Download or read book DNA Helicases and DNA Motor Proteins written by Maria Spies and published by Springer Science & Business Media. This book was released on 2012-11-19 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, a number of groundbreaking structural and mechanistic studies deepened our understanding of helicase mechanisms and established new approaches for their analyses. Many fundamental mechanistic questions ranging from the mechanism of force generation, mechanochemical coupling to distinct mechanisms by which the same enzyme translocates on DNA removing obstacles, unwinds DNA and/or remodels nucleoprotein complexes, however, remain to be answered. It is even less understood how the helicase motors are incorporated into a wide range of genome maintenance and repair machines. The field has reached a stage when the studies of molecular mechanisms and basic biology of helicases can and shall be integrated with the studies of development, cancer and longevity. The objective of this book is to provide the first systematic overview of structure, function and regulation of DNA helicases and related molecular motors. By integrating the knowledge obtained through the diverse technical approaches ranging from single-molecule biophysics to cellular and molecular biological studies the editors aim to provide a unified view on how helicases function in the cell, are regulated in response to different cellular stresses and are integrated into large macromolecular assemblies to form a complex and adaptive living system.
Download or read book Single Stranded DNA Binding Proteins written by James L. Keck and published by Humana Press. This book was released on 2016-05-01 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: This Methods in Molecular Biology book offers techniques for examining fundamental properties of SSBs and for exploiting the biochemical functions of SSBs as in vitro and in vivo reagents. Includes materials lists, protocols, troubleshooting tips and more."
Download or read book Single Stranded DNA Binding Proteins written by Marcos T. Oliveira and published by Humana. This book was released on 2021-05-30 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a comprehensive set of protocols that can be used by any research lab to investigate diverse functional and structural properties of Single Stranded DNA Binding Proteins (SSBs) from eubacterial, archaeal, eukaryotic, mitochondrial and viral systems. Written in the highly successful Methods in 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Single Stranded DNA Binding Proteins aims to be a useful practical guide to researchers to help further their study in this field.
Download or read book Single molecule Studies of Single stranded DNA Binding Proteins Involved in DNA Repair written by Jeffrey Mauritz Schaub and published by . This book was released on 2021 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA Protein Interactions written by G. Geoff Kneale and published by Springer Science & Business Media. This book was released on 2008-02-02 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of protein-nucleic acid interactions is currently one of the most rapidly growing areas of molecular biology. DNA binding proteins are at the very heart of the regulation and control of gene expression, replication, and recombination: Enzymes that recognize and either modify or cleave specific DNA sequences are equally important to the cell. Some of the techniques reported in this volume can be used to identify previously unknown DNA binding proteins from crude cell extracts. Virtually all are capable of giving direct information on the molecular basis of the interaction—the location of the DNA binding site; the strength and specificity of binding; the identities of individual groups on specific bases involved in binding; the specific amino acid residues of the protein that interact with the DNA; or the effects of protein binding on gross conformation and local structure of DNA. The recognition of DNA sequences by proteins is a complex phenomenon, involving specific hydrogen bonding contacts to the DNA bases ("direct readout") and/or interactions with the sugar-phos phate backbone ("indirect readout"). The latter interactions can also be highly specific because of sequence-dependent conformational changes in the DNA. In addition, intercalation of planar aromatic amino acid side-chains between the DNA bases can occur, most notably with single-stranded DNA binding proteins. Furthermore, when bound, many DNA binding proteins induce drastic structural changes in the DNA as an integral part of their function.
Download or read book The Biology of Nonspecific DNA Protein Interactions written by Arnold Revzin and published by CRC Press. This book was released on 1990-08-27 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: This important publication addresses the interactions of proteins with nonspecific binding sites on DNA as they play critical roles in fundamental cellular processes such as transcription, DNA replication, and recombination. The book presents current reviews of the biochemistry of representative nonspecific DNA-protein systems, and of their physiological functions. It includes chapters on the techniques used to characterize the complexes, on their thermodynamic properties, and on the role of nonspecific binding as gene regulatory proteins search for specific target sites on the chromosome. Systems considered include the effects of nonspecific binding in regulation of the lactose operon of Escherichia coli, the T4 bacteriophage gene 32 protein, the E. coli single strand binding (SSB) protein and recA protein, eukaryotic SSB's and histone-DNA complexes. The book presents those proteins displaying multiple modes of DNA binding as participants in more than one cellular process. This monograph combines rigorous descriptions of new findings for these important systems with provocative interpretations of the biological significance of the results. It is of great value to researchers ranging from graduate students to senior scientists in the areas of biochemistry, microbiology and molecular/cell biology.
