LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 41

Search options

  1. Book ; Online: The DNA Replication Machinery as Therapeutic Targets

    Gardner, Andrew F. / Kelman, Zvi

    2019  

    Keywords Science: general issues ; Antibacterial drug ; CMG ; DNA polymerase ; DNA Replication ; therapeutic targets
    Size 1 electronic resource (144 pages)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021230814
    ISBN 9782889459278 ; 2889459276
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Book ; Online: DNA Polymerases in Biotechnology

    Gardner, Andrew F. / Kelman, Zvi

    2015  

    Abstract: DNA polymerases are core tools for molecular biology including PCR, whole genome amplification, DNA sequencing and genotyping. Research has focused on discovery of novel DNA polymerases, characterization of DNA polymerase biochemistry and development of ... ...

    Abstract DNA polymerases are core tools for molecular biology including PCR, whole genome amplification, DNA sequencing and genotyping. Research has focused on discovery of novel DNA polymerases, characterization of DNA polymerase biochemistry and development of new replication assays. These studies have accelerated DNA polymerase engineering for biotechnology. For example, DNA polymerases have been engineered for increased speed and fidelity in PCR while lowering amplification sequence bias. Inhibitor resistant DNA polymerase variants enable PCR directly from tissue (i.e. blood). Design of DNA polymerases that efficiently incorporate modified nucleotide have been critical for development of next generation DNA sequencing, synthetic biology and other labeling and detection technologies. The Frontiers in Microbiology Research Topic on DNA polymerases in Biotechnology aims to capture current research on DNA polymerases and their use in emerging technologies
    Keywords Microbiology ; Science (General)
    Size 1 electronic resource (146 p.)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020090921
    ISBN 9782889194551 ; 2889194558
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: Detection and Quantitation of DNA Damage on a Genome-wide Scale Using RADAR-seq.

    Zatopek, Kelly M / Potapov, Vladimir / Ong, Jennifer L / Gardner, Andrew F

    Current protocols

    2022  Volume 2, Issue 11, Page(s) e595

    Abstract: The formation and persistence of DNA damage can impact biological processes such as DNA replication and transcription. To maintain genome stability and integrity, organisms rely on robust DNA damage repair pathways. Techniques to detect and locate DNA ... ...

    Abstract The formation and persistence of DNA damage can impact biological processes such as DNA replication and transcription. To maintain genome stability and integrity, organisms rely on robust DNA damage repair pathways. Techniques to detect and locate DNA damage sites across a genome enable an understanding of the consequences of DNA damage as well as how damage is repaired, which can have key diagnostic and therapeutic implications. Importantly, advancements in technology have enabled the development of high-throughput sequencing-based DNA damage detection methods. These methods require DNA enrichment or amplification steps that limit the ability to quantitate the DNA damage sites. Further, each of these methods is typically tailored to detect only a specific type of damage. RAre DAmage and Repair (RADAR) sequencing is a DNA sequencing workflow that overcomes these limitations and enables detection and quantitation of DNA damage sites in any organism on a genome-wide scale. RADAR-seq works by replacing DNA damage sites with a patch of modified bases that can be directly detected by Pacific Biosciences Single-Molecule Real Time sequencing. Here, we present three protocols that enable detection of thymine dimers and ribonucleotides in bacterial and archaeal genomes. Basic Protocol 1 enables construction of a reference genome required for RADAR-seq analyses. Basic Protocol 2 describes how to locate, quantitate, and compare thymine dimer levels in Escherichia coli exposed to varying amounts of UV light. Basic Protocol 3 describes how to locate, quantitate, and compare ribonucleotide levels in wild-type and ΔRNaseH2 Thermococcus kodakarensis. Importantly, all three protocols provide in-depth steps for data analysis. Together they serve as proof-of-principle experiments that will allow users to adapt the protocols to locate and quantitate a wide variety of DNA damage sites in any organism. © 2022 New England Biolabs. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Constructing a reference genome utilizing SMRT sequencing Basic Protocol 2: Mapping and quantitating genomic thymine dimer formation in untreated versus UV-irradiated E. coli using RADAR-seq Basic Protocol 3: Mapping and quantitating genomic ribonucleotide incorporation in wildtype versus ΔRNaseH2 T. kodakarensis using RADAR-seq.
    MeSH term(s) Pyrimidine Dimers/genetics ; DNA Repair/genetics ; Escherichia coli/genetics ; DNA Damage/genetics ; Ribonucleotides ; Genome, Archaeal
    Chemical Substances Pyrimidine Dimers ; Ribonucleotides
    Language English
    Publishing date 2022-11-14
    Publishing country United States
    Document type Journal Article
    ISSN 2691-1299
    ISSN (online) 2691-1299
    DOI 10.1002/cpz1.595
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article: Editorial: The DNA Replication Machinery as Therapeutic Targets.

