A Structural and Biochemical Investigation of Human DNA Polymerase Beta PDF Download
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Author: Andrew James Reed
Publisher:
ISBN:
Category : DNA polymerases
Languages : en
Pages : 244
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Book Description
Adenosine, guanosine, cytidine, and thymidine nucleotides are the building blocks of life and are arranged in distinct combinations to give unique genomic DNA sequences. These DNA encode for all biological molecules and processes and therefore the preservation of genomic integrity is essential for cell growth and viability. To do so the cell has evolved specialized enzymes for efficient and faithful DNA replication. However, genomic DNA is continually damaged by reactive agents occurring from host processes or those encountered through the environment. The resulting DNA damage can act as mutagens causing errors in DNA replication and ultimately leading to disease states or can cause blocks to DNA replication causing replication fork collapse and potentially cell death. To counteract the onslaught of DNA damage cells have evolved a multitude of DNA damage repair mechanisms that can directly revert damaged DNA bases back to the canonical bases, remove and replace single DNA bases (base excision repair), or remove and resynthesize segments of DNA containing damage (nucleotide excision repair and mismatch repair). Base excision repair (BER) in humans is initiated by a damage specific DNA glycosylase that recognizes and removes a single damaged base from DNA, resulting in a product abasic site. This action is followed by cleavage of the abasic site containing DNA strand by apyrimidinic/apurinic endonuclease 1 generating a single-nucleotide gapped DNA substrate with a deoxyribophosphate-aducted 5'-end (5'-dRP). This gap is then filled and the 5'-dRP removed by DNA polymerase ß (Polß) resulting in a nicked DNA substrate. Finally, this nick is ligated by DNA LigaseIII/XRCC1 to complete repair. Here I have investigated the structure and function of Polß to better define its role in DNA repair. Through time-resolved X-ray crystallography and pre-steady-state gel-based kinetics, I have identified and characterized a third divalent metal ion utilized in the synthesis of DNA, determined the mechanism of nucleotide stereoselectivity, and elucidated distinct mechanistic steps following nucleotide incorporation.
Author: Andrew James Reed
Publisher:
ISBN:
Category : DNA polymerases
Languages : en
Pages : 244
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Book Description
Adenosine, guanosine, cytidine, and thymidine nucleotides are the building blocks of life and are arranged in distinct combinations to give unique genomic DNA sequences. These DNA encode for all biological molecules and processes and therefore the preservation of genomic integrity is essential for cell growth and viability. To do so the cell has evolved specialized enzymes for efficient and faithful DNA replication. However, genomic DNA is continually damaged by reactive agents occurring from host processes or those encountered through the environment. The resulting DNA damage can act as mutagens causing errors in DNA replication and ultimately leading to disease states or can cause blocks to DNA replication causing replication fork collapse and potentially cell death. To counteract the onslaught of DNA damage cells have evolved a multitude of DNA damage repair mechanisms that can directly revert damaged DNA bases back to the canonical bases, remove and replace single DNA bases (base excision repair), or remove and resynthesize segments of DNA containing damage (nucleotide excision repair and mismatch repair). Base excision repair (BER) in humans is initiated by a damage specific DNA glycosylase that recognizes and removes a single damaged base from DNA, resulting in a product abasic site. This action is followed by cleavage of the abasic site containing DNA strand by apyrimidinic/apurinic endonuclease 1 generating a single-nucleotide gapped DNA substrate with a deoxyribophosphate-aducted 5'-end (5'-dRP). This gap is then filled and the 5'-dRP removed by DNA polymerase ß (Polß) resulting in a nicked DNA substrate. Finally, this nick is ligated by DNA LigaseIII/XRCC1 to complete repair. Here I have investigated the structure and function of Polß to better define its role in DNA repair. Through time-resolved X-ray crystallography and pre-steady-state gel-based kinetics, I have identified and characterized a third divalent metal ion utilized in the synthesis of DNA, determined the mechanism of nucleotide stereoselectivity, and elucidated distinct mechanistic steps following nucleotide incorporation.
Author: Giovanni Maga
Publisher: World Scientific
ISBN: 9813226420
Category : Science
Languages : en
Pages : 398
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Book Description
Maintenance of the information embedded in the genomic DNA sequence is essential for life. DNA polymerases play pivotal roles in the complex processes that maintain genetic integrity. Besides their tasks in vivo, DNA polymerases are the workhorses in numerous biotechnology applications such as the polymerase chain reaction (PCR), cDNA cloning, next generation sequencing, nucleic acids based diagnostics and in techniques to analyze ancient and otherwise damaged DNA (e.g. for forensic applications). Moreover, some diseases are related to DNA polymerase defects and chemotherapy through inhibition of DNA polymerases is used to fight HIV, Herpes and Hepatitis B and C infections. This book focuses on (i) biology of DNA polymerases, (ii) medical aspects of DNA polymerases and (iii) biotechnological applications of DNA polymerases. It is intended for a wide audience from basic scientists, to diagnostic laboratories, to companies and to clinicians, who seek a better understanding and the practical use of these fascinating enzymes.
