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  1. Article ; Online: The UvrD303 hyper-helicase exhibits increased processivity.

    Meiners, Matthew J / Tahmaseb, Kambiz / Matson, Steven W

    The Journal of biological chemistry

    2014  Volume 289, Issue 24, Page(s) 17100–17110

    Abstract: DNA helicases use energy derived from nucleoside 5'-triphosphate hydrolysis to catalyze the separation of double-stranded DNA into single-stranded intermediates for replication, recombination, and repair. Escherichia coli helicase II (UvrD) functions in ... ...

    Abstract DNA helicases use energy derived from nucleoside 5'-triphosphate hydrolysis to catalyze the separation of double-stranded DNA into single-stranded intermediates for replication, recombination, and repair. Escherichia coli helicase II (UvrD) functions in methyl-directed mismatch repair, nucleotide excision repair, and homologous recombination. A previously discovered 2-amino acid substitution of residues 403 and 404 (both Asp → Ala) in the 2B subdomain of UvrD (uvrD303) confers an antimutator and UV-sensitive phenotype on cells expressing this allele. The purified protein exhibits a "hyper-helicase" unwinding activity in vitro. Using rapid quench, pre-steady state kinetic experiments we show the increased helicase activity of UvrD303 is due to an increase in the processivity of the unwinding reaction. We suggest that this mutation in the 2B subdomain results in a weakened interaction with the 1B subdomain, allowing the helicase to adopt a more open conformation. This is consistent with the idea that the 2B subdomain may have an autoregulatory role. The UvrD303 mutation may enable the helicase to unwind DNA via a "strand displacement" mechanism, which is similar to the mechanism used to processively translocate along single-stranded DNA, and the increased unwinding processivity may contribute directly to the antimutator phenotype.
    MeSH term(s) Amino Acid Sequence ; Binding Sites ; DNA Helicases/chemistry ; DNA Helicases/genetics ; DNA Helicases/metabolism ; DNA, Bacterial/metabolism ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Molecular Sequence Data ; Mutation, Missense ; Protein Binding
    Chemical Substances DNA, Bacterial ; Escherichia coli Proteins ; UvrD protein, E coli (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-)
    Language English
    Publishing date 2014-05-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M114.565309
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Rapid purification of helicase proteins and in vitro analysis of helicase activity.

    Tahmaseb, Kambiz / Matson, Steven W

    Methods (San Diego, Calif.)

    2010  Volume 51, Issue 3, Page(s) 322–328

    Abstract: Most processes involving an organism's genetic material, including replication, repair and recombination, require access to single-stranded DNA as a template or reaction intermediate. To disrupt the hydrogen bonds between the two strands in double- ... ...

    Abstract Most processes involving an organism's genetic material, including replication, repair and recombination, require access to single-stranded DNA as a template or reaction intermediate. To disrupt the hydrogen bonds between the two strands in double-stranded DNA, organisms utilize proteins called DNA helicases. DNA helicases use duplex DNA as a substrate to create single-stranded DNA in a reaction that requires ATP hydrolysis. Due to their critical role in cellular function, understanding the reaction catalyzed by helicases is essential to understanding DNA metabolism. Helicases are also important in many disease processes due to their role in DNA maintenance and replication. Here we discuss ways to rapidly purify helicases in sufficient quantity for biochemical analysis. We also briefly discuss potential substrates to use with helicases to establish some of their critical biochemical parameters. Through the use of methods that simplify the study of helicases, our understanding of these essential proteins can be accelerated.
    MeSH term(s) DNA Helicases/genetics ; DNA Helicases/isolation & purification ; DNA Helicases/metabolism ; Escherichia coli/genetics ; Eukaryota/genetics
    Chemical Substances DNA Helicases (EC 3.6.4.-)
    Language English
    Publishing date 2010-02-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2010.02.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Intrinsic hTRF1 fluorescence quenching reveals details of telomere DNA binding activity: impact of DNA length, structure and position of telomeric repeats.

    Tahmaseb, Kambiz / Turchi, John J

    Archives of biochemistry and biophysics

    2009  Volume 493, Issue 2, Page(s) 207–212

    Abstract: The myb-DNA binding domain is characterized by a 3-alpha helical bundle and three repeats of this domain drive sequence specific DNA binding of the c-myb transcription factor. Human TRF1 contains a single myb-related domain and as a homodimer, enables ... ...

