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 Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biophysics of DNA Protein Interactions written by Mark C. Williams and published by Springer Science & Business Media. This book was released on 2010-10-05 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Depite the rapid expansion of the field of biophysics, there are very few books that comprehensively treat specific topics in this area. Recently, the field of single molecule biophysics has developed very quickly, and a few books specifically treating single molecule methods are beginning to appear. However, the promise of single molecule biophysics is to contribute to the understanding of specific fields of biology using new methods. This book would focus on the specific topic of the biophysics of DNA-protein interactions, and would include the use of new approaches, including both bulk methods as well as single molecule methods. This would make the book attractive to anyone working in the general area of DNA-protein interactions, which is of course a much wider market than just single molecule biophysicists or even biophysicists. The subject of the book will be the biophysics of DNA-protein interactions, and will include new methods and results that describe the physical mechanism by which proteins interact with DNA. For example, there has been much recent work on the mechanism by which proteins search for specific binding sites on DNA. A few chapters will be devoted to experiments and theory that shed light on this important problem. We will also cover proteins that alter DNA properties to facilitate interactions important for transcription or replication. Another section of the book will cover the biophysical mechanism by which motor proteins interact with DNA. Finally, we will cover larger protein-DNA complexes, such as replication forks, recombination complexes, DNA repair interactions, and their chromatin context.
Download or read book DNA Repair in Cancer Therapy written by Mark R. Kelley and published by Academic Press. This book was released on 2016-06-07 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Repair and Cancer Therapy: Molecular Targets and Clinical Applications, Second Edition provides a comprehensive and timely reference that focuses on the translational and clinical use of DNA repair as a target area for the development of diagnostic biomarkers and the enhancement of cancer treatment. Experts on DNA repair proteins from all areas of cancer biology research take readers from bench research to new therapeutic approaches. This book provides a detailed discussion of combination therapies, in other words, how the inhibition of repair pathways can be coupled with chemotherapy, radiation, or DNA damaging drugs. Newer areas in this edition include the role of DNA repair in chemotherapy induced peripheral neuropathy, radiation DNA damage, Fanconi anemia cross-link repair, translesion DNA polymerases, BRCA1-BRCA2 pathway for HR and synthetic lethality, and mechanisms of resistance to clinical PARP inhibitors. - Provides a comprehensive overview of the basic and translational research in DNA repair as a cancer therapeutic target - Includes timely updates from the earlier edition, including Fanconi Anemia cross-link repair, translesion DNA polymerases, chemotherapy induced peripheral neuropathy, and many other new areas within DNA repair and cancer therapy - Saves academic, medical, and pharma researchers time by allowing them to quickly access the very latest details on DNA repair and cancer therapy - Assists researchers and research clinicians in understanding the importance of the breakthroughs that are contributing to advances in disease-specific research
Download or read book Single molecule and Ensemble Studies of DNA Replication System written by Cheng Liu and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA replication is one the most important and complex systems in biology. In this dissertation, we first started from ensemble experiments, studying the clamp (PCNA) and the clamp loader (RFC) from the mesophilic archaeon Methanosarcina acetivorans, and then moved to the single-molecule level trying to reconstitute the DNA replication machinery protein by protein. In the first study, by developing a real-time fluorescence assay, we discovered that RFC can assemble a PCNA ring from monomers in solution. A motion-based DNA polymerization assay showed that the PCNA assembled by RFC is functional. This PCNA assembly activity required the ATP-bound conformation of RFC. Our work demonstrated a reverse-chaperoning activity for an AAA+ protein that can act as a template for the assembly of another protein complex. In the second study, by applying fluorescence resonance energy transfer (FRET) to the archaeal replication, we reconstituted part of replication machine, up to four different protein components, at the single-molecule level. We developed a surface-based assay where the loading of the PCNA to the DNA by the RFC was visualized in real time. We discovered an intermediate step likely due to ATP hydrolysis by RFC before PCNA was released on the DNA. Although PCNA itself was not stable as a trimeric ring, once loaded, PCNA remained stably associated with the DNA for hours, allowing us to investigate the subsequent reactions. We found that PCNA prefers to stay near the primer/template junction but still diffuses on both double and single stranded DNA. This is only the second example of direct observation of protein diffusion on single stranded DNA. Diffusion on the single strand, however, is two orders of magnitude slower than on double stranded DNA, and is prevented by cognate single strand binding protein. By adding the DNA polymerase to the loaded clamp, we could follow DNA synthesis by the polymerase-clamp complex by visualizing the motion of the clamp downstream. Interestingly, PCNA frequently slipped back or paused during synthesis, suggesting that spontaneous diffusion of PCNA or its complex with the polymerase is an integral feature even during polymerization. In the last chapter and appendices, some additional works regarding new instrument development and statistical algorithms for programming are also included.
