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Full-Text Articles in Physical Sciences and Mathematics
Exploration Of Nucleic Acid Hydrogran Bonding Using Molecular Mechanics And Dft Calculations, Simi Kaur
Exploration Of Nucleic Acid Hydrogran Bonding Using Molecular Mechanics And Dft Calculations, Simi Kaur
Biological Sciences
Many recent theoretical and experimental techniques have been developed to probe the structurefunction relationships of complex biomolecules. The roles of RNAs are dependent upon various intricate structural motifs and interactions, including hairpins, pseudoknots, long range territory contacts, bulges and internal loops, that are not easily captured by these methods. We had previously developed an enhanced replica exchange molecular dynamics method that incorporated secondary structure information in the form of distance restraints in order to effectively overcome kinetic barriers and sample conformational space. In several structures, restrained RNA base pairs near large bulges displayed a preference for stacking over hydrogen bonding …
Spontaneous Recombination Of Short Rnas To Increase Length And Complexity In Prebiotically Plausible Conditions, Benedict Arthur Smail
Spontaneous Recombination Of Short Rnas To Increase Length And Complexity In Prebiotically Plausible Conditions, Benedict Arthur Smail
Dissertations and Theses
The RNA World hypothesis is an influential theory of how life arose on earth which posits that the earliest life forms carried out essential activities with RNA catalysts instead of proteins. Substantial evidence to support this theory comes from among others, the fact that the ribosome is a ribozyme, the existence of small RNA catalysts capable of high activity, and self-assembling ribozymes such as the Azoarcus ribozyme. Additional support has been provided by the directed evolution of various ribozymes and the reputed prebiotic synthesis of nucleotides and small RNA oligomers. However, it has long been challenging to show how long …
Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese
Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese
MSU Graduate Theses
Nanoparticles have become very useful as delivery systems in biomedicine. The nanoparticles can be layered with different compounds to produce a vessel for transport of biological materials. Specifically, gold nanoparticles layered with a reducing agent, lysozyme, and polyelectrolytes can be synthesized to transport lysozyme into a cell. However, zinc oxide nanoparticles are cheaper, biocompatible nanoparticles that can be used for the same process. Here in, zinc oxide nanoparticle conjugates were synthesized, modified, and analyzed to be used as a biological material delivery system. The zinc oxide nanoparticles were synthesized using zinc chloride and sodium hydroxide. The particles were then layered …
Infrared Laser Ablation For Biomolecule Sampling, Kelin Wang
Infrared Laser Ablation For Biomolecule Sampling, Kelin Wang
LSU Doctoral Dissertations
In this research, an infrared laser at a wavelength of 3 µm was used to ablate material from tissue sections for biomolecule analysis. Pulsed infrared (IR) irradiation of tissue with a focused laser beam efficiently removed biomolecules, such as proteins, enzymes, DNA, and RNA from tissue sections for further analysis. In a proteomics project, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) was used to determine regions of interest (ROI) for laser ablation. The matrix was then washed off. By overlaying the MSI generated heat-map, the section was sampled using IR laser ablation and custom stage-control software. Two ROI were selected …
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 …