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Chemistry Faculty Publications

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Articles 31 - 60 of 159

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Periplasmic Binding Proteins In Thermophiles: Characterization And Potential Application Of An Arginine-Binding Protein From Thermotoga Maritima: A Brief Thermo-Story, Alessio Ausili, Maria Staiano, Jonathan D. Dattelbaum, Antonio Varriale, Alessandro Capo, Sabato D'Auria Jan 2013

Periplasmic Binding Proteins In Thermophiles: Characterization And Potential Application Of An Arginine-Binding Protein From Thermotoga Maritima: A Brief Thermo-Story, Alessio Ausili, Maria Staiano, Jonathan D. Dattelbaum, Antonio Varriale, Alessandro Capo, Sabato D'Auria

Chemistry Faculty Publications

Arginine-binding protein from the extremophile Thermotoga maritima is a 27.7 kDa protein possessing the typical two-domain structure of the periplasmic binding proteins family. The protein is characterized by a very high specificity and affinity to bind to arginine, also at high temperatures. Due to its features, this protein could be taken into account as a potential candidate for the design of a biosensor for arginine. It is important to investigate the stability of proteins when they are used for biotechnological applications. In this article, we review the structural and functional features of an arginine-binding protein from the extremophile Thermotoga ...


Spectroscopic Analysis Of Polymerization And Exonuclease Proofreading By A High-Fidelity Dna Polymerase During Translesion Dna Synthesis, Babho Devadoss, Irene Lee, Anthony J. Berdis Jan 2013

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 ...


Voltage-Controlled Enzyme-Catalyzed Glucose–Gluconolactone Conversion Using A Field-Effect Enzymatic Detector, Siu Tung Yau, Yan Xu, Yang Song, Ye Feng, Jiapeng Wang Jan 2013

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 ...


Exploring The Role Of A Conserved Class A Residue In The Ω-Loop Of Kpc-2 Β-Lactamase: A Mechanism For Ceftazidime Hydrolysis Sep 2012

Exploring The Role Of A Conserved Class A Residue In The Ω-Loop Of Kpc-2 Β-Lactamase: A Mechanism For Ceftazidime Hydrolysis

Chemistry Faculty Publications

Gram-negative bacteria harboring KPC-2, a class A β-lactamase, are resistant to all β-lactam antibiotics and pose a major public health threat. Arg-164 is a conserved residue in all class A β-lactamases and is located in the solvent-exposed Ω-loop of KPC-2. To probe the role of this amino acid in KPC-2, we performed site-saturation mutagenesis. When compared with wild type, 11 of 19 variants at position Arg-164 in KPC-2 conferred increased resistance to the oxyimino-cephalosporin, ceftazidime (minimum inhibitory concentration; 32→128 mg/liter) when expressed in Escherichia coli. Using the R164S variant of KPC-2 as a representative β-lactamase for more detailed ...


Understanding The Molecular Determinants Of Substrate And Inhibitor Specificities In The Carbapenemase Kpc-2: Exploring The Roles Of Arg220 And Glu276 Aug 2012

Understanding The Molecular Determinants Of Substrate And Inhibitor Specificities In The Carbapenemase Kpc-2: Exploring The Roles Of Arg220 And Glu276

Chemistry Faculty Publications

β-Lactamases are important antibiotic resistance determinants expressed by bacteria. By studying the mechanistic properties of β-lactamases, we can identify opportunities to circumvent resistance through the design of novel inhibitors. Comparative amino acid sequence analysis of class A β-lactamases reveals that many enzymes possess a localized positively charged residue (e.g., R220, R244, or R276) that is critical for interactions with β-lactams and β-lactamase inhibitors. To better understand the contribution of these residues to the catalytic process, we explored the roles of R220 and E276 in KPC-2, a class A β-lactamase that inactivates carbapenems and β-lactamase inhibitors. Our study reveals that ...


