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  1. Article ; Online: Bacterial DnaB helicase interacts with the excluded strand to regulate unwinding.

    Carney, Sean M / Gomathinayagam, Shivasankari / Leuba, Sanford H / Trakselis, Michael A

    The Journal of biological chemistry

    2017  Volume 292, Issue 46, Page(s) 19001–19012

    Abstract: Replicative hexameric helicases are thought to unwind duplex DNA by steric exclusion (SE) where one DNA strand is encircled by the hexamer and the other is excluded from the central channel. However, interactions with the excluded strand on the exterior ... ...

    Abstract Replicative hexameric helicases are thought to unwind duplex DNA by steric exclusion (SE) where one DNA strand is encircled by the hexamer and the other is excluded from the central channel. However, interactions with the excluded strand on the exterior surface of hexameric helicases have also been shown to be important for DNA unwinding, giving rise to the steric exclusion and wrapping (SEW) model. For example, the archaeal
    MeSH term(s) Amino Acid Sequence ; DNA, Bacterial/chemistry ; DNA, Bacterial/metabolism ; DnaB Helicases/chemistry ; DnaB Helicases/metabolism ; Escherichia coli/chemistry ; Escherichia coli/metabolism ; Fluorescence Resonance Energy Transfer ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Sequence Alignment ; Static Electricity
    Chemical Substances DNA, Bacterial ; dnaB protein, E coli (EC 3.6.1.-) ; DnaB Helicases (EC 3.6.4.12)
    Language English
    Publishing date 2017-09-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M117.814178
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Optimal practices for surface-tethered single molecule total internal reflection fluorescence resonance energy transfer analysis.

    Fagerburg, Matt V / Leuba, Sanford H

    Methods in molecular biology (Clifton, N.J.)

    2011  Volume 749, Page(s) 273–289

    Abstract: Single molecule fluorescence microscopy can be used to follow the mechanics of molecular biology processes in real time. However, many factors, from flow cell preparation to improper data analysis can negatively impact single molecule fluorescence ... ...

    Abstract Single molecule fluorescence microscopy can be used to follow the mechanics of molecular biology processes in real time. However, many factors, from flow cell preparation to improper data analysis can negatively impact single molecule fluorescence resonance energy transfer (smFRET) experiments. Here, we describe some best practices for ensuring that smFRET data are of the highest quality. In addition to instrumentation, we describe sample preparation and data analysis.
    MeSH term(s) Fluorescence Resonance Energy Transfer/instrumentation ; Fluorescence Resonance Energy Transfer/methods ; Micromanipulation/methods ; Nanotechnology/methods ; Surface Properties
    Language English
    Publishing date 2011-06-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-61779-142-0_19
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Dynamics of DNA nicking and unwinding by the RepC-PcrA complex.

    Carrasco, Carolina / Pastrana, Cesar L / Aicart-Ramos, Clara / Leuba, Sanford H / Khan, Saleem A / Moreno-Herrero, Fernando

    Nucleic acids research

    2019  Volume 48, Issue 4, Page(s) 2013–2025

    Abstract: The rolling-circle replication is the most common mechanism for the replication of small plasmids carrying antibiotic resistance genes in Gram-positive bacteria. It is initiated by the binding and nicking of double-stranded origin of replication by a ... ...