    Abstract The myb-DNA binding domain is characterized by a 3-alpha helical bundle and three repeats of this domain drive sequence specific DNA binding of the c-myb transcription factor. Human TRF1 contains a single myb-related domain and as a homodimer, enables the sequence specific binding of telomeric DNA. In this report we provide a kinetic assessment of hTRF1 DNA binding activity. Using intrinsic fluorescence quenching we present evidence that hTRF1 binds to both telomeric and non-telomeric DNA with kinetic discrimination to allow stable binding to telomeric tracts of DNA. The position of telomere repeats does not impact binding though the number of repeats and structure does impact binding. Kinetic analysis of DNA-dependent intrinsic tryptophan fluorescence quenching of hTRF1 revealed a two step binding process that is impacted by telomere repeat length, position, and structure. These data are consistent with existing structural and equilibrium binding data for hTRF1 recognition and binding of telomere DNA.
    MeSH term(s) Animals ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; Fluorescence ; Humans ; Kinetics ; Protein Binding/physiology ; Protein Multimerization/physiology ; Protein Structure, Quaternary/physiology ; Protein Structure, Secondary/physiology ; Protein Structure, Tertiary/physiology ; Repetitive Sequences, Nucleic Acid/physiology ; Telomere/chemistry ; Telomere/genetics ; Telomere/metabolism ; Telomeric Repeat Binding Protein 1/chemistry ; Telomeric Repeat Binding Protein 1/genetics ; Telomeric Repeat Binding Protein 1/metabolism
    Chemical Substances Telomeric Repeat Binding Protein 1 ; DNA (9007-49-2)
    Language English
    Publishing date 2009-11-01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 523-x
    ISSN 1096-0384 ; 0003-9861
    ISSN (online) 1096-0384
    ISSN 0003-9861
    DOI 10.1016/j.abb.2009.10.015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Resolving Holliday junctions with Escherichia coli UvrD helicase.

    Carter, Annamarie S / Tahmaseb, Kambiz / Compton, Sarah A / Matson, Steven W

    The Journal of biological chemistry

    2012  Volume 287, Issue 11, Page(s) 8126–8134

    Abstract: The Escherichia coli UvrD helicase is known to function in the mismatch repair and nucleotide excision repair pathways and has also been suggested to have roles in recombination and replication restart. The primary intermediate DNA structure in these two ...

    Abstract The Escherichia coli UvrD helicase is known to function in the mismatch repair and nucleotide excision repair pathways and has also been suggested to have roles in recombination and replication restart. The primary intermediate DNA structure in these two processes is the Holliday junction. UvrD has been shown to unwind a variety of substrates including partial duplex DNA, nicked DNA, forked DNA structures, blunt duplex DNA and RNA-DNA hybrids. Here, we demonstrate that UvrD also catalyzes the robust unwinding of Holliday junction substrates. To characterize this unwinding reaction we have employed steady-state helicase assays, pre-steady-state rapid quench helicase assays, DNaseI footprinting, and electron microscopy. We conclude that UvrD binds initially to the junction compared with binding one of the blunt ends of the four-way junction to initiate unwinding and resolves the synthetic substrate into two double-stranded fork structures. We suggest that UvrD, along with its mismatch repair partners, MutS and MutL, may utilize its ability to unwind Holliday junctions directly in the prevention of homeologous recombination. UvrD may also be involved in the resolution of stalled replication forks by unwinding the Holliday junction intermediate to allow bypass of the blockage.
    MeSH term(s) Adenosine Triphosphatases/chemistry ; Adenosine Triphosphatases/genetics ; Adenosine Triphosphatases/metabolism ; DNA Footprinting/methods ; DNA Helicases/chemistry ; DNA Helicases/genetics ; DNA Helicases/metabolism ; DNA, Bacterial/chemistry ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; DNA, Cruciform/chemistry ; DNA, Cruciform/genetics ; DNA, Cruciform/metabolism ; Deoxyribonuclease I/chemistry ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; MutL Proteins ; MutS DNA Mismatch-Binding Protein/chemistry ; MutS DNA Mismatch-Binding Protein/genetics ; MutS DNA Mismatch-Binding Protein/metabolism ; Nucleic Acid Heteroduplexes/chemistry ; Nucleic Acid Heteroduplexes/genetics ; Nucleic Acid Heteroduplexes/metabolism
    Chemical Substances DNA, Bacterial ; DNA, Cruciform ; Escherichia coli Proteins ; MutL protein, E coli ; Nucleic Acid Heteroduplexes ; Deoxyribonuclease I (EC 3.1.21.1) ; Adenosine Triphosphatases (EC 3.6.1.-) ; UvrD protein, E coli (EC 3.6.1.-) ; MutL Proteins (EC 3.6.1.3) ; MutS DNA Mismatch-Binding Protein (EC 3.6.1.3) ; MutS protein, E coli (EC 3.6.1.3) ; DNA Helicases (EC 3.6.4.-)
    Language English
    Publishing date 2012-01-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.M111.314047
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Telomerase-associated Protein 1, HSP90, and Topoisomerase IIα Associate Directly with the BLM Helicase in Immortalized Cells Using ALT and Modulate Its Helicase Activity Using Telomeric DNA Substrates

    Bhattacharyya, Saumitri / Keirsey, Jeremy / Russell, Beatriz / Kavecansky, Juraj / Lillard-Wetherell, Kate / Tahmaseb, Kambiz / Turchi, John J / Groden, Joanna

    Journal of biological chemistry. 2009 May 29, v. 284, no. 22

    2009  

    Abstract: The BLM helicase associates with the telomere structural proteins TRF1 and TRF2 in immortalized cells using the alternative lengthening of telomere (ALT) pathways. This work focuses on identifying protein partners of BLM in cells using ALT. Mass ... ...

