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Full-Text Articles in Biochemistry
Combining Orthogonal Trna/Synthatase Pair And Amber Codon Suppression To Genetically Encode Oxidative Damage In High Density Lipoproteins, Jaclyn Alatrash, Nicholas Gilliam, Alisha House, Valentin Gogonea
Combining Orthogonal Trna/Synthatase Pair And Amber Codon Suppression To Genetically Encode Oxidative Damage In High Density Lipoproteins, Jaclyn Alatrash, Nicholas Gilliam, Alisha House, Valentin Gogonea
Undergraduate Research Posters 2013
Apolipoprotein A-I (apoA-I) is the main protein constituent of high density lipoprotein (HDL - the “good cholesterol”). Oxidatively damaged apoA-I has been isolated from circulating plasma and atherosclerosis plaque with the amino acid residue tryptophan 72 (W72) of apoA-I identified as a primary oxidation site. ApoA-I designed to include specific oxidized amino acids can be used to further investigate the role of site-specific oxidative damage in atherosclerosis. Genetic encoding of oxidized amino acids through orthogonal tRNA/aminoacyl-tRNA synthetase (aaRS) pairs offers a reliable method for producing site-specific oxidized proteins. Our project involves the generation of Saccharomyces tryptophan-RS mutants for recognition of …
Insights Into The Roles Of Desolvation And Π-Electron Interactions During Dna Polymerization, Edward A. Motea, Irene Lee, Anthony J. Berdis
Insights Into The Roles Of Desolvation And Π-Electron Interactions During Dna Polymerization, Edward A. Motea, Irene Lee, Anthony J. Berdis
Chemistry Faculty Publications
This report describes the use of several isosteric non-natural nucleotides as probes to evaluate the roles of nucleobase shape, size, solvation energies, and π-electron interactions as forces influencing key kinetic steps of the DNA polymerization cycle. Results are provided using representative high- and low-fidelity DNA polymerases. Results generated with the E. coli Klenow fragment reveal that this high-fidelity polymerase utilizes hydrophobic nucleotide analogues with higher catalytic efficiencies compared to hydrophilic analogues. These data support a major role for nucleobase desolvation during nucleotide selection and insertion. In contrast, the low-fidelity HIV-1 reverse transcriptase discriminates against hydrophobic analogues and only tolerates non-natural …
Spectroscopic Analysis Of Polymerization And Exonuclease Proofreading By A High-Fidelity Dna Polymerase During Translesion Dna Synthesis, Babho Devadoss, Irene Lee, Anthony J. Berdis
Spectroscopic Analysis Of Polymerization And Exonuclease Proofreading By A High-Fidelity Dna Polymerase During Translesion Dna Synthesis, Babho Devadoss, Irene Lee, Anthony J. Berdis
Chemistry Faculty Publications
High fidelity DNA polymerases maintain genomic fidelity through a series of kinetic steps that include nucleotide binding, conformational changes, phosphoryl transfer, polymerase translocation, and nucleotide excision. Developing a comprehensive understanding of how these steps are coordinated during correct and pro-mutagenic DNA synthesis has been hindered due to lack of spectroscopic nucleotides that function as efficient polymerase substrates. This report describes the application of a non-natural nucleotide designated 5-naphthyl-indole-2′-deoxyribose triphosphate which behaves as a fluorogenic substrate to monitor nucleotide incorporation and excision during the replication of normal DNA versus two distinct DNA lesions (cyclobutane thymine dimer and an abasic site). Transient …
Voltage-Controlled Enzyme-Catalyzed Glucose–Gluconolactone Conversion Using A Field-Effect Enzymatic Detector, Siu Tung Yau, Yan Xu, Yang Song, Ye Feng, Jiapeng Wang
Voltage-Controlled Enzyme-Catalyzed Glucose–Gluconolactone Conversion Using A Field-Effect Enzymatic Detector, Siu Tung Yau, Yan Xu, Yang Song, Ye Feng, Jiapeng Wang
Chemistry Faculty Publications
The field-effect enzymatic detection (FEED) technique was used to control the kinetics of the enzymatic conversion of glucose to gluconolactone. The glucose–gluconolactone conversion occurring at an enzyme-immobilized electrode, a well-studied process, was confirmed using mass spectrometry. Electrochemical studies showed that the glucose oxidation current depends on the gating voltage VG and the ion concentration of the sample solution. Additionally, the depletion of glucose in the sample also showed a dependence on VG. FEED was used to detect H2O2 on the zepto-molar level in order to show the ultrasensitive detection capability of the technique. These results, while providing evidence for the …