Download or read book Grab Manipulate and Watch Single DNA Molecule Replication written by and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA replication is a critical process intrinsic to the sustenance and propagation of life, involving a symphony of enzymes including helicases, polymerases, and single-stranded DNA binding proteins (SSBs). These enzymes collaboratively ensure the precise duplication of genetic information, a process that, despite significant research, has elements yet to be fully elucidated, especially intermediary steps and the dynamic engagements between replicative proteins. Single-molecule techniques have recently blossomed, offering enhanced insights into the real-time dynamics and interactions of individual molecules in their natural settings, unveiling obscured intermediate steps and enzyme conformational changes. Chapter 1 outlines the thesis's primary aim, elucidating DNA replication mechanisms. Starting with fundamental biological notions, this chapter transitions to discuss the non-equilibrium nature of living systems, emphasizing the role of single-molecule investigations. Such studies have enhanced our understanding of non-equilibrium systems, revealing cellular mechanisms and influencing factors. SSBs are crucial for maintaining genome integrity as they bind to ssDNA and coordinate with various proteins involved in DNA replication, recombination, and repair. Chapter 2 offers a comprehensive overview of recent advances in our understanding of SSBs, as elucidated by single-molecule assays such as optical tweezers, magnetic tweezers, Förster resonance energy transfer, and their combinations. These techniques have provided novel insights into the dynamics of SSB binding to ssDNA and its interactions with other proteins, emphasizing the central role of SSB in modulating the activities of other proteins. Chapter 3 presents the single-molecule observations of the T7 bacteriophage single-stranded DNA-binding protein (gp2.5) binding to ssDNA. Our experiments demonstrate the significant influence of the base sequence, ssDNA conformation, and the acidic terminal domain of T7 gp2.
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 molecule and Ensemble Fluorescence Studies of Single stranded DNA and Replication Proteins written by Mary Cathleen McKinney and published by . This book was released on 2006 with total page 216 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA replication is a complex process involving many proteins that must be performed for a cell to proliferate. In this work, we will study three members of the replication system: single-stranded DNA, single-stranded DNA binding proteins, and the sliding clamp and clamp loader proteins. Fluorescence studies have been widely used to study the properties of biomolecules and here we will use both Fluorescence Polarization Anisotropy (FPA) and Fluorescence Resonance Energy Transfer (FRET) to study these biomolecules. First, we present a method by which single molecule FRET measurements can be used to determine the persistence length of single-stranded DNA. Our results indicate that the persistence length decreases from 3.0nm to 1.5nm as the salt concentration increases from 50mM NaCl to 2M NaCl. Furthermore, we use fluoresce anisotropy and FRET measurements in ensemble studies to examine properties of single stranded DNA binding proteins from archaeal organisms. Our results will show that the Archaea have exploited the single stranded DNA binding fold motif unlike the other domains of life to create a wide variety of proteins that have different binding properties leading to the probable conclusion that many of the proteins area a result of gene duplication and recombination events. Finally, we will examine the properties of the clamp loader protein as it loads a fluorescently labeled clamp to DNA on both the ensemble and single molecule measurements. Our findings show that loading the clamp is a multi-step process with different conformational states that can be observed for the first time at a single molecule level. We also will examine mutations of the clamp loader protein to bring further insight into the not fully understood Methanosarcina acetivorans clamp loader.