    Abstract The BLM helicase associates with the telomere structural proteins TRF1 and TRF2 in immortalized cells using the alternative lengthening of telomere (ALT) pathways. This work focuses on identifying protein partners of BLM in cells using ALT. Mass spectrometry and immunoprecipitation techniques have identified three proteins that bind directly to BLM and TRF2 in ALT cells: telomerase-associated protein 1 (TEP1), heat shock protein 90 (HSP90), and topoisomerase IIα (TOPOIIα). BLM predominantly co-localizes with these proteins in foci actively synthesizing DNA during late S and G₂/M phases of the cell cycle when ALT is thought to occur. Immunoprecipitation studies also indicate that only HSP90 and TOPOIIα are components of a specific complex containing BLM, TRF1, and TRF2 but that this complex does not include TEP1. TEP1, TOPOIIα, and HSP90 interact directly with BLM in vitro and modulate its helicase activity on telomere-like DNA substrates but not on non-telomeric substrates. Initial studies suggest that knockdown of BLM in ALT cells reduces average telomere length but does not do so in cells using telomerase.
    Language English
    Dates of publication 2009-0529
    Size p. 14966-14977.
    Publishing place American Society for Biochemistry and Molecular Biology
    Document type Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Telomerase-associated protein 1, HSP90, and topoisomerase IIalpha associate directly with the BLM helicase in immortalized cells using ALT and modulate its helicase activity using telomeric DNA substrates.

    Bhattacharyya, Saumitri / Keirsey, Jeremy / Russell, Beatriz / Kavecansky, Juraj / Lillard-Wetherell, Kate / Tahmaseb, Kambiz / Turchi, John J / Groden, Joanna

    The Journal of biological chemistry

    2009  Volume 284, Issue 22, Page(s) 14966–14977

    Abstract: The BLM helicase associates with the telomere structural proteins TRF1 and TRF2 in immortalized cells using the alternative lengthening of telomere (ALT) pathways. This work focuses on identifying protein partners of BLM in cells using ALT. Mass ... ...

    Abstract The BLM helicase associates with the telomere structural proteins TRF1 and TRF2 in immortalized cells using the alternative lengthening of telomere (ALT) pathways. This work focuses on identifying protein partners of BLM in cells using ALT. Mass spectrometry and immunoprecipitation techniques have identified three proteins that bind directly to BLM and TRF2 in ALT cells: telomerase-associated protein 1 (TEP1), heat shock protein 90 (HSP90), and topoisomerase IIalpha (TOPOIIalpha). BLM predominantly co-localizes with these proteins in foci actively synthesizing DNA during late S and G(2)/M phases of the cell cycle when ALT is thought to occur. Immunoprecipitation studies also indicate that only HSP90 and TOPOIIalpha are components of a specific complex containing BLM, TRF1, and TRF2 but that this complex does not include TEP1. TEP1, TOPOIIalpha, and HSP90 interact directly with BLM in vitro and modulate its helicase activity on telomere-like DNA substrates but not on non-telomeric substrates. Initial studies suggest that knockdown of BLM in ALT cells reduces average telomere length but does not do so in cells using telomerase.
    MeSH term(s) Antigens, Neoplasm/metabolism ; Blotting, Western ; Carrier Proteins/metabolism ; Cell Line, Transformed ; Cell Nucleus Structures/metabolism ; DNA/biosynthesis ; DNA/metabolism ; DNA Topoisomerases, Type II/metabolism ; DNA-Binding Proteins/metabolism ; HSP90 Heat-Shock Proteins/metabolism ; Humans ; Mass Spectrometry ; Protein Transport ; RNA-Binding Proteins ; RecQ Helicases/chemistry ; RecQ Helicases/metabolism ; Telomere/metabolism ; Telomeric Repeat Binding Protein 2/chemistry
    Chemical Substances Antigens, Neoplasm ; Carrier Proteins ; DNA-Binding Proteins ; HSP90 Heat-Shock Proteins ; RNA-Binding Proteins ; TEP1 protein, human ; TERF2 protein, human ; Telomeric Repeat Binding Protein 2 ; DNA (9007-49-2) ; Bloom syndrome protein (EC 3.6.1.-) ; RecQ Helicases (EC 3.6.4.12) ; DNA Topoisomerases, Type II (EC 5.99.1.3)
    Language English
    Publishing date 2009-03-27
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; 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.M900195200
    Database MEDical Literature Analysis and Retrieval System OnLINE

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