Author: Renee Ann Beardslee
Publisher:
ISBN:
Category :
Languages : en
Pages : 145
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Book Description
Author: Kevin Andrew Fiala
Publisher:
ISBN:
Category : DNA damage
Languages : en
Pages :
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Book Description
Abstract: DNA polymerases are the enzymes responsible for the vital task of faithfully duplicating genomes in order to pass on these genetically encoded instructions to their offspring. However, the process of faithfully propagating this information is hindered in all organisms due to endogenous and exogenous agents that damage DNA. While DNA repair mechanisms correct the vast majority of the resulting DNA lesions, unrepaired lesions do persist in the presence of fully functional repair mechanisms. Fortunately cells have evolved a class of promiscuous enzymes known as lesion bypass polymerases that have been shown to bypass DNA lesions that stall the high fidelity replicative DNA polymerases. Here, we have studied two DNA polymerases, human DNA polymerase [lambda] and Sulfolobus solfataricus DNA polymerase IV (Dpo4), which are thought to be involved in the previously mentioned cellular processes of DNA repair and DNA lesion bypass respectively. In the process of establishing a minimal kinetic mechanism for the incorporation of a single nucleotide into undamaged DNA catalyzed by human DNA polymerase [lambda], we discovered a novel mechanism in which one of its non-enzymatic N-terminal domains, the Proline-rich domain, dramatically increases the fidelity of the C-terminal DNA polymerase [beta]-like domain by 10- to 100-fold to the level equivalent to that observed with DNA polymerase [beta], with which it shares 33% sequence identity. Moreover, we have also explored the effects of various structurally distinct DNA substrates on the catalytic efficiency of nucleotide incorporation where we determined the downstream strand and its 5'-phosphate increase the incorporation efficiency by 15- and 11-fold respectively. We have used S. solfataricus Dpo4 as a model Y-family DNA polymerase to elucidate the kinetic mechanism for nucleotide incorporation at both 37 °C and 56 °C, demonstrating that Dpo4 uses an induced-fit mechanism to select and incorporate a correct nucleotide into undamaged DNA independent of reaction temperature. We have also demonstrated using a variety of techniques that Dpo4 predominantly uses two distinct pathways (A-rule and lesion loop-out mechanism) to bypass an abasic site lesion. Taken together, these observations provide compelling evidence for the observation made by Joyce and Benkovic that DNA polymerases defy a unified description.
Author: Ajay Ummat
Publisher:
ISBN:
Category :
Languages : en
Pages : 121
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Book Description
Author: Vern L. Schramm
Publisher: Elsevier
ISBN: 0323149987
Category : Science
Languages : en
Pages : 448
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Book Description
Manganese in Metabolism and Enzyme Function provides an understanding of the various biological roles of the trace levels of manganese found in mammalian systems. This text discusses the nutritional aspects of manganese in mammals. This book is organized into three sections encompassing 19 chapters. Section I discusses the effects of manganese deficiency, including abnormal pancreatic action and reduced pancreatic manganese in humans and laboratory animals. This text considers the criteria for adding manganese to infant formulas that are commercially available. Section II explores the effects of Mn(II) in protein kinases, protein phosphatases, and other enzymes. The reader is introduced to the electron paramagnetic resonance spectroscopic probes of manganese function. Other chapters discuss the extrinsic tag technique used to study the bioavailability of trace elements, such as iron and zinc. Finally, Section III examines the biophysical, biochemical, and physiological properties and uses of manganese. Nutritionists, toxicologists, scientists, and researchers will find this book extremely useful.
Author:
Publisher:
ISBN: 9780815332183
Category : Cells
Languages : en
Pages : 0
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Book Description
Author: Panagiotis A. Tsonis
Publisher: Cambridge University Press
ISBN: 9780521804745
Category : Science
Languages : en
Pages : 300
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Book Description
Table of contents
Author: Irina Artsimovitch
Publisher: Humana
ISBN: 9781493954674
Category : Science
Languages : en
Pages : 0
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Book Description
This volume is designed to be a resource of proven techniques and approaches for probing the activities of bacterial, eukaryotic, and archaeal RNA polymerases. This book features a collection of in vitro and in vivo technologies that will permit researchers to purify and probe the position and stability of RNA polymerase complexes at different points of the transcription cycle, analyze the various translocations and intermolecular movements associated with catalysis, define recruitment strategies, probe the roles of transcription factors in each stage of the cycle, highlight conserved and disparate fidelity mechanisms, analyze the resultant transcripts, and study coordination of the nascent mRNA synthesis by the RNA polymerase and mRNA translation by the ribosome. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubles troubleshooting and avoiding known pitfalls. Practical and timely, Bacterial Transcriptional Controls: Methods and Protocols highlights the breadth and depth of techniques that are likely to continue shaping the transcription community in the future.
Author: Ulrich Hubscher
Publisher: World Scientific
ISBN: 9814465453
Category : Medical
Languages : en
Pages : 338
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Book Description
Maintenance of the information embedded in the genomic DNA sequence is essential for life. DNA polymerases play pivotal roles in the complex processes that maintain genetic integrity. Besides their tasks in vivo, DNA polymerases are the workhorses in numerous biotechnology applications such as the polymerase chain reaction (PCR), cDNA cloning, genome sequencing, nucleic acids-based diagnostics and in techniques to analyze ancient and otherwise damaged DNA. Moreover, some diseases are related to DNA polymerase defects, and chemotherapy through inhibition of DNA polymerases is used to fight HIV, Herpes and Hepatitis B and C infections. We have recently witnessed the discovery of an abundance of novel DNA polymerases in viruses, bacteria, archaea and eukaryotes with specialized properties whose physiological functions are only beginning to be understood. This book summarizes the current knowledge of these fascinating enzymes. It is intended for a wide audience from basic scientists, to diagnostic laboratories and to clinicians who seek a better understanding of these fascinating enzymes.
