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Quadruplex molecular beacons (QMBs) are DNA strands that have shown promise in research for cancer screening. This is achieved by the QMB acting as a sensor, capable of binding to miRNA, a class of non-coding RNA that is upregulated within the human body when cancer is present. A substantial challenge when designing QMBs is making them stable enough to withstand the human body and bind to miRNA. In this project, we investigated dual-loop quadruplexes, a modification made to standard single loop quadruplexes by adding on another recognition loop capable of binding another miRNA strand of a same or different type.
Faculty Sponsor: Cooper Battle
Discipline: Chemistry
Methyl halides contribute to the destruction of the stratospheric ozone layer. S-Adenosyl-L-Methionine (SAM)-dependent thiol/halide methyltransferase enzymes, encoded by HARMLESS TO OZONE LAYER (HOL) genes, have been shown to catalyze the production of methyl halides in several plant species. We developed a High-Performance Liquid Chromatography (HPLC) assay to use to characterize the activity of novel SAM-dependent thiol/halide methyltransferase enzymes in plants. We validated the method using the known halide/thiol methyltransferase AtHOL1 from Arabidopsis thaliana, and we used the assay in an attempt to characterize the activity of the putative halide/thiol methyltransferase PhyscoHOL from the moss Physcomitrella patens.
Faculty Sponsor: Alison Fisher
Discipline: Chemistry
This project investigates the use of chitin-based polymers as a delivery system for the hydrophobic antioxidants caffeic acid and ferulic acid. These phenolic compounds aid the body’s natural response to imbalanced levels of reactive oxygen species (ROS), which cause oxidative stress. Oxidative stress damages proteins, enzymes, nucleic acids, and membranes in the body’s cells, causing a variety of health problems. In this project we have optimized the synthesis of antioxidant-polymer conjugates and investigated the relationship between antioxidant loading and antioxidant activity.
Faculty Sponsor: Andrew Duncan
Discipline: Chemistry
Methyl halide production in plants is catalyzed by S-adenosyl-L-methionine (SAM)-dependent thiol/halide methyltransferase enzymes, encoded by HARMLESS TO OZONE LAYER (HOL) genes. By characterizing a variety of thiol/halide methyltransferase enzymes from diverse plants, we can better understand the evolution and function of HOL proteins. We developed a High-Performance Liquid Chromatography (HPLC)-based thiol/halide methyltransferase enzyme assay and used it to characterize the enzymatic activity of AtHOL1, from the flowering plant Arabidopsis thaliana, and PhyscoHOL, from the moss Physcomitrella patens, in Michaelis-Menten experiments. Thiocyanate and iodide were the substrates of focus for this study.
Faculty Sponsor: Alison Fisher
Discipline: Chemistry
Drug purification often involves the use of liquid-liquid extraction systems to isolate a compound of interest. Volatile organic solvents are commonly used in extractions, so finding environmentally friendly “green” solvents is important. One replacement is the low vapor pressure ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([Bmim]BF 4 ) and water system. This system has an impractical upper critical temperature of 5 °C, which can be raised by adding zinc sulfate. It also has been useful in isolating the antibiotic cephalexin To characterize the impact of zinc sulfate we will be studying a slice of the [Bmim]BF 4 + water + zinc sulfate coexistence surface.
Faculty Sponsor: Chuck Williamson
Discipline: Chemistry
Methyl halides are volatile organic compounds (VOCs) that contribute to ozone layer depletion. Thiol/halide methyltransferase enzymes, encoded by HARMLESS TO OZONE LAYER (HOL) genes in plants, are a major source of methyl halides to the atmosphere. In this study we sought to develop a headspace solid-phase microextraction gas chromatography mass spectrometry (HS SPME GC-MS) method to confirm the production of methyl bromide (CH 3 Br), methyl chloride (CH 3 Cl), methyl thiocyanate (CH 3 SCN), and methyl iodide (CH 3 I) in reactions with known and putative thiol/halide methyltransferase enzymes. Our method successfully determined the presence of CH 3 Br, CH 3 SCN, and CH 3 I in vial headspace.
Faculty Sponsor: Alison Fisher
Discipline: Chemistry
This study investigates the interactions that occur between the protein human serum albumin (HSA) and the ruthenium-based anticancer drug RAPTA-C in physiological conditions with varying pH levels. Changes in fluorescence intensity of the tryptophan residue in HSA were monitored as RAPTA-C was titrated into buffered solutions of HSA. The results from these experiments and the implications of these findings on the role of HSA in drug transport will be discussed.
Faculty Sponsor: Karen Holman
Discipline: Chemistry
To better understand the complex folding patterns of intramolecular quadruplexes with long stems, sequences differing only in the number of guanines (3G vs 4G) were designed. Additionally, FRET pairs were placed in two differing positions such that the relative efficiency of transfer could be used to assess the likelihood of different folding conformations. By pairing UV-Visible absorbance and fluorescence melting, relative stability and potential conformation changes of the quadruplexes were assessed. Unexpectedly, FRET pairs in some positions showed significant alterations in stability relative to the unmodified quadruplexes, hindering the initial comparisons but opening up a new area to study.
Faculty Sponsor: Cooper Battle
Discipline: Chemistry
RAPTA-C, a ruthenium-based anti-cancer drug, has been found to be promising because of its selectivity and low toxicity which could minimize side effects in cancer patients. Research is ongoing to understand which biomolecules are crucial to the mechanism of action for RAPTA-C. One biologically relevant molecule of interest is glutathione (GSH). This study investigates the reaction between RAPTA-C and GSH further using UV-Visible spectroscopy kinetics to determine the effect of pH on the reaction. The reaction between RAPTA-C and GSH was also examined using 1 H and 31 P NMR spectroscopy to investigate the reaction and the structure of the product.
Faculty Sponsor: Karen Holman
Discipline: Chemistry
Quadruplex molecular beacons (QMBs) are promising biosensors for miRNA biomarkers of diseases, including the detection of miR21 for breast cancer. With a goal of optimizing a QMB scaffold, we investigated the impact on FRET pair position & attachment chemistry on the fluorescence increase of the QMB in the presence of the miR21 target sequence. Our results suggest that the attachment of the FRET pair via thymine nucleobases yields stronger fluorescence response than attachment via phosphate diesters. With this we will be able to optimize our sensor design for future use in both diagnostic and therapeutic medical fields.
Faculty Sponsor: Cooper Battle
Discipline: Chemistry
Non-coding RNA known as microRNA (miRNA) are upregulated with the onset of Cancer and pose as a promising biomarker for early detection. Quadruplex molecular beacons for miRNA detection with fluorescence emission resonance transfer (FRET) pairs were synthesized and studied. Thermal denaturation was used to measure the dependence of quadruplex stability on attachment chemistry and position of the FRET pair to optimize a scaffold design for use in detection of miRNAs. We found FRET pairs on thymine bases within loop regions increased quadruplex stability relative to terminal phosphodiester linkages and that mild destabilization with additional thymine bases in loops was observed.
Faculty Sponsor: Cooper Battle
Discipline: Chemistry