Open Access. Powered by Scholars. Published by Universities.®
Physical Sciences and Mathematics Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Institution
Articles 1 - 6 of 6
Full-Text Articles in Physical Sciences and Mathematics
On The Conformational Dynamics Of Dna: A Perspective From Molecular Dynamics Simulations, Ning Ma
On The Conformational Dynamics Of Dna: A Perspective From Molecular Dynamics Simulations, Ning Ma
USF Tampa Graduate Theses and Dissertations
The main focus of my dissertation is on the conformational motion of DNA, studied by applying tools from the computational chemistry field. In addition, studies of relative α- and 310 helical stabilities in peptides/mini-proteins, and a molecular flooding study of the retinoid X-receptor as part of a continuing drug design effort are presented. In molecular biology, it has been well known that sequence determines structure, and structure controls function. For proteins or DNA to work properly, the correct configuration is required. Mutations may alter the structure, which can cause malfunction. Non-mutational effects, such as a change in environment may also …
Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver
Mutagenic And Spectroscopic Investigation Of Ph Dependent Cooa Dna Binding, Brian R. Weaver
Chemistry Honors Papers
The carbon monoxide (CO) sensing heme protein, CooA, is a transcription factor which exists in several bacteria that utilize CO as an energy source. CooA positively regulates the expression of coo genes in the presence of CO such that the corresponding proteins may metabolize CO. The present studies have yielded the unexpected result that Fe(III) CooA binds DNA tightly at pH < 7, deviating from all previously reported work which indicate that CooA DNA binding is initiated only when the exogenous CO effector reacts with the Fe(II) CooA heme. This observation suggests that the disruption of one or more salt bridges upon effector binding may be a critical feature of the normal CooA activation mechanism. To test this possibility, several protein variants that eliminated a selected salt bridge for the CooA homolog from Rhodospirillum rubrum were prepared via site-directed mutagenesis. Samples of these variant proteins, which were overexpressed in Escherichia coli, were then characterized by spectroscopic methods and functional assays to investigate the impact these mutations had on CooA heme coordination …
Gas-Phase Ion Spectroscopy Of Nucleobases And Mononucleotides: Models For Higher Order Nucleic Acids, Yuan-Wei Nei
Gas-Phase Ion Spectroscopy Of Nucleobases And Mononucleotides: Models For Higher Order Nucleic Acids, Yuan-Wei Nei
Wayne State University Dissertations
Experiments examining the structures and stabilities of protonated and sodium cationized nucleobases, and deprotonated DNA and RNA mononucleotides are presented and discussed in this dissertation. These studies were carried out using the infrared multiple photon dissociation (IRMPD) action spectroscopy technique that utilizes a Fourier transform ion cyclotron mass spectrometer (FT-ICR MS) coupled to a free electron laser (FEL) located at the Radboud University Nijmegen. Ionic species of these biologically important complexes were generated using an electrospray ionization source and then mass isolated to have their infrared (IR) spectra measured by the experimental apparatus. Detailed analysis of the IR spectra measured …
Dna Aptamer-Based Smart Mri Contrast Agent For Dopamine, Angel D. Thompson
Dna Aptamer-Based Smart Mri Contrast Agent For Dopamine, Angel D. Thompson
Legacy Theses & Dissertations (2009 - 2024)
A smart contrast agent is a molecule whose relaxivity changes in response to a biological trigger such as a biomolecule, enzymatic activity, or pH. The focus of my graduate project was to develop a DNA aptamer-based smart MRI contrast agent capable of sensing dopamine. Aptamers are single-stranded oligonucleotides that form stable three-dimensional structures efficient in binding with high affinity and specificity for a range of targets. The DNA aptamer has an attached lanthanide-based probe, consisting of a metal ion Gd(III) and a macrocyclic DOTA ligand. The aptamer was assembled using solid phase oligonucleotide synthesis. Nuclear magnetic resonance was used to …
Literature Review On The Use Of Nucleic Acid-Based Logic Gates For The Detection Of Human Diseases, Enrique J. Blanco Martinez
Literature Review On The Use Of Nucleic Acid-Based Logic Gates For The Detection Of Human Diseases, Enrique J. Blanco Martinez
Honors Undergraduate Theses
Conventional methods for diagnosis of human disease are, at times, limited in different regards including time requirement, either experimental or data processing, sensitivity, and selectivity. It is then that a Point of Care Criteria, which considers the true utility and usefulness of the device, is employed to propose new diagnostic devices capable of overcoming the aforementioned shortcomings of conventional tools. Nucleic acid, characterized for its predictable base-pairing nature, is considered to be a highly-selective, yet greatly modifiable device. Its behavior is then described through Boolean Logic, where “true” or “false” outputs are mathematically described as “1” and “0”, respectively. This …
Silica Nanoparticles For The Delivery Of Dna And Rnai In Cancer Treatment, Michael Aaron Vrolijk
Silica Nanoparticles For The Delivery Of Dna And Rnai In Cancer Treatment, Michael Aaron Vrolijk
Graduate College Dissertations and Theses
DNA and interfering RNA (RNAi) – short interfering RNA (siRNA) and micro RNA (miRNA) – are promising new cancer therapies, especially for drug resistant lines. However, they require a delivery system in vivo to prevent degradation and off target effects. Silica based nanoparticles, both solid and mesoporous, are a promising option due to their biocompatibility, ease of preparation and morphology control, reproducibility, and facile addition of functional groups including targeting ligands.
After a brief introduction to cancer treatment and review of the current nanoparticle treatments undergoing clinical trials, this thesis details the many methods explored over the past ten years …