Download or read book Dissertation Abstracts International written by and published by . This book was released on 2008 with total page 1006 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book DNA Repair Enzymes Structure Biophysics and Mechanism written by and published by Academic Press. This book was released on 2017-07-11 with total page 378 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Repair Enzymes, Part B, Volume 592 is the latest volume in the Methods in Enzymology series and the first part of a thematic that focuses on DNA Repair Enzymes. Topics in this updated volume include MacroBac: New Technologies for Robust and Efficient Large-Scale Production of Recombinant Multiprotein Complexes, Production and Assay of Recombinant Multisubunit Chromatin Remodeling Complexes, Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR, the Use of Single-Cysteine Variants for Trapping Transient States in DNA Mismatch Repair, and Structural Studies of RNases H2 as an Example of Crystal Structure Determination of Protein-Nucleic Acid Complexes. Includes contributions from leading authorities working in enzymology Focuses on DNA repair enzymes Informs and updates on all the latest developments in the field of enzymology
Download or read book Helicase SSB Interactions In Recombination Dependent DNA Repair and Replication written by Christian S. Jordan and published by . This book was released on 2014 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dda, one of three helicases encoded by bacteriophage T4, has been well- characterized biochemically but its biological role remains unclear. It is thought to be involved in origin-dependent replication, recombination-dependent replication, anti- recombination, recombination repair, as well as in replication fork progression past template-bound nucleosomes and RNA polymerase. One of the proteins that most strongly interacts with Dda, Gp32, is the only single-stranded DNA binding protein (SSB) encoded by T4, is essential for DNA replication, recombination, and repair. Previous studies have shown that Gp32 is essential for Dda stimulation of replication fork progression. Our studies show that interactions between Dda and Gp32 play a critical role in regulating replication fork restart during recombination repair. When the leading strand polymerase stalls at a site of ssDNA damage and the lagging strand machinery continues, Gp32 binds the resulting ssDNA gap ahead of the stalled leading strand polymerase. We found that a Gp32 cluster on leading strand ssDNA blocks Dda loading on the lagging strand ssDNA, blocks stimulation of fork progression by Dda, and stimulates Dda to displace the stalled polymerase and the 3' end of the daughter strand. This unwinding generates conditions necessary for polymerase template switching in order to regress the DNA damage-stalled replication fork. Helicase trafficking by Gp32 could play a role in preventing premature fork progression until the events required for error-free translesion DNA synthesis have taken place. Interestingly, we found that Dda helicase activity is strongly stimulated by the N-terminal deletion mutant Gp32-B, suggesting the N-terminal truncation to generate Gp32-B reveals a cryptic helicase stimulatory activity of Gp32 that may be revealed in the context of a moving polymerase, or through direct interactions of Gp32 with other replisome components. Additionally, our findings support a role for Dda-Gp32 interactions in double strand break (DSB) repair by homology-directed repair (HDR), which relies on homologous recombination and the formation of a displacement loop (D-loop) that can initiate DNA synthesis. We examined the D-loop unwinding activity of Dda, Gp41, and UvsW, the D-loop strand extension activity of Gp43 polymerase, and the effect of the helicases and their modulators on D-loop extension. Dda and UvsW, but not Gp41, catalyze D-loop invading strand by DNA unwinding. The relationship between Dda and Gp43 was modulated by the presence of Gp32. Dda D-loop unwinding competes with D- loop extension by Gp43 only in the presence of Gp32, resulting in a decreased frequency of invading strand extension when all three proteins are present. These data suggest Dda functions as an antirecombinase and negatively regulates the replicative extension of D- loops. Invading strand extension is observed in the presence of Dda, indicating that invading strand extension and unwinding can occur in a coordinated manner. The result is a translocating D-loop, called bubble migration synthesis, a hallmark of break-induced repair (BIR) and synthesis dependent strand annealing (SDSA). Gp41 did not unwind D- loops studied and may serve as a secondary helicase loaded subsequent to D-loop processing by Dda. Dda is proposed to be a mixed function helicase that can work both as an antirecombinase and to promote recombination-dependent DNA synthesis, consistent with the notion that Dda stimulates branch migration. These results have implications on the repair of ssDNA damage, DSB repair, and replication fork regulation, which are highly conserved processes sustained in all organisms.