Removal Of Uracil By Uracil Dna Glycosylase Limits Pemetrexed Cytotoxicity: Overriding The Limit With Methoxyamine To Inhibit Base Excision Repair, A. D. Bulgar, L. D. Weeks, Y. Miao, S. Yang, Yan Xu, C. Guo, S. Markowitz, N. Oleinick, S. L. Gerson, Lili Liu Jan 2012

Removal Of Uracil By Uracil Dna Glycosylase Limits Pemetrexed Cytotoxicity: Overriding The Limit With Methoxyamine To Inhibit Base Excision Repair, A. D. Bulgar, L. D. Weeks, Y. Miao, S. Yang, Yan Xu, C. Guo, S. Markowitz, N. Oleinick, S. L. Gerson, Lili Liu

Chemistry Faculty Publications

Uracil DNA glycosylase (UDG) specifically removes uracil bases from DNA, and its repair activity determines the sensitivity of the cell to anticancer agents that are capable of introducing uracil into DNA. In the present study, the participation of UDG in the response to pemetrexed-induced incorporation of uracil into DNA was studied using isogenic human tumor cell lines with or without UDG (UDG+/+/UDG−/−). UDG−/− cells were very sensitive to pemetrexed. Cell killing by pemetrexed was associated with genomic uracil accumulation, stalled DNA replication, and catastrophic DNA strand breaks. By contrast, UDG+/+ cells were >10 times more resistant to pemetrexed due ...


Development Of A ‘Clickable’ Non-Natural Nucleotide To Visualize The Replication Of Non-Instructional Dna Lesions, Edward A. Motea, Irene Lee, Anthony J. Berdis Jan 2012

Development Of A ‘Clickable’ Non-Natural Nucleotide To Visualize The Replication Of Non-Instructional Dna Lesions, Edward A. Motea, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The misreplication of damaged DNA is an important biological process that produces numerous adverse effects on human health. This report describes the synthesis and characterization of a non-natural nucleotide, designated 3-ethynyl-5-nitroindolyl-2′-deoxyriboside triphosphate (3-Eth-5-NITP), as a novel chemical reagent that can probe and quantify the misreplication of damaged DNA. We demonstrate that this non-natural nucleotide is efficiently inserted opposite an abasic site, a commonly formed and potentially mutagenic non-instructional DNA lesion. The strategic placement of the ethynyl moiety allows the incorporated nucleoside triphosphate to be selectively tagged with an azide-containing fluorophore using ‘click’ chemistry. This reaction provides a facile way ...


Exploring The Roles Of Nucleobase Desolvation And Shape Complementarity During The Misreplication Of O6-Methylguanine, Delia Chavarria, Andrea Ramos Serrano, Ichiro Hirao, Anthony J. Berdis Sep 2011

Exploring The Roles Of Nucleobase Desolvation And Shape Complementarity During The Misreplication Of O6-Methylguanine, Delia Chavarria, Andrea Ramos Serrano, Ichiro Hirao, Anthony J. Berdis

Chemistry Faculty Publications

O6-methylguanine is a miscoding DNA lesion arising from the alkylation of guanine. This report uses the bacteriophage T4 DNA polymerase as a model to probe the roles hydrogen-bonding interactions, shape/size, and nucleobase desolvation during the replication of this miscoding lesion. This was accomplished by using transient kinetic techniques to monitor the kinetic parameters for incorporating and extending natural and non-natural nucleotides. In general, the efficiency of nucleotide incorporation does not depend on the hydrogen-bonding potential of the incoming nucleotide. Instead, nucleobase hydrophobicity and shape complementarity appear to be the preeminent factors controlling nucleotide incorporation. In addition, shape complementarity plays ...


The Exonuclease Activity Of Hpmc2 Is Required For Transcriptional Regulation Of The Qr Gene And Repair Of Estrogen-Induced Abasic Sites, N. Krishnamurthy, C. R. Ngam, Anthony J. Berdis, M. M. Montano May 2011

The Exonuclease Activity Of Hpmc2 Is Required For Transcriptional Regulation Of The Qr Gene And Repair Of Estrogen-Induced Abasic Sites, N. Krishnamurthy, C. R. Ngam, Anthony J. Berdis, M. M. Montano

Chemistry Faculty Publications

We have previously reported that the expression of antioxidative stress enzymes is upregulated by trans-hydroxytamoxifen (TOT) in breast epithelial cell lines providing protection against estrogen-induced DNA damage. This regulation involves Estrogen Receptor β (ERβ) recruitment to the Electrophile Response Element (EpRE) and a novel protein, human homolog of Xenopus gene which Prevents Mitotic Catastrophe (hPMC2). We have also demonstrated that ERβ and hPMC2 are required for TOT-dependent recruitment of poly (ADP-ribose) polymerase 1 (PARP-1) and Topoisomerase IIβ (Topo IIβ) to the EpRE. Sequence analysis reveals that the C-terminus of hPMC2 encodes a putative exonuclease domain. Using in vitro kinetic assays ...