    Abstract The rolling-circle replication is the most common mechanism for the replication of small plasmids carrying antibiotic resistance genes in Gram-positive bacteria. It is initiated by the binding and nicking of double-stranded origin of replication by a replication initiator protein (Rep). Duplex unwinding is then performed by the PcrA helicase, whose processivity is critically promoted by its interaction with Rep. How Rep and PcrA proteins interact to nick and unwind the duplex is not fully understood. Here, we have used magnetic tweezers to monitor PcrA helicase unwinding and its relationship with the nicking activity of Staphylococcus aureus plasmid pT181 initiator RepC. Our results indicate that PcrA is a highly processive helicase prone to stochastic pausing, resulting in average translocation rates of 30 bp s-1, while a typical velocity of 50 bp s-1 is found in the absence of pausing. Single-strand DNA binding protein did not affect PcrA translocation velocity but slightly increased its processivity. Analysis of the degree of DNA supercoiling required for RepC nicking, and the time between RepC nicking and DNA unwinding, suggests that RepC and PcrA form a protein complex on the DNA binding site before nicking. A comprehensive model that rationalizes these findings is presented.
    MeSH term(s) Bacterial Proteins/genetics ; DNA Breaks, Single-Stranded/drug effects ; DNA Helicases/genetics ; DNA Replication/genetics ; DNA-Binding Proteins/genetics ; Drug Resistance, Bacterial/genetics ; Geobacillus stearothermophilus/drug effects ; Geobacillus stearothermophilus/genetics ; Geobacillus stearothermophilus/pathogenicity ; Plasmids/drug effects ; Plasmids/genetics ; Protein Binding/genetics ; Protein Interaction Domains and Motifs/genetics ; Staphylococcus aureus/drug effects ; Staphylococcus aureus/genetics ; Staphylococcus aureus/pathogenicity ; Tetracycline/pharmacology ; Trans-Activators/genetics
    Chemical Substances Bacterial Proteins ; DNA-Binding Proteins ; RepC protein, Staphylococcus aureus ; Trans-Activators ; pcrA protein, Bacteria ; replication initiator protein ; DNA Helicases (EC 3.6.4.-) ; Tetracycline (F8VB5M810T)
    Language English
    Publishing date 2019-11-02
    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/gkz1200
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  4. Article: Jörg Langowski: his scientific legacy and the future it promises.

    Chirico, Giuseppe / Gansen, Alexander / Leuba, Sanford H / Olins, Ada L / Olins, Donald E / Smith, Jeremy C / Tóth, Katalin

    BMC biophysics

    2018  Volume 11, Page(s) 5

    Abstract: Background: With the passing of Jörg Langowski 6 May 2017 in a sailplane accident, the scientific community was deprived of a strident and effective voice for DNA and chromatin molecular and computational biophysics, for open access publishing and for ... ...

    Abstract Background: With the passing of Jörg Langowski 6 May 2017 in a sailplane accident, the scientific community was deprived of a strident and effective voice for DNA and chromatin molecular and computational biophysics, for open access publishing and for the creation of effective scientific research networks.
    Methods: Here, after reviewing some of Jörg's key research contributions and ideas, we offer through the personal remembrance of his closest collaborators, a deep analysis of the major results of his research and the future directions they have engendered.
    Conclusions: The legacy of Jörg Langowski has been to propel a way of viewing biological function that considers living systems as dynamic and in three dimensions. This physical view of biology that he pioneered is now, finally, becoming established also because of his great effort.
    Language English
    Publishing date 2018-07-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2600208-5
    ISSN 2046-1682
    ISSN 2046-1682
    DOI 10.1186/s13628-018-0045-1
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  5. Book: Chromatin structure and dynamics

    Leuba, Sanford H / Zlatanova, Jordanka

    state-of-the-art

    (New comprehensive biochemistry ; 39)

    2004  

    Author's details ed. J. Zlatanova; S.H. Leuba
    Series title New comprehensive biochemistry ; 39
    Language English
    Size XXV, 507 S, Ill., graf. Darst
    Edition 1. ed
    Publisher Elsevier
    Publishing place Amsterdam u.a.
    Document type Book
    Note Literaturangaben
    ISBN 0444515941 ; 044451595X ; 9780444515940 ; 9780444515957
    Database Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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  6. Article ; Online: Mechanism of allosteric inhibition of HIV-1 reverse transcriptase revealed by single-molecule and ensemble fluorescence.