    Gardner, Andrew F / Kelman, Zvi

    Frontiers in molecular biosciences

    2019  Volume 6, Page(s) 35

    Language English
    Publishing date 2019-05-21
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2019.00035
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  5. Article ; Online: Molecular basis for proofreading by the unique exonuclease domain of Family-D DNA polymerases.

    Betancurt-Anzola, Leonardo / Martínez-Carranza, Markel / Delarue, Marc / Zatopek, Kelly M / Gardner, Andrew F / Sauguet, Ludovic

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 8306

    Abstract: Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found ... ...

    Abstract Replicative DNA polymerases duplicate entire genomes at high fidelity. This feature is shared among the three domains of life and is facilitated by their dual polymerase and exonuclease activities. Family D replicative DNA polymerases (PolD), found exclusively in Archaea, contain an unusual RNA polymerase-like catalytic core, and a unique Mre11-like proofreading active site. Here, we present cryo-EM structures of PolD trapped in a proofreading mode, revealing an unanticipated correction mechanism that extends the repertoire of protein domains known to be involved in DNA proofreading. Based on our experimental structures, mutants of PolD were designed and their contribution to mismatch bypass and exonuclease kinetics was determined. This study sheds light on the convergent evolution of structurally distinct families of DNA polymerases, and the domain acquisition and exchange mechanism that occurred during the evolution of the replisome in the three domains of life.
    MeSH term(s) Exonucleases/genetics ; Exonucleases/metabolism ; DNA-Directed DNA Polymerase/metabolism ; DNA Replication/genetics ; Catalytic Domain ; Protein Domains
    Chemical Substances Exonucleases (EC 3.1.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2023-12-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-44125-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article ; Online: Overview of Next-Generation Sequencing Technologies.

    Slatko, Barton E / Gardner, Andrew F / Ausubel, Frederick M

    Current protocols in molecular biology

    2018  Volume 122, Issue 1, Page(s) e59

    Abstract: High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding ... ...

    Abstract High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. © 2018 by John Wiley & Sons, Inc.
    MeSH term(s) Genome ; High-Throughput Nucleotide Sequencing/methods ; Humans
    Language English
    Publishing date 2018-05-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ISSN 1934-3647
    ISSN (online) 1934-3647
    DOI 10.1002/cpmb.59
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  7. Article ; Online: Archaeal DNA replication and repair: new genetic, biophysical and molecular tools for discovering and characterizing enzymes, pathways and mechanisms.

    Zatopek, Kelly M / Gardner, Andrew F / Kelman, Zvi

    FEMS microbiology reviews

    2018  Volume 42, Issue 4, Page(s) 477–488

    Abstract: DNA replication and repair are essential biological processes needed for the survival of all organisms. Although these processes are fundamentally conserved in the three domains, archaea, bacteria and eukarya, the proteins and complexes involved differ. ... ...

    Abstract DNA replication and repair are essential biological processes needed for the survival of all organisms. Although these processes are fundamentally conserved in the three domains, archaea, bacteria and eukarya, the proteins and complexes involved differ. The genetic and biophysical tools developed for archaea in the last several years have accelerated the study of DNA replication and repair in this domain. In this review, the current knowledge of DNA replication and repair processes in archaea will be summarized, with emphasis on the contribution of genetics and other recently developed biophysical and molecular tools, including capillary gel electrophoresis, next-generation sequencing and single-molecule approaches. How these new tools will continue to drive archaeal DNA replication and repair research will also be discussed.
    MeSH term(s) Archaea/genetics ; Archaea/physiology ; Archaeal Proteins/metabolism ; DNA Repair ; DNA Replication/genetics ; DNA, Archaeal/genetics
    Chemical Substances Archaeal Proteins ; DNA, Archaeal
    Language English
    Publishing date 2018-06-18
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 283740-7
    ISSN 1574-6976 ; 0168-6445
    ISSN (online) 1574-6976
    ISSN 0168-6445
    DOI 10.1093/femsre/fuy017
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2165: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article ; Online: Pre-steady-state Kinetic Analysis of a Family D DNA Polymerase from Thermococcus sp. 9°N Reveals Mechanisms for Archaeal Genomic Replication and Maintenance.

    Schermerhorn, Kelly M / Gardner, Andrew F

    The Journal of biological chemistry

    2015  Volume 290, Issue 36, Page(s) 21800–21810

    Abstract: Family D DNA polymerases (polDs) have been implicated as the major replicative polymerase in archaea, excluding the Crenarchaeota branch, and bear little sequence homology to other DNA polymerase families. Here we report a detailed kinetic analysis of ... ...