Epistatic Roles For Pseudomonas Aeruginosa Muts And Dinb (Dna Pol Iv) In Coping With Reactive Oxygen Species-Induced Dna Damage, Laurie H. Sanders, Babho Devadoss, Geraldine V. Raja, Jaime O'Connor, Shengchang Su, Daniel J. Wozniak, Daniel J. Hassett, Anthony J. Berdis, Mark D. Sutton Apr 2011

Epistatic Roles For Pseudomonas Aeruginosa Muts And Dinb (Dna Pol Iv) In Coping With Reactive Oxygen Species-Induced Dna Damage, Laurie H. Sanders, Babho Devadoss, Geraldine V. Raja, Jaime O'Connor, Shengchang Su, Daniel J. Wozniak, Daniel J. Hassett, Anthony J. Berdis, Mark D. Sutton

Chemistry Faculty Publications

Pseudomonas aeruginosa is especially adept at colonizing the airways of individuals afflicted with the autosomal recessive disease cystic fibrosis (CF). CF patients suffer from chronic airway inflammation, which contributes to lung deterioration. Once established in the airways, P. aeruginosa continuously adapts to the changing environment, in part through acquisition of beneficial mutations via a process termed pathoadaptation. MutS and DinB are proposed to play opposing roles in P. aeruginosa pathoadaptation: MutS acts in replication-coupled mismatch repair, which acts to limit spontaneous mutations; in contrast, DinB (DNA polymerase IV) catalyzes error-prone bypass of DNA lesions, contributing to mutations. As part of ...


Her2 Targeted Molecular Mr Imaging Using A De Novo Designed Protein Contrast Agent, Jingjuan Qiao, Shunyi Li, Lixia Wei, Jie Jiang, Robert Long, Hui Mao, Ling Wei, Liya Wang, Hua Yang, Hans E. Grossniklaus, Zhi-Ren Liu, Jenny J. Yang Mar 2011

Her2 Targeted Molecular Mr Imaging Using A De Novo Designed Protein Contrast Agent, Jingjuan Qiao, Shunyi Li, Lixia Wei, Jie Jiang, Robert Long, Hui Mao, Ling Wei, Liya Wang, Hua Yang, Hans E. Grossniklaus, Zhi-Ren Liu, Jenny J. Yang

Chemistry Faculty Publications

The application of magnetic resonance imaging (MRI) to non-invasively assess disease biomarkers has been hampered by the lack of desired contrast agents with high relaxivity, targeting capability, and optimized pharmacokinetics. We have developed a novel MR imaging probe targeting to HER2, a biomarker for various cancer types and a drug target for anti-cancer therapies. This multimodal HER20targeted MR imaging probe integrates a de novo designed protein contrast agent with a high affinity HER2 affibody and a near IR fluorescent dye. Our probe can differentially monitor tumors with different expression levels of HER2 in both human cell lines and xenograft mice ...


Quantifying The Energetic Contributions Of Desolvation And Π-Electron Density During Translesion Dna Synthesis, Edward A. Motea, Irene Lee, Anthony J. Berdis Mar 2011

Quantifying The Energetic Contributions Of Desolvation And Π-Electron Density During Translesion Dna Synthesis, Edward A. Motea, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

This report examines the molecular mechanism by which high-fidelity DNA polymerases select nucleotides during the replication of an abasic site, a non-instructional DNA lesion. This was accomplished by synthesizing several unique 5-substituted indolyl 2′-deoxyribose triphosphates and defining their kinetic parameters for incorporation opposite an abasic site to interrogate the contributions of π-electron density and solvation energies. In general, the Kd, app values for hydrophobic non-natural nucleotides are ∼10-fold lower than those measured for isosteric hydrophilic analogs. In addition, kpol values for nucleotides that contain less π-electron densities are slower than isosteric analogs possessing higher degrees of π-electron density. The ...


