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Full-Text Articles in Computational Chemistry
Effect Of Bond Strength Variation And Ionizing Radiation On Mutations In Cytosine-Guanine Islands, Joshua Robert Bedwell, Yan Poniatovskyi, Vola Andrianarijaona
Effect Of Bond Strength Variation And Ionizing Radiation On Mutations In Cytosine-Guanine Islands, Joshua Robert Bedwell, Yan Poniatovskyi, Vola Andrianarijaona
Achieve
Ionizing radiation produces free electrons within cells which then ionizes DNA and has the potential to cause carcinogenic mutations. Cytosine-Guanine (CpG) islands are regions that are rich in cytosine and guanine bases and are common sites of single point mutations and strand breaks. In this study, density function theory (DFT) is used to calculate the potential energy of DNA nucleotide dimers varying bond lengths in five different ionized states. Crossing between two ionized states can be seen in the potential energy curves, indicating the possibility of natural transition between the two states. Potential energy curves are used to determine bond …
Analyzing The Strength Of The Amine Bond Of Guanine Via Potential Curve Analysis: A Computational Approach, Yan Poniatovskyi, Joshua Robert Bedwell, Vola Andrianarijaona
Analyzing The Strength Of The Amine Bond Of Guanine Via Potential Curve Analysis: A Computational Approach, Yan Poniatovskyi, Joshua Robert Bedwell, Vola Andrianarijaona
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The deamination of guanine can be a cause of single point DNA mutations. In this study, the strength of the amine bond was examined using DFT and B3LYP to map out the bond’s potential curves under conditions of various charges being imposed on the molecule. Such an approach yielded a few potential curves that do not exhibit the expected behavior and rather, show crossings in potential energy curves. Discussions regarding the suspected causes of these unexpected behaviors are included in the poster presentation. The Mulliken charge analysis of guanine under these conditions is coherent with the proposition that the deamination …
Investigating Dna Damage Caused By Reactive Oxygen And Nitrogen Species Via Guided-Ion-Beam Scattering And Computational Techniques, Jonathan Benny
Investigating Dna Damage Caused By Reactive Oxygen And Nitrogen Species Via Guided-Ion-Beam Scattering And Computational Techniques, Jonathan Benny
Dissertations, Theses, and Capstone Projects
Among DNA nucleobases, guanine (G) is the primary target for one-electron ionization and oxidation, generating G●+ through various processes, including photooxidation, electrocatalytic oxidation, DNA-binding transition metals, ionizing radiation, and photolysis. This is due to the low adiabatic ionization potential and oxidation potential of guanine. Electron holes from other nucleobases can move to guanine, proving that G●+ production traps oxidative DNA damage. G●+ formation can exacerbate DNA damages and cause secondary reactions from reactive oxygen species (ROS) and reactive nitrogen species (RNS) during pathological processes. The following three projects were conducted using a customized electrospray ionization (ESI) guided-ion-beam tandem mass spectrometer, …
Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan
Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan
Legacy Theses & Dissertations (2009 - 2024)
Computational methods can be used for a wide range of applications, especially regarding DNA and RNA. Interactions such as sugar torsions, receptor-ligand interactions, ligand docking/drug docking, receptor modeling, and drug design are excellent candidates for computational analysis and in silico experiments. The use of molecular dynamics software (GROMACS) coupled with molecular design software (MOE) produce insights that may have been otherwise difficult to assess. All these problems are academic in nature but have practical uses outside of academia. Understanding alternate linkages can lead to antibiotic assays to address potential superbug epidemics. Modeling DNA superstructures can provide insight into how large …