    Abstract Family D DNA polymerases (polDs) have been implicated as the major replicative polymerase in archaea, excluding the Crenarchaeota branch, and bear little sequence homology to other DNA polymerase families. Here we report a detailed kinetic analysis of nucleotide incorporation and exonuclease activity for a Family D DNA polymerase from Thermococcus sp. 9°N. Pre-steady-state single-turnover nucleotide incorporation assays were performed to obtain the kinetic parameters, kpol and Kd, for correct nucleotide incorporation, incorrect nucleotide incorporation, and ribonucleotide incorporation by exonuclease-deficient polD. Correct nucleotide incorporation kinetics revealed a relatively slow maximal rate of polymerization (kpol ∼ 2.5 s(-1)) and especially tight nucleotide binding (Kd (dNTP) ∼ 1.7 μm), compared with DNA polymerases from Families A, B, C, X, and Y. Furthermore, pre-steady-state nucleotide incorporation assays revealed that polD prevents the incorporation of incorrect nucleotides and ribonucleotides primarily through reduced nucleotide binding affinity. Pre-steady-state single-turnover assays on wild-type 9°N polD were used to examine 3'-5' exonuclease hydrolysis activity in the presence of Mg(2+) and Mn(2+). Interestingly, substituting Mn(2+) for Mg(2+) accelerated hydrolysis rates > 40-fold (kexo ≥ 110 s(-1) versus ≥ 2.5 s(-1)). Preference for Mn(2+) over Mg(2+) in exonuclease hydrolysis activity is a property unique to the polD family. The kinetic assays performed in this work provide critical insight into the mechanisms that polD employs to accurately and efficiently replicate the archaeal genome. Furthermore, despite the unique properties of polD, this work suggests that a conserved polymerase kinetic pathway is present in all known DNA polymerase families.
    MeSH term(s) Algorithms ; Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; DNA Replication ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Exonucleases/metabolism ; Genome, Archaeal/genetics ; Hydrolysis/drug effects ; Kinetics ; Magnesium/metabolism ; Magnesium/pharmacology ; Manganese/metabolism ; Manganese/pharmacology ; Nucleotides/genetics ; Nucleotides/metabolism ; Thermococcus/enzymology ; Thermococcus/genetics ; Thermococcus/metabolism
    Chemical Substances Archaeal Proteins ; Nucleotides ; Manganese (42Z2K6ZL8P) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; Exonucleases (EC 3.1.-) ; Magnesium (I38ZP9992A)
    Language English
    Publishing date 2015-07-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M115.662841
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Uc I Zs.108: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article: DNA polymerases in biotechnology.

    Gardner, Andrew F / Kelman, Zvi

    Frontiers in microbiology

    2014  Volume 5, Page(s) 659

    Language English
    Publishing date 2014-12-01
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2014.00659
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: Novel ribonucleotide discrimination in the RNA polymerase-like two-barrel catalytic core of Family D DNA polymerases.

    Zatopek, Kelly M / Alpaslan, Ece / Evans, Thomas C / Sauguet, Ludovic / Gardner, Andrew F

    Nucleic acids research

    2020  Volume 48, Issue 21, Page(s) 12204–12218

    Abstract: Family D DNA polymerase (PolD) is the essential replicative DNA polymerase for duplication of most archaeal genomes. PolD contains a unique two-barrel catalytic core absent from all other DNA polymerase families but found in RNA polymerases (RNAPs). ... ...

    Abstract Family D DNA polymerase (PolD) is the essential replicative DNA polymerase for duplication of most archaeal genomes. PolD contains a unique two-barrel catalytic core absent from all other DNA polymerase families but found in RNA polymerases (RNAPs). While PolD has an ancestral RNA polymerase catalytic core, its active site has evolved the ability to discriminate against ribonucleotides. Until now, the mechanism evolved by PolD to prevent ribonucleotide incorporation was unknown. In all other DNA polymerase families, an active site steric gate residue prevents ribonucleotide incorporation. In this work, we identify two consensus active site acidic (a) and basic (b) motifs shared across the entire two-barrel nucleotide polymerase superfamily, and a nucleotide selectivity (s) motif specific to PolD versus RNAPs. A novel steric gate histidine residue (H931 in Thermococcus sp. 9°N PolD) in the PolD s-motif both prevents ribonucleotide incorporation and promotes efficient dNTP incorporation. Further, a PolD H931A steric gate mutant abolishes ribonucleotide discrimination and readily incorporates a variety of 2' modified nucleotides. Taken together, we construct the first putative nucleotide bound PolD active site model and provide structural and functional evidence for the emergence of DNA replication through the evolution of an ancestral RNAP two-barrel catalytic core.
    MeSH term(s) Amino Acid Sequence ; Archaeal Proteins/chemistry ; Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; Binding Sites ; Catalytic Domain ; Cloning, Molecular ; DNA Replication ; DNA, Archaeal/genetics ; DNA, Archaeal/metabolism ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Gene Expression ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Histidine/chemistry ; Histidine/metabolism ; Kinetics ; Models, Molecular ; Mutation ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Ribonucleotides/chemistry ; Ribonucleotides/genetics ; Ribonucleotides/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Thermococcus/enzymology ; Thermococcus/genetics
    Chemical Substances Archaeal Proteins ; DNA, Archaeal ; Recombinant Proteins ; Ribonucleotides ; Histidine (4QD397987E) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2020-11-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkaa986
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top