Crystallization And Preliminary X-Ray Crystallographic Analysis Of Ligand-Free And Arginine-Bound Forms Of Thermotoga Maritima Arginine-Binding Protein, Alessia Ruggiero, Jonathan D. Dattelbaum, Anna Pennacchio, Luisa Iozzion, Maria Staiano, Matthew S. Luchansky, Bryan S. Der, Rita Berisio, Sabato D'Auria, Luigi Vitagliano Jan 2011

Crystallization And Preliminary X-Ray Crystallographic Analysis Of Ligand-Free And Arginine-Bound Forms Of Thermotoga Maritima Arginine-Binding Protein, Alessia Ruggiero, Jonathan D. Dattelbaum, Anna Pennacchio, Luisa Iozzion, Maria Staiano, Matthew S. Luchansky, Bryan S. Der, Rita Berisio, Sabato D'Auria, Luigi Vitagliano

Chemistry Faculty Publications

The arginine-binding protein from Thermotoga maritima (TmArgBP) is an arginine-binding component of the ATP-binding cassette (ABC) transport system in this hyperthermophilic bacterium. This protein is endowed with an extraordinary stability towards thermal and chemical denaturation. Its structural characterization may provide useful insights for the clarification of structure– stability relationships and for the design of new biosensors. Crystallization trials were set up for both arginine-bound and ligand-free forms of TmArgBP and crystals suitable for crystallographic investigations were obtained for both forms. Ordered crystals of the arginine adduct of TmArgBP could only be obtained by using the detergent LDAO as an additive ...


Dnmt1 Stability Is Regulated By Proteins Coordinating Deubiquitination And Acetylation-Driven Ubiquitination, Zhanwen Du, Jing Song, Yong Wang, Yiqing Zhao, Kishore Guda, Shuming Yang, Hung Ying Kao, Yan Xu, Joseph Willis, Sanford D. Markowitz, David Sedwick, Robert M. Ewing, Zhenghe Wang Nov 2010

Dnmt1 Stability Is Regulated By Proteins Coordinating Deubiquitination And Acetylation-Driven Ubiquitination, Zhanwen Du, Jing Song, Yong Wang, Yiqing Zhao, Kishore Guda, Shuming Yang, Hung Ying Kao, Yan Xu, Joseph Willis, Sanford D. Markowitz, David Sedwick, Robert M. Ewing, Zhenghe Wang

Chemistry Faculty Publications

DNA methyltransferase 1 (DNMT1) is the primary enzyme that maintains DNA methylation. We describe a previously unknown mode of regulation of DNMT1 protein stability through the coordinated action of an array of DNMT1-associated proteins. DNMT1 was destabilized by acetylation by the acetyltransferase Tip60, which triggered ubiquitination by the E3 ligase UHRF1, thereby targeting DNMT1 for proteasomal degradation. In contrast, DNMT1 was stabilized by histone deacetylase 1 (HDAC1) and the deubiquitinase HAUSP (herpes virus–associated ubiquitin-specific protease). Analysis of the abundance of DNMT1 and Tip60, as well as the association between HAUSP and DNMT1, suggested that during the cell cycle the ...


Terminal Deoxynucleotidyl Transferase: The Story Of A Misguided Dna Polymerase, Edward A. Motea, Anthony J. Berdis May 2010

Terminal Deoxynucleotidyl Transferase: The Story Of A Misguided Dna Polymerase, Edward A. Motea, Anthony J. Berdis

Chemistry Faculty Publications

Nearly every DNA polymerase characterized to date exclusively catalyzes the incorporation of mononucleotides into a growing primer using a DNA or RNA template as a guide to direct each incorporation event. There is, however, one unique DNA polymerase designated terminal deoxynucleotidyl transferase that performs DNA synthesis using only single-stranded DNA as the nucleic acid substrate. In this chapter, we review the biological role of this enigmatic DNA polymerase and the biochemical mechanism for its ability to perform DNA synthesis in the absence of a templating strand. We compare and contrast the molecular events for template-independent DNA synthesis catalyzed by terminal ...


Dna Polymerases: Perfect Enzymes For An Imperfect World, Anthony J. Berdis May 2010

Dna Polymerases: Perfect Enzymes For An Imperfect World, Anthony J. Berdis

Chemistry Faculty Publications

This Special Thematic Issue explores the molecular properties of DNA polymerases as extraordinary biological catalysts. In this short introductory chapter, I briefly highlight some of the most important concepts from the articles contained within this Special Issue. The contents of this Special Issue are arranged into distinct sub-categories corresponding to mechanistic studies of faithful DNA polymerization, studies of "specialized" DNA polymerases that function on damaged DNA, and DNA polymerases that are of therapeutic importance against various diseases. Emphasis is placed on understanding the dynamic cellular roles and biochemical functions of DNA polymerases, and how their structure and mechanism impact their ...