Download or read book DNA Repair Part B written by and published by Elsevier. This book was released on 2011-09-21 with total page 613 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume emphasizes the intracellular consequences of DNA damage, describing procedures for analysis of checkpoint responses, DNA repair in vivo, replication fork encounter of DNA damage, as well as biological methods for analysis of mutation production and chromosome rearrangements. It also describes molecular methods for analysis of a number of genome maintenance activities including DNA ligases, helicases, and single-strand binding proteins.*Part B of a 2-part series*Addresses DNA maintenance enzymes*Discusses damage signaling*Presents In vivo analysis of DNA repair*Covers mutation and chromosome rearrangements
Download or read book Single Molecule Analysis written by Erwin J. G. Peterman and published by Humana Press. This book was released on 2011-09-15 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt: Life scientists believe that life is driven, directed, and shaped by biomolecules working on their own or in concert. It is only in the last few decades that technological breakthroughs in sensitive fluorescence microscopy and single-molecule manipulation techniques have made it possible to observe and manipulate single biomolecules and measure their individual properties. The methodologies presented in Single Molecule Techniques: Methods and Protocols are being applied more and more to the study of biologically relevant molecules, such as DNA, DNA-binding proteins, and motor proteins, and are becoming commonplace in molecular biophysics, biochemistry, and molecular and cell biology. The aim of Single Molecule Techniques: Methods and Protocols is to provide a broad overview of single-molecule approaches applied to biomolecules on the basis of clear and concise protocols, including a solid introduction to the most widely used single-molecule techniques, such as optical tweezers, single-molecule fluorescence tools, atomic force microscopy, magnetic tweezers, and tethered particle motion. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Single Molecule Techniques: Methods and Protocols serves as an ideal guide to scientists of all backgrounds and provides a broad and thorough overview of the exciting and still-emerging field of single-molecule biology.
Download or read book Viral Replication Enzymes and their Inhibitors Part A written by and published by Academic Press. This book was released on 2021-10-23 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: Viral Replication Enzymes and their Inhibitors Part A, Volume 49, the latest release in the Enzymes series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of related topics. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in The Enzymes series
Download or read book Single molecule Studies Reveal the Dynamics of DNA Repair and Transcription associated Proteins written by Yoori Kim and published by . This book was released on 2018 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: Intrinsically disordered regions (IDR) are protein segments that lack a defined tertiary structure. IDRs are enriched in eukaryotic chromatin-binding proteins, where they modulate protein-DNA and protein-protein interactions. In this thesis, I probe the function(s) of IDRs via two case studies: the yeast mismatch repair (MMR) protein Mlh1- Pms1 and transcription factors (TFs) derived from C. albicans, a pathogenic yeast. Using single-molecule DNA curtain assays, I demonstrate novel roles for IDRs in promoting facilitated diffusion of Mlh1-Pms1 on DNA. IDRs improve Mlh1-Pms1’s ability to bypass a single nucleosome and to navigate dense nucleosome arrays that resemble chromatin. Moreover, these IDRs are critical for the Mlh1-Pms1 ATPase activity and also for nicking of the DNA substrate. I propose that conformational changes in the Mlh1-Pms1 IDRs alter DNA interactions and the nucleolytic activity of neighboring structured domains. I also examine the dynamics of PCNA, another essential MMR factor, in the context of trinucleotide repeat (TNR) instability. I show that Replication Factor C preferentially loads PCNA onto (CAG)13 structures. The (CAG)13 repeat captures the loaded PCNA and prevents PCNA from diffusing. Lastly, I reveal a novel role for IDRs in DNA condensation by studying Efg1, a TF that regulates a cell-type switching network in C. albicans. Efg1 encodes a specific IDR of low complexity, referred to as the prion-like domain (PrLD). I show that the PrLD is critical for the DNA condensation and recruiting other PrLD-containing TFs, wherein nucleosomes regulate the TF-DNA dynamics. I propose a model where transcription factors become concentrated via phase separation and bring gene regulatory elements together to promote gene activation. Overall, this study provides mechanistic insights into the functions of IDRs in the dynamic behavior of DNA-binding proteins
Download or read book Structural and Biophysical Studies of Single stranded DNA Binding Proteins and DnaB Helicases Proteins Involved in DNA Replication and Repair written by Vinu Johnson and published by . This book was released on 2007 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: The processes of DNA replication, repair and recombination have been studied for many years using model systems such as E. coli. One key aspect of DNA replication is the role of proteins at the replication fork. It is important to understand the interactions of these proteins with the other proteins involved in the process or with a DNA substrate. In PART I of this dissertation, studies of the Archaeal Aeropyrum pernix and Archaeoglobus fulgidus single-stranded DNA binding protein are presented. Archaea are more closely related to eukaryotes than the commonly studied E. coli model system. The SSB proteins have an involvement in Okazaki fragment processing. The FEN-1 enzyme removes DNA flaps that are 3 to 5 nucleotides long. If the length of the flap is more than 5 to 7 nucleotides, two other proteins are then involved in the removal of these flaps, the SSB protein that binds to the flap, and dna2 needed to shorten the flap. Using PCR and molecular cloning techniques and protein chemistry, milligram quantities of the purified Ape SSB protein were obtained. Preliminary attempts to crystallize the full length protein failed, most likely due to highly flexible C-terminal region. To overcome this problem, a truncated version of the protein was prepared. The truncated protein crystallized in two different crystallization conditions. One produced beautiful large 1mm hexagonal crystals that appeared twinned on diffraction. The other crystal form, rod shaped small crystals, diffracted to almost 1.6 [alpha]. The structure of the truncated protein was solved using molecular replacement with an already known SSB protein from the species Sulfolobus sulfataricus. Biophysical studies, Dynamic Light Scattering (DLS) and Fluorescence Anisotropy, have been carried out to characterize the Ape SSB protein. In PART II, work done on DNA helicases (dnaB) from different organisms is presented. Expression and purification protocols for Vibrio cholerae dnaB were successfully established and crystal screens set up. Few hits were obtained in the screens but expansion of some of the conditions did not yield any crystals. Cloning, expression and purification protocols were established for Yersinia pestis dnaB and Helicobacter pylori dnaB.
Download or read book Single molecule Studies of DNA binding Proteins in Live Bacteria written by Mathew Stracy and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Understanding DNA written by Chris R. Calladine and published by Elsevier. This book was released on 2004-03-13 with total page 349 pages. Available in PDF, EPUB and Kindle. Book excerpt: The functional properties of any molecule are directly related to, and affected by, its structure. This is especially true for DNA, the molecular that carries the code for all life on earth. The third edition of Understanding DNA has been entirely revised and updated, and expanded to cover new advances in our understanding. It explains, step by step, how DNA forms specific structures, the nature of these structures and how they fundamentally affect the biological processes of transcription and replication. Written in a clear, concise and lively fashion, Understanding DNA is essential reading for all molecular biology, biochemistry and genetics students, to newcomers to the field from other areas such as chemistry or physics, and even for seasoned researchers, who really want to understand DNA. - Describes the basic units of DNA and how these form the double helix, and the various types of DNA double helix - Outlines the methods used to study DNA structure - Contains over 130 illustrations, some in full color, as well as exercises and further readings to stimulate student comprehension
Download or read book DNA Repair written by and published by Academic Press. This book was released on 2019-10-16 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA Repair, Volume 45 in The Enzymes series highlights new advances in the field, with this new volume presenting interesting chapters on DNA polymerase beta and other gap-filling enzymes in mammalian base excision repair, Translesion polymerases, mechanism and function, The Rev1-Pol? Mutasome: Structure and Interactions in Translesion Synthesis, Challenges for base excision repair enzymes: acquiring access to damaged DNA in chromatin Nucleotide excision repair, DNA damage recognition mechanisms in mammalian nucleotide excision repair, Advances in understanding DNA mismatch repair, and more. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in The Enzymes series
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.