    Schauer, Grant D / Huber, Kelly D / Leuba, Sanford H / Sluis-Cremer, Nicolas

    Nucleic acids research

    2014  Volume 42, Issue 18, Page(s) 11687–11696

    Abstract: Non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are routinely used to treat HIV-1 infection, yet their mechanism of action remains unclear despite intensive investigation. In this study, we developed complementary single-molecule ... ...

    Abstract Non-nucleoside reverse transcriptase (RT) inhibitors (NNRTIs) are routinely used to treat HIV-1 infection, yet their mechanism of action remains unclear despite intensive investigation. In this study, we developed complementary single-molecule fluorescence and ensemble fluorescence anisotropy approaches to discover how NNRTIs modulate the intra-molecular conformational changes and inter-molecular dynamics of RT-template/primer (T/P) and RT-T/P-dNTP complexes. We found that NNRTI binding to RT induces opening of the fingers and thumb subdomains, which increases the dynamic sliding motion of the enzyme on the T/P and reduces dNTP binding affinity. Further, efavirenz promotes formation of the E138-K101 salt bridge between the p51 and p66 subunits of RT, which contributes to opening of the thumb/fingers subdomains. Engineering a more polar salt bridge between p51 and p66 resulted in even greater increases in the thumb/fingers opening, RT sliding, dNTP binding disruption and in vitro and in vivo RT inhibition than were observed with wild-type RT. We also observed that K103N, a clinically relevant NNRTI resistance mutation, does not prevent binding between efavirenz and RT-T/P but instead allows formation of a stable and productive RT-T/P-dNTP complex, possibly through disruption of the E138-K101 salt bridge. Collectively, these data describe unique structure-activity-resistance relationships that could be exploited for drug development.
    MeSH term(s) Alkynes ; Allosteric Regulation ; Benzoxazines/pharmacology ; Cyclopropanes ; DNA Primers ; Deoxyribonucleotides/metabolism ; Fluorescence Polarization ; HIV Reverse Transcriptase/antagonists & inhibitors ; HIV Reverse Transcriptase/chemistry ; HIV Reverse Transcriptase/genetics ; HIV Reverse Transcriptase/metabolism ; Mutation ; Protein Subunits/chemistry ; Reverse Transcriptase Inhibitors/pharmacology ; Templates, Genetic
    Chemical Substances Alkynes ; Benzoxazines ; Cyclopropanes ; DNA Primers ; Deoxyribonucleotides ; Protein Subunits ; Reverse Transcriptase Inhibitors ; reverse transcriptase, Human immunodeficiency virus 1 (EC 2.7.7.-) ; HIV Reverse Transcriptase (EC 2.7.7.49) ; efavirenz (JE6H2O27P8)
    Language English
    Publishing date 2014-09-17
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    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/gku819
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  7. Article ; Online: Force and twist dependence of RepC nicking activity on torsionally-constrained DNA molecules.

    Pastrana, Cesar L / Carrasco, Carolina / Akhtar, Parvez / Leuba, Sanford H / Khan, Saleem A / Moreno-Herrero, Fernando

    Nucleic acids research

    2016  Volume 44, Issue 18, Page(s) 8885–8896

    Abstract: Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA ... ...