Non-Natural Nucleotides As Probes For The Mechanism And Fidelity Of Dna Polymerases, Irene Lee, Anthony J. Berdis May 2010

Non-Natural Nucleotides As Probes For The Mechanism And Fidelity Of Dna Polymerases, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

DNA is a remarkable macromolecule that functions primarily as the carrier of the genetic information of organisms ranging from viruses to bacteria to eukaryotes. The ability of DNA polymerases to efficiently and accurately replicate genetic material represents one of the most fundamental yet complex biological processes found in nature. The central dogma of DNA polymerization is that the efficiency and fidelity of this biological process is dependent upon proper hydrogen-bonding interactions between an incoming nucleotide and its templating partner. However, the foundation of this dogma has been recently challenged by the demonstration that DNA polymerases can effectively and, in some ...


Amino Acid Transport In Thermophiles: Characterization Of An Arginine-Binding Protein In Thermotoga Maritima, Matthew S. Luchansky, Bryan S. Der, Sabato D'Auria, Gabriella Pocsfalvi, Luisa Iozzion, Daniela Marasco, Jonathan D. Dattelbaum Jan 2010

Amino Acid Transport In Thermophiles: Characterization Of An Arginine-Binding Protein In Thermotoga Maritima, Matthew S. Luchansky, Bryan S. Der, Sabato D'Auria, Gabriella Pocsfalvi, Luisa Iozzion, Daniela Marasco, Jonathan D. Dattelbaum

Chemistry Faculty Publications

Members of the periplasmic binding protein superfamily are involved in the selective passage of ligands through bacterial cell membranes. The hyperthermophilic eubacterium Thermotoga maritima was found to encode a highly stable and specific periplasmic arginine-binding protein (TM0593). Following signal sequence removal and overexpression in Escherichia coli, TM0593 was purified by thermoprecipitation and affinity chromatography. The ultra-stable protein with a monomeric molecular weight of 27.7 kDa was found to exist as both a homodimer and homotrimer at appreciable concentrations even under strongly denaturing conditions, with an estimated transition temperature of 116 °C. Its multimeric structure may provide further evidence of ...


Amino Acid Transport In Thermophiles: Characterization Of An Arginine-Binding Protein In Thermotoga Maritima. 2. Molecular Organization And Structural Stability, Andrea Scirè, Anna Marabotti, Maria Staiano, Luisa Iozzion, Matthew S. Luchansky, Bryan S. Der, Jonathan D. Dattelbaum, Fabio Tanfani, Sabato D'Auria Jan 2010

Amino Acid Transport In Thermophiles: Characterization Of An Arginine-Binding Protein In Thermotoga Maritima. 2. Molecular Organization And Structural Stability, Andrea Scirè, Anna Marabotti, Maria Staiano, Luisa Iozzion, Matthew S. Luchansky, Bryan S. Der, Jonathan D. Dattelbaum, Fabio Tanfani, Sabato D'Auria

Chemistry Faculty Publications

ABC transport systems provide selective passage of metabolites across cell membranes and typically require the presence of a soluble binding protein with high specificity to a specific ligand. In addition to their primary role in nutrient gathering, the binding proteins associated with bacterial transport systems have been studied for their potential to serve as design scaffolds for the development of fluorescent protein biosensors. In this work, we used Fourier transform infrared spectroscopy and molecular dynamics simulations to investigate the physicochemical properties of a hyperthermophilic binding protein from Thermotoga maritima. We demonstrated preferential binding for the polar amino acid arginine and ...


Plasticity Of Acquired Secondary Metabolites In Clathria Prolifera (Demospongia: Poecilosclerida): Putative Photoprotective Role Of Carotenoids In A Temperate Intertidal Sponge, Jonathan D. Dattelbaum, Drew Sieg, Malcolm Hill, Chris M. Manieri, Giles Thomson Jan 2010

Plasticity Of Acquired Secondary Metabolites In Clathria Prolifera (Demospongia: Poecilosclerida): Putative Photoprotective Role Of Carotenoids In A Temperate Intertidal Sponge, Jonathan D. Dattelbaum, Drew Sieg, Malcolm Hill, Chris M. Manieri, Giles Thomson

Chemistry Faculty Publications

Several marine sponges sequester high concentrations of carotenoids in their tissues. The diversity of carotenoid compounds has been described in detail for a handful of species, but to date, little attention has been paid to natural variability in the concentration and constituency of carotenoid pools. Also lacking are experimental tests of some of the proposed adaptive benefits of carotenoids to the sponge. To address some of these deficits in our understanding of sponge ecology, we used a combination of analytic chemistry, field surveys, and manipulative experiments to determine what function these compounds might play. Attention was focused on the common ...


4-Hydroxyphenylretinamide (4hpr) Derivatives Regulate Aromatase Activity And Expression In Breast Cancer Cells, Bin Su, Serena M. Mershon, Laura A. Stonerock, Robert W. Curley Jr., Robert W. Brueggemeier Mar 2008

4-Hydroxyphenylretinamide (4hpr) Derivatives Regulate Aromatase Activity And Expression In Breast Cancer Cells, Bin Su, Serena M. Mershon, Laura A. Stonerock, Robert W. Curley Jr., Robert W. Brueggemeier

Chemistry Faculty Publications

Recent studies exhibit that 4-hydroxyphenylretinamide (4HPR) decreases aromatase activity in breast and placental cells. The effect of synthetic 4HPR analogs on aromatase and expression was examined in three breast cancer cell lines. Most derivatives did not decrease cellular aromatase activity. Two of the analogs even stimulated aromatase activity at the transcriptional level. Only one derivative significantly decreased aromatase in all three breast cancer cell lines and also suppressed CYP19 gene expression in one of the cell line. Placental microsomal aromatase assay rule out the possibility that this compound directly inhibits the aromatase enzyme. A non-genomic mechanism in suppression of cellular ...


Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis Oct 2007

Optimization Of Non-Natural Nucleotides For Selective Incorporation Opposite Damaged Dna, Diana Vineyard, Xuemei Zhang, Alison Donnelley, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The promutagenic process known as translesion DNA synthesis reflects the ability of a DNA polymerase to misinsert a nucleotide opposite a damaged DNA template. To study the underlying mechanism of nucleotide selection during this process, we quantified the incorporation of various non-natural nucleotide analogs opposite an abasic site, a non-templating DNA lesion. Our kinetic studies using the bacteriophage T4 DNA polymerase reveal that the π-electron surface area of the incoming nucleotide substantially contributes to the efficiency of incorporation opposite an abasic site. A remaining question is whether the selective insertion of these non-hydrogen-bonding analogs can be achieved through optimization of ...


The Use Of Non-Natural Nucleotides To Probe Template-Independent Dna Synthesis, Anthony J. Berdis, David Mccutcheon Aug 2007

The Use Of Non-Natural Nucleotides To Probe Template-Independent Dna Synthesis, Anthony J. Berdis, David Mccutcheon

Chemistry Faculty Publications

The vast majority of DNA polymerases use the complementary templating strand of DNA to guide each nucleotide incorporation. There are instances, however, in which polymerases can efficiently incorporate nucleotides in the absence of templating information. This process, known as translesion DNA synthesis, can alter the proper genetic code of an organism. To further elucidate the mechanism of template-independent DNA synthesis, we monitored the incorporation of various nucleotides at the “blunt-end” of duplex DNA by the high-fidelity bacteriophage T4 DNA polymerase. Although natural nucleotides are not incorporated at the blunt-end, a limited subset of non-natural indolyl analogues containing extensive π-electron surface ...


Curriculum Vitae, Donald Dudley Clarke Phd Jan 2007

Curriculum Vitae, Donald Dudley Clarke Phd

Chemistry Faculty Publications

Curriculum vitae of Donald Clarke, PhD, professor of chemistry at Fordham University, Rose Hill campus


Effect Of N-Halosucinimides On 5-, 7- And 5,7-8-Quinolinol Sulfonic Acids / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd Jan 2007

Effect Of N-Halosucinimides On 5-, 7- And 5,7-8-Quinolinol Sulfonic Acids / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

8-Quinolinol 5-, 7- and 5,7-sulfonic acids were treated with N-halosuccinimides (NXS) where the halogen atom was chlorine, bromine or iodine under different conditions of solvent, temperature and time. Under neutral or basic conditions the sulfonic acid group was retained while in dilute acid the S03H group was largely displaced by halogen. Excess NXS caused additional electrophilic substitution. Mild hydrolysis of 5-iodo-8-quinolinol- 7-sulfonic acid and 7-iodo-8-quinolinol-5-sulfonic acid with 15% sulfuric acid in acetic acid formed the 5- and 7-iodo-8-quinolinol respectively in high yield