Download or read book DNA Repair and Replication written by and published by Elsevier. This book was released on 2004-12-24 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Repair and Replication contains an up-to-date review of general principles of DNA replication and an overview of the multiple pathways involved in DNA repair. Specific DNA repair pathways, including base-excision repair, light-dependent direct reversal of UV-damage, nucleotide-excision repair, transcription-coupled repair, double-strand break repair, and mismatch repair, are each discussed in separate chapters.Selected Contents: - Base Excision Repair - Eukaryotic DNA Mismatch Repair - Double Strand Break Repair - Functions of DNA Polymerases - Somatic Hypermutation: A Mutational Panacea
Download or read book Mechanism of Homologous Recombination Through Studies of DNA Strand Exchange Recombination Mediator annealing and SsDNA Binding Proteins written by Noriko Kantake and published by . This book was released on 2001 with total page 512 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structure and Function of the Escherichia Coli Ribonuclease HI single stranded DNA binding Protein Complex written by and published by . This book was released on 2016 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: The DNA replication machinery (replisome) is a dynamic multi-protein complex that efficiently achieves the task of genome duplication. However, DNA replication is a vulnerable process to organisms due to the generation of single-stranded (ss) DNA intermediates. In addition, the DNA replication fork must overcome obstacles, such as template damage or frozen protein complexes, that threaten accurate and complete genome duplication. Cells encode specialized ssDNA-binding proteins (SSBs) to bind ssDNA and ensure the genomic template is maintained. The Escherichia coli (E. coli) SSB has also been found to interact with over a dozen proteins involved in the major genome maintenance pathways. The RNase HI enzyme specifically hydrolyzes the RNA in RNA:DNA hybrids and is involved in processing DNA replication lagging strand RNA primers as well as removing transcription-dependent R-loops that block replication fork progression. In this work I have confirmed and characterized the interaction between E. coli RNase HI and SSB. The protein complex is maintained through SSB’s highly conserved C-terminal tail (SSB-Ct). I located the SSB-Ct docking site on RNase HI and identified the binding pocket residues that are essential for maintaining the interaction in vitro. The RNase HI/SSB interaction stimulates RNase HI-mediated RNA:DNA hybrid hydrolysis by lowering the reaction’s Km, suggesting that SSB recruits RNase HI to its substrate. I have tested this hypothesis in cells by incorporating an SSB binding mutant identified from in vitro experiments, rnhAK60E, into the chromosome. The SSB interaction mediates the localization of RNase HI to the DNA replication fork but does not impact the role of RNase HI in lagging strand RNA primer processing. However, combining the point mutant with a Rep (accessory helicase localized to the replication fork) null mutant (rnhAK60E rep) renders cells sensitive to rich media and increases DNA damage. The rnhAK60E rep phenotype is influenced by mutations in RNA Polymerase likely arising from changes to levels of transcription-dependent R-loops. From the data presented in this thesis we have generated a model for the function of the RNase HI/SSB complex that provides a mechanism for localizing the cellular activity of the RNase HI enzyme.