    Abstract Many bacterial plasmids replicate by an asymmetric rolling-circle mechanism that requires sequence-specific recognition for initiation, nicking of one of the template DNA strands and unwinding of the duplex prior to subsequent leading strand DNA synthesis. Nicking is performed by a replication-initiation protein (Rep) that directly binds to the plasmid double-stranded origin and remains covalently bound to its substrate 5'-end via a phosphotyrosine linkage. It has been proposed that the inverted DNA sequences at the nick site form a cruciform structure that facilitates DNA cleavage. However, the role of Rep proteins in the formation of this cruciform and the implication for its nicking and religation functions is unclear. Here, we have used magnetic tweezers to directly measure the DNA nicking and religation activities of RepC, the replication initiator protein of plasmid pT181, in plasmid sized and torsionally-constrained linear DNA molecules. Nicking by RepC occurred only in negatively supercoiled DNA and was force- and twist-dependent. Comparison with a type IB topoisomerase in similar experiments highlighted a relatively inefficient religation activity of RepC. Based on the structural modeling of RepC and on our experimental evidence, we propose a model where RepC nicking activity is passive and dependent upon the supercoiling degree of the DNA substrate.
    MeSH term(s) DNA Breaks, Single-Stranded ; DNA Helicases/chemistry ; DNA Helicases/metabolism ; DNA Replication ; Models, Biological ; Plasmids/genetics ; Protein Binding ; Protein Multimerization ; Recombinant Proteins ; Trans-Activators/chemistry ; Trans-Activators/metabolism
    Chemical Substances Recombinant Proteins ; Trans-Activators ; replication initiator protein ; DNA Helicases (EC 3.6.4.-)
    Language English
    Publishing date 2016-08-03
    Publishing country England
    Document type Journal Article
    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/gkw689
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Robust methods for purification of histones from cultured mammalian cells with the preservation of their native modifications.

    Rodriguez-Collazo, Pedro / Leuba, Sanford H / Zlatanova, Jordanka

    Nucleic acids research

    2009  Volume 37, Issue 11, Page(s) e81

    Abstract: Post-translational modifications (PTMs) of histones play a role in modifying chromatin structure for DNA-templated processes in the eukaryotic nucleus, such as transcription, replication, recombination and repair; thus, histone PTMs are considered major ... ...

    Abstract Post-translational modifications (PTMs) of histones play a role in modifying chromatin structure for DNA-templated processes in the eukaryotic nucleus, such as transcription, replication, recombination and repair; thus, histone PTMs are considered major players in the epigenetic control of these processes. Linking specific histone PTMs to gene expression is an arduous task requiring large amounts of highly purified and natively modified histones to be analyzed by various techniques. We have developed robust and complementary procedures, which use strong protein denaturing conditions and yield highly purified core and linker histones from unsynchronized proliferating, M-phase arrested and butyrate-treated cells, fully preserving their native PTMs without using enzyme inhibitors. Cell hypotonic swelling and lysis, nuclei isolation/washing and chromatin solubilization under mild conditions are bypassed to avoid compromising the integrity of histone native PTMs. As controls for our procedures, we tested the most widely used conventional methodologies and demonstrated that they indeed lead to drastic histone dephosphorylation. Additionally, we have developed methods for preserving acid-labile histone modifications by performing non-acid extractions to obtain highly purified H3 and H4. Importantly, isolation of histones H3, H4 and H2A/H2B is achieved without the use of HPLC. Functional supercoiling assays reveal that both hyper- and hypo-phosphorylated histones can be efficiently assembled into polynucleosomes. Notably, the preservation of fully phosphorylated mitotic histones and their assembly into polynucleosomes should open new avenues to investigate an important but overlooked question: the impact of mitotic phosphorylation in chromatin structure and function.
    MeSH term(s) Acetylation ; Animals ; Cell Line ; Chemical Fractionation/methods ; Chromatography, Agarose ; Histones/isolation & purification ; Histones/metabolism ; Humans ; Mice ; Mitosis ; Molecular Chaperones/metabolism ; Nucleosomes/metabolism ; Phosphorylation ; Protein Processing, Post-Translational ; Sepharose/analogs & derivatives ; Sodium Chloride/chemistry ; Urea/chemistry
    Chemical Substances Histones ; Molecular Chaperones ; Nucleosomes ; Sodium Chloride (451W47IQ8X) ; thiopropyl-sepharose (68517-67-9) ; Urea (8W8T17847W) ; Sepharose (9012-36-6)
    Language English
    Publishing date 2009-05-13
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    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/gkp273
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  9. Article ; Online: Steric exclusion and wrapping of the excluded DNA strand occurs along discrete external binding paths during MCM helicase unwinding.

