Analytical Chemistry Commons^™

Molecular-Level Studies Of Nanopatterned Biomolecules With Atomic Force Microscopy, Ashley R. Walker

LSU Doctoral Dissertations

Atomic force microscopy (AFM) is an analytical technique in which a tipped probe is gently scanned across the surface in a raster pattern to generate digital images of a sample at the nanoscale. The AFM instrument has three general operational modes, which are contact, non-contact and tapping-mode, that can be used to examine materials at the atomic level. Single-molecular details of biological molecules and other soft organic materials can be captured with minimal denaturation in either ambient or liquid environments when using tapping-mode AFM. In tapping-mode, the probe is driven to oscillate vertically while the tip is scanned across the …

Electrostatic Denaturation Of Dna-Cisplatin Adducts, Eddie Madrigal

Master's Theses

In this thesis, electrochemical approaches are used to determine the properties of deoxyribonucleic acid (DNA) by electrostatic denaturation. The electrochemical routine involves an application of a destabilization potential, an equilibration potential, and a square wave voltammogram (SWV) to monitor the extent of melting. Our method uses a monolayer consisting of thiol modified DNA and mercaptohexanol on a gold electrode. These electrodes are then incubated in a complementary sequence tagged with methylene blue. By using our electrostatic denaturation technique, different parameters are explored, such as surface densities, surface coverages, and ionic strengths. As proof of concept, these techniques were applied toward …

Study Of Reaction Dynamics Of Protonated/Deprotonated And Radical Cations Of Guanine In Nucleobases And Nucleosides: Singlet Oxygen Oxidation, C8-Water Addition, Cross-Linking With Lysine And Base-Pair Dissociation, Yan Sun

Dissertations, Theses, and Capstone Projects

Among the four DNA nucleobases, guanine (G) has the lowest oxidation potential and represents a preferential target for oxidation and ionization. This leads to the formation of guanine radical cation (G^•+) in various oxidative environments. Of the biologically relevant oxidants, electronically excited singlet oxygen (¹O₂) exclusively damages the guanine bases and gives rise to mutagenesis, DNA-protein cross-linking and cellular death. Combining our home-made electrospray ionization (ESI) guided-ion-beam tandem mass spectrometer, with reaction potential surface calculations and kinetics modeling, five projects have been accomplished as described below.

In project 1, the reactions of deuterated water …

Dna Recovery From Handwritten Documents Using A Novel Vacuum Technique, Patrick M. Mclaughlin

Student Theses

Investigations of many crimes such as robberies, kidnappings, and terrorism are often associated with the recovery of a paper document which has been written by the perpetrator. Paper can provide a variety of forensic evidence such as DNA, latent fingermarks, and indented writing. The focus of this study was the collection of probative DNA profiles from the text region of a handwritten note through a vacuum suction device without altering or destroying the document. Collection of DNA evidence was carried out in two separate groups. The first group involved 11 volunteers providing a handwritten note sample with unwashed hands. The …

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 …

Atomic Force Microscopy Tip-Enhanced Laser Ablation, Fan Cao

LSU Doctoral Dissertations

In the present work, an apertureless atomic force microscope (AFM) tip-enhanced laser ablation (TELA) system was developed and investigated. An AFM was coupled to an optical parametric oscillator (OPO) wavelength tunable laser for sample ablation with a submicron sampling size. The AFM was used to image the surface and hold the AFM tip 10 nm above the sample surface. The AFM tip is coated with a layer of gold with a thickness of 35 nm. The incident laser wavelength was tuned in the visible and near-infrared (IR) region and focused on the AFM tip. With the tip-enhancement effect, ablation craters …

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 …

Specific Binding Affinity Of The Non-Catalytic Domain Of Eukaryotic Like Type Ib Topoisomerase Of Vaccinia Virus, Benjamin R. Reed

Dissertations, Theses, and Capstone Projects

Topoisomerases are ubiquitous proteins that alter supercoiling in double stranded DNA (dsDNA) during transcription and replication and. vaccinia and the closely related poxvirus variola virus, at 314 amino acids in length, encode the smallest of the type I topoisomerases(TopIB). TopIB is a two domain protein that recognizes the sequence 5’-T/CCCTT, cleaves at the 3’-end and relaxes supercoiling through rotation. The C-terminal domain (CTD) alone contains the catalytic activity and specificity. Deletion of the N-terminal domain results in a greatly reduced rate of relaxation and rapid dissociation. Biochemical data suggests that the N-terminal domain (NTD) is important for pre-cleavage binding and …

Polymers For Dna Binding, Sue Yuan Li

Seton Hall University Dissertations and Theses (ETDs)

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