(Review) Green Fluorescent Proteins, Marc Zimmer Jun 2006

(Review) Green Fluorescent Proteins, Marc Zimmer

Chemistry Faculty Publications

Reviews the book:Green Fluorescent Protein: Properties, Applications, and Protocols. Second Edition. Methods of Biochemical Analysis, Volume 47. Edited by Martin Chalfie and Steven R Kain.Green Fluorescent Protein: Properties, Applications, and Protocols. Second Edition. Methods of Biochemical Analysis, Volume 47. Edited by Martin Chalfie and Steven R Kain. Hoboken (New Jersey): Wiley-Interscience. $89.95. xv + 443 p + 24 pl; ill.; index. ISBN: 0–471–73682–1. 2006.


Effect Of Geometry Of Molecules On Penetrability Of Fungal Wall And Antifungal Activity Of Cooper(Ii) Biscomplexes Of Substituted 8-Quinolinols And Their 2-Methyl Analogues / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd Jan 2006

Effect Of Geometry Of Molecules On Penetrability Of Fungal Wall And Antifungal Activity Of Cooper(Ii) Biscomplexes Of Substituted 8-Quinolinols And Their 2-Methyl Analogues / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

It was shown that the lack of fungitoxicity of some classes of square planar compounds can be altered by adding substituents that make the potential toxicant non-planar and/or dipolar. Corrections were made of errors in a number of published papers. Calculations were made to approximate the sizes and shapes of the perforations in the fungal wall


Further Evidence That Geometries Of Fungicides And Pores In Fungal Wall Must Be Compatible To Show Bioavailability / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd Jan 2006

Further Evidence That Geometries Of Fungicides And Pores In Fungal Wall Must Be Compatible To Show Bioavailability / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

Copper(II) biscomplexes of 3-bromo-6-chloro-8- quinolinol and 6-bromo-3-chloro-8-quinolinol were prepared, the long axes ofwhich were 16.8 A and 17.6 A respectively. The long axes of the pores in the walls of the test fungi were determined: A niger (15.0 A), A. oryzae (16.8 A), M verrucaria (17.4 A), T viride (15.0 A). M circinelloides (not determined), and T mentagrophytes (11 .4 A). When the long axis of the copper(II) complex was was shorter or equal to that of the pore, there was fungitoxicity. When the long axis of the complex was longer than ...


Recent Developments Inthe Mechanistic Enzymology Of The Atp-Dependent Lon Protease From Escherichia Coli: Highlights From Kinetic Studies, Irene Lee, Anthony J. Berdis, Carolyn K. Suzuki Jan 2006

Recent Developments Inthe Mechanistic Enzymology Of The Atp-Dependent Lon Protease From Escherichia Coli: Highlights From Kinetic Studies, Irene Lee, Anthony J. Berdis, Carolyn K. Suzuki

Chemistry Faculty Publications

Lon protease, also known as protease La, is one of the simplest ATP-dependent proteases that plays vital roles in maintaining cellular functions by selectively eliminating misfolded, damaged and certain short-lived regulatory proteins. Although Lon is a homo-oligomer, each subunit of Lon contains both an ATPase and a protease active site. This relatively simple architecture compared to other hetero-oligomeric ATP-dependent proteases such as the proteasome makes Lon a useful paradigm for studying the mechanism of ATP-dependent proteolysis. In this article, we survey some recent developments in the mechanistic characterization of Lon with an emphasis on the utilization of pre-steady-state enzyme kinetic ...


Fluorescent Analysis Of Translesion Dna Synthesis By Using A Novel, Non-Natural Nucleotide Analogue, Irene Lee, Anthony J. Berdis Jan 2006

Fluorescent Analysis Of Translesion Dna Synthesis By Using A Novel, Non-Natural Nucleotide Analogue, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

The replication of damaged DNA is a promutagenic process that can lead to disease development. This report evaluates the dynamics of nucleotide incorporation opposite an abasic site, a commonly formed DNA lesion, by using two fluorescent nucleotide analogues, 2-aminopurine deoxyribose triphosphate (2-APTP) and 5-phenylindole deoxyribose triphosphate (5-PhITP). In both cases, the kinetics of incorporation were compared by using a 32 P-radiolabel extension assay versus a fluorescence-quenching assay. Although 2-APTP is efficiently incorporated opposite a templating nucleobase (thymine), the kinetics for incorporation opposite an abasic site are significantly slower. The lower catalytic efficiency hinders its use as a probe to study ...