    Graham, Brian W / Schauer, Grant D / Leuba, Sanford H / Trakselis, Michael A

    Nucleic acids research

    2011  Volume 39, Issue 15, Page(s) 6585–6595

    Abstract: The minichromosome maintenance (MCM) helicase complex is essential for the initiation and elongation of DNA replication in both the eukaryotic and archaeal domains. The archaeal homohexameric MCM helicase from Sulfolobus solfataricus serves as a model ... ...

    Abstract The minichromosome maintenance (MCM) helicase complex is essential for the initiation and elongation of DNA replication in both the eukaryotic and archaeal domains. The archaeal homohexameric MCM helicase from Sulfolobus solfataricus serves as a model for understanding mechanisms of DNA unwinding. In this report, the displaced 5'-tail is shown to provide stability to the MCM complex on DNA and contribute to unwinding. Mutations in a positively charged patch on the exterior surface of the MCM hexamer destabilize this interaction, alter the path of the displaced 5'-tail DNA and reduce unwinding. DNA footprinting and single-molecule fluorescence experiments support a previously unrecognized wrapping of the 5'-tail. This mode of hexameric helicase DNA unwinding is termed the steric exclusion and wrapping (SEW) model, where the 3'-tail is encircled by the helicase while the displaced 5'-tail wraps around defined paths on the exterior of the helicase. The novel wrapping mechanism stabilizes the MCM complex in a positive unwinding mode, protects the displaced single-stranded DNA tail and prevents reannealing.
    MeSH term(s) Archaeal Proteins/chemistry ; Archaeal Proteins/genetics ; Archaeal Proteins/metabolism ; DNA/metabolism ; DNA Helicases/chemistry ; DNA Helicases/genetics ; DNA Helicases/metabolism ; Mutation ; Plant Proteins/metabolism ; Protein Binding ; Single-Strand Specific DNA and RNA Endonucleases/metabolism ; Sulfolobus solfataricus/enzymology
    Chemical Substances Archaeal Proteins ; Mung Bean Nuclease ; Plant Proteins ; DNA (9007-49-2) ; Single-Strand Specific DNA and RNA Endonucleases (EC 3.1.30.1) ; DNA Helicases (EC 3.6.4.-)
    Language English
    Publishing date 2011-05-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; 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/gkr345
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  10. Article: Single-molecule studies of chromatin fibers: a personal report.

    Leuba, Sanford H / Zlatanova, Jordanka

    Archives of histology and cytology

    2003  Volume 65, Issue 5, Page(s) 391–403

    Abstract: With the advent of single-molecule techniques, macromolecular science has reached new horizons. Nowadays, we can observe, touch, stretch and twist biological macromolecules or their complexes, one-at-a time, in attempts to better understand their ... ...

    Abstract With the advent of single-molecule techniques, macromolecular science has reached new horizons. Nowadays, we can observe, touch, stretch and twist biological macromolecules or their complexes, one-at-a time, in attempts to better understand their mechanical properties and to gain insights into their behavior in the living cell. Chromatin structure and function has been the focus of our research interests for many years. In the past decade, we have added some of the newly emerged single-molecule approaches to the more traditional biochemical and biophysical methods that we have been using throughout the years. This paper briefly summaries our studies on individual chromatin fibers using the atomic force microscope (AFM), optical tweezers, and magnetic tweezers. We believe that our results so far have contributed significantly to our understanding of chromatin, but we also hope that this is only the beginning, and that more exciting times lie ahead.
    MeSH term(s) Biophysical Phenomena ; Biophysics ; Chromatin/chemistry ; Chromatin/ultrastructure ; Humans ; Microscopy, Atomic Force/methods
    Chemical Substances Chromatin
    Language English
    Publishing date 2003-11-03
    Publishing country Japan
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Review
    ZDB-ID 392577-8
    ISSN 0914-9465
    ISSN 0914-9465
    DOI 10.1679/aohc.65.391
    Database MEDical Literature Analysis and Retrieval System OnLINE

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