Download or read book DNA Replication Recombination and Repair written by Fumio Hanaoka and published by Springer. This book was released on 2016-01-22 with total page 548 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a comprehensive review of the detailed molecular mechanisms of and functional crosstalk among the replication, recombination, and repair of DNA (collectively called the "3Rs") and the related processes, with special consciousness of their biological and clinical consequences. The 3Rs are fundamental molecular mechanisms for organisms to maintain and sometimes intentionally alter genetic information. DNA replication, recombination, and repair, individually, have been important subjects of molecular biology since its emergence, but we have recently become aware that the 3Rs are actually much more intimately related to one another than we used to realize. Furthermore, the 3R research fields have been growing even more interdisciplinary, with better understanding of molecular mechanisms underlying other important processes, such as chromosome structures and functions, cell cycle and checkpoints, transcriptional and epigenetic regulation, and so on. This book comprises 7 parts and 21 chapters: Part 1 (Chapters 1–3), DNA Replication; Part 2 (Chapters 4–6), DNA Recombination; Part 3 (Chapters 7–9), DNA Repair; Part 4 (Chapters 10–13), Genome Instability and Mutagenesis; Part 5 (Chapters 14–15), Chromosome Dynamics and Functions; Part 6 (Chapters 16–18), Cell Cycle and Checkpoints; Part 7 (Chapters 19–21), Interplay with Transcription and Epigenetic Regulation. This volume should attract the great interest of graduate students, postdoctoral fellows, and senior scientists in broad research fields of basic molecular biology, not only the core 3Rs, but also the various related fields (chromosome, cell cycle, transcription, epigenetics, and similar areas). Additionally, researchers in neurological sciences, developmental biology, immunology, evolutionary biology, and many other fields will find this book valuable.
Download or read book Impact of DNA Structure and Aeropyrum Pernix Single strand DNA Binding Protein on Oxidative Damage to DNA written by Nicholas J. Amato and published by . This book was released on 2013 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA replication is essential to life. To successfully replicate DNA and preserve the genomic code, many replication proteins are coordinated to facilitate the generation of the daughter strands.(1) Unfortunately, the fidelity of DNA replication can be compromised by DNA damage resulting from assault by reactive oxygen species (ROS). It has been shown that elevated levels of ROS during DNA replication result in a prolonged S-phase and if left unrepaired, can lead to apoptosis.(2) Despite the prevalence of DNA repair pathways, DNA damage during replication exists as a significant source of genomic instability.(3) Such DNA damaging events lead to the onset of many diseases and illnesses, such as cancer.(4) Specifically, the participation of single-stranded DNA binding proteins (SSBs) in DNA replication and repair processes are essential to maintaining genomic integrity.(5) Currently, the role of SSBs is well documented, but their functions have not been fully elucidated. One particular role of SSBs that remains highly conjectured is their ability to protect regions of ssDNA from DNA damage. When the SSBs associate with DNA, the sugar-phosphate backbone remains solvent exposed being accessible to DNA damaging agents such as ROS. Thus, we hypothesize that the 2'-deoxyribose moiety of DNA in the SSB-DNA complex is susceptible to hydrogen atom abstraction, of which the DNA damage products are anticipated to be influenced by the presence of the SSB. In order to elucidate the impact of protein binding on DNA damage, a complete understanding of DNA damage in the absence of proteins must be first assessed. This research project establishes an in vitro model system for determining the interplay of DNA-protein binding on C3'-oxidative DNA damage. A C3'-radical precursor was synthesized and incorporated into DNA using automated DNA synthesis. Selective C3'-radical generation was achieved in DNA replication relevant architectures to evaluate the impact of DNA structure and sequence on the fate of the C3'-oxidative damage products. The resulting damage products were quantified using tandem IEX/RP HPLC and identified using MALDI-TOF MS. Next, the thermodynamic and structural effects of the DNA damage lesions generated were characterized using circular dichroism, differential scanning calorimetry and UV melting temperature analysis. Finally, the impact of the oxidative DNA damage lesions on SSB-DNA complex formation were evaluated by fluorescence anisotropy. Together, these results provide the foundation required for determining the impact of SSBs, and other proteins, on oxidative DNA damage.
Download or read book Structural Studies of the Interaction Between the RecQ Helicase Sgs1 and the Single stranded DNA Binding Protein RFA written by Philipp Amsler and published by . This book was released on 2009 with total page 109 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Binding Studies of Human Single stranded Dna Binding and Repair Proteins written by Aishwarya Prakash and published by . This book was released on 2010 with total page 600 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cumulated Index Medicus written by and published by . This book was released on 1990 with total page 1420 pages. Available in PDF, EPUB and Kindle. Book excerpt:
