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  1. Article ; Online: Four cases: Human immunodeficiency virus and novel coronavirus 2019 Co-infection in patients from Long Island, New York.

    Benkovic, Scott / Kim, Michelle / Sin, Eric

    Journal of medical virology

    2020  Volume 92, Issue 11, Page(s) 2338–2340

    MeSH term(s) Aged ; COVID-19/diagnosis ; Coinfection/diagnosis ; Coinfection/virology ; HIV Infections/diagnosis ; Humans ; Male ; Middle Aged ; New York ; Risk Factors
    Keywords covid19
    Language English
    Publishing date 2020-06-16
    Publishing country United States
    Document type Case Reports ; Letter
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.26029
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  2. Article ; Online: Purine synthesis suppression reduces the development and progression of pulmonary hypertension in rodent models.

    Ma, Qian / Yang, Qiuhua / Xu, Jiean / Sellers, Hunter G / Brown, Zach L / Liu, Zhiping / Bordan, Zsuzsanna / Shi, Xiaofan / Zhao, Dingwei / Cai, Yongfeng / Pareek, Vidhi / Zhang, Chunxiang / Wu, Guangyu / Dong, Zheng / Verin, Alexander D / Gan, Lin / Du, Quansheng / Benkovic, Stephen J / Xu, Suowen /
    Asara, John M / Ben-Sahra, Issam / Barman, Scott / Su, Yunchao / Fulton, David J R / Huo, Yuqing

    European heart journal

    2023  Volume 44, Issue 14, Page(s) 1265–1279

    Abstract: Aims: Proliferation of vascular smooth muscle cells (VSMCs) is a hallmark of pulmonary hypertension (PH). Proliferative cells utilize purine bases from the de novo purine synthesis (DNPS) pathways for nucleotide synthesis; however, it is unclear whether ...

    Abstract Aims: Proliferation of vascular smooth muscle cells (VSMCs) is a hallmark of pulmonary hypertension (PH). Proliferative cells utilize purine bases from the de novo purine synthesis (DNPS) pathways for nucleotide synthesis; however, it is unclear whether DNPS plays a critical role in VSMC proliferation during development of PH. The last two steps of DNPS are catalysed by the enzyme 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine monophosphate cyclohydrolase (ATIC). This study investigated whether ATIC-driven DNPS affects the proliferation of pulmonary artery smooth muscle cells (PASMCs) and the development of PH.
    Methods and results: Metabolites of DNPS in proliferative PASMCs were measured by liquid chromatography-tandem mass spectrometry. ATIC expression was assessed in platelet-derived growth factor-treated PASMCs and in the lungs of PH rodents and patients with pulmonary arterial hypertension. Mice with global and VSMC-specific knockout of Atic were utilized to investigate the role of ATIC in both hypoxia- and lung interleukin-6/hypoxia-induced murine PH. ATIC-mediated DNPS at the mRNA, protein, and enzymatic activity levels were increased in platelet-derived growth factor-treated PASMCs or PASMCs from PH rodents and patients with pulmonary arterial hypertension. In cultured PASMCs, ATIC knockdown decreased DNPS and nucleic acid DNA/RNA synthesis, and reduced cell proliferation. Global or VSMC-specific knockout of Atic attenuated vascular remodelling and inhibited the development and progression of both hypoxia- and lung IL-6/hypoxia-induced PH in mice.
    Conclusion: Targeting ATIC-mediated DNPS compromises the availability of purine nucleotides for incorporation into DNA/RNA, reducing PASMC proliferation and pulmonary vascular remodelling and ameliorating the development and progression of PH.
    MeSH term(s) Mice ; Animals ; Hypertension, Pulmonary ; Pulmonary Arterial Hypertension ; Rodentia/metabolism ; Vascular Remodeling/physiology ; Pulmonary Artery ; Purines/metabolism ; Cells, Cultured ; Hypoxia/metabolism ; RNA, Messenger/metabolism ; Platelet-Derived Growth Factor/metabolism ; Cell Proliferation ; Myocytes, Smooth Muscle/metabolism
    Chemical Substances Purines ; RNA, Messenger ; Platelet-Derived Growth Factor
    Language English
    Publishing date 2023-01-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 603098-1
    ISSN 1522-9645 ; 0195-668X
    ISSN (online) 1522-9645
    ISSN 0195-668X
    DOI 10.1093/eurheartj/ehad044
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  3. Article ; Online: Response of the bacteriophage T4 replisome to noncoding lesions and regression of a stalled replication fork.

    Nelson, Scott W / Benkovic, Stephen J

    Journal of molecular biology

    2010  Volume 401, Issue 5, Page(s) 743–756

    Abstract: DNA is constantly damaged by endogenous and exogenous agents. The resulting DNA lesions have the potential to halt the progression of the replisome, possibly leading to replication fork collapse. Here, we examine the effect of a noncoding DNA lesion in ... ...

    Abstract DNA is constantly damaged by endogenous and exogenous agents. The resulting DNA lesions have the potential to halt the progression of the replisome, possibly leading to replication fork collapse. Here, we examine the effect of a noncoding DNA lesion in either leading strand template or lagging strand template on the bacteriophage T4 replisome. A damaged base in the lagging strand template does not affect the progression of the replication fork. Instead, the stalled lagging strand polymerase recycles from the lesion and initiates the synthesis of a new Okazaki fragment upstream of the damaged base. In contrast, when the replisome encounters a blocking lesion in the leading strand template, the replication fork only travels approximately 1 kb beyond the point of the DNA lesion before complete replication fork collapse. The primosome and the lagging strand polymerase remain active during this period, and an Okazaki fragment is synthesized beyond the point of the leading strand lesion. There is no evidence for a new priming event on the leading strand template. Instead, the DNA structure that is produced by the stalled replication fork is a substrate for the DNA repair helicase UvsW. UvsW catalyzes the regression of a stalled replication fork into a "chicken-foot" structure that has been postulated to be an intermediate in an error-free lesion bypass pathway.
    MeSH term(s) Bacteriophage T4/genetics ; Bacteriophage T4/physiology ; DNA ; DNA Helicases/physiology ; DNA Replication ; Electrophoresis, Agar Gel ; Viral Proteins/physiology
    Chemical Substances Okazaki fragments ; Viral Proteins ; DNA (9007-49-2) ; DNA Helicases (EC 3.6.4.-) ; UvsW protein, Bacteriophage T4 (EC 5.99.-)
    Language English
    Publishing date 2010-06-25
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2010.06.027
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  4. Article ; Online: Interaction of T4 UvsW helicase and single-stranded DNA binding protein gp32 through its carboxy-terminal acidic tail.

    Perumal, Senthil K / Nelson, Scott W / Benkovic, Stephen J

    Journal of molecular biology

    2013  Volume 425, Issue 16, Page(s) 2823–2839

    Abstract: Bacteriophage T4 UvsW helicase contains both unwinding and annealing activities and displays some functional similarities to bacterial RecG and RecQ helicases. UvsW is involved in several DNA repair pathways, playing important roles in recombination- ... ...

    Abstract Bacteriophage T4 UvsW helicase contains both unwinding and annealing activities and displays some functional similarities to bacterial RecG and RecQ helicases. UvsW is involved in several DNA repair pathways, playing important roles in recombination-dependent DNA repair and the reorganization of stalled replication forks. The T4 single-stranded DNA (ssDNA) binding protein gp32 is a central player in nearly all DNA replication and repair processes and is thought to facilitate their coordination by recruiting and regulating the various proteins involved. Here, we show that the activities of the UvsW protein are modulated by gp32. UvsW-catalyzed unwinding of recombination intermediates such as D-loops and static X-DNA (Holliday junction mimic) to ssDNA products is enhanced by the gp32 protein. The enhancement requires the presence of the protein interaction domain of gp32 (the acidic carboxy-terminus), suggesting that a specific interaction between UvsW and gp32 is required. In the absence of this interaction, the ssDNA annealing and ATP-dependent translocation activities of UvsW are severely inhibited when gp32 coats the ssDNA lattice. However, when UvsW and gp32 do interact, UvsW is able to efficiently displace the gp32 protein from the ssDNA. This ability of UvsW to remove gp32 from ssDNA may explain its ability to enhance the strand invasion activity of the T4 recombinase (UvsX) and suggests a possible new role for UvsW in gp32-mediated DNA transactions.
    MeSH term(s) Bacteriophage T4/enzymology ; DNA Helicases/metabolism ; DNA, Single-Stranded/metabolism ; DNA, Viral/metabolism ; DNA-Binding Proteins/metabolism ; Models, Biological ; Protein Binding ; Protein Interaction Domains and Motifs ; Viral Proteins/metabolism
    Chemical Substances DNA, Single-Stranded ; DNA, Viral ; DNA-Binding Proteins ; Viral Proteins ; gp32 protein, Enterobacteria phage T4 