescence Resonance Energy Transfer (smFRET) techniques that provide information about heterogeneity and dynamic behaviors of molecules have been developed to investigate inter- and intra-molecular interactions. Here we have used FRET in combination with smFRET to study three very …
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Examining Post-Translational Modifications In Alpha-Synuclein Through Semi-Synthesis And Single Molecule Spectroscopy
… molecule Förster resonance energy transfer (smFRET) measurements reveal changes in monomer conformation that underlie a possible mechanism for the differential aggregation profile of phosphorylated αS. In addition to its disease-relevant characteristics, we examine the function of modified αS …
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Single Molecule Förster Resonance Energy Transfer and Super Resolution Force Spectroscopy Study of Elongation Factor G Evolution, Conformation, and Function
… molecule Förster resonance energy transfer (smFRET) experiments determined this inhibition stems from the mutants becoming trapped in a ‘super’-compact conformation on the ribosome. The Thr48 mutations were modeled using AlphaFold predictions and MSAs. This revealed the mutations shifted the …
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Single molecule studies of helicase mechanisms
… many biological systems. Single molecule FRET (smFRET) microscopy provides these abilities with a distance scale of 2-8 nm, 8 ms time resolution, and the ability to look at single molecules. smFRET experiments on BLM have shown several interesting new behaviors which are unavailable to ensemble …
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The Role of Initiation Factor Dynamics in Translation Initiation
… fluorescence resonance energy transfer (smFRET) as a primary tool for investigating how the dynamics of IF1 and IF3 regulate the accuracy with which the translational machinery selects an initiator transfer RNA (tRNA) and the correct messenger RNA (mRNA) start codon during the initiation …
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Characterization of splicing mechanisms by single-molecule fluorescence
… conditions <i>in vitro</i>. Furthermore, smFRET data indicate that the Mss116-mediated group II intron folding pathway is a multi-step process that consists of both ATP-independent and ATP-dependent steps. </p> <p> Structurally and mechanistically group II introns are similar to …
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Investigations of The Structure-Function Relationship In Kainate Receptors Using FöRster Resonance Energy Transfer
… Förster Resonance Energy Transfer (smFRET) in order to address this gap in the knowledge. We have characterized the structural arrangement and dynamics of the homomeric (GluK2) receptors and identified structural changes involved in the functional modulation by ions and auxiliary …
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Effect of oxidative stress on human telomeric DNA structural dynamics and accessibility
… molecule Förster Resonance Energy Transfer (smFRET) to characterize the effect of 8OG on the structural dynamics and accessibility of ssTEL. We show that the stable GQ folding observed in ssTEL is disrupted by a single 8OG, generating dynamic conformational fluctuations of the DNA. Such …
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Understanding the activation-deactivation mechanism of glutamate receptor proteins at the single molecule level
… molecule Förster Resonance Energy Transfer (smFRET) spectroscopy to provide a mechanistic understanding of the activation processes that the receptors undergo. We have probed, at a single molecule level, the structural changes explored by the NMDA receptor proteins, upon binding with several …
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A single molecule study on the structural basis of ion selective permeation in voltage-gated sodium channels
… and membrane voltages. Surprisingly, my smFRET data showed large spontaneous FRET transitions which suggest significant structural dynamics at the NavAb selectivity filter. Moreover, I also detected significant FRET changes at the NavAb selectivity filter induced by activating voltage. My …
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Fret-Based Investigations of The Structure-Function Relationships In The Nmda Receptor
… molecule Förster Resonance Energy Transfer (smFRET) as a means to address that gap. We have examined the question of partial agonism of the NMDA receptor, noting a mechanism of a dynamically graded cleft closure. We have pushed the bounds of the temporal resolution of such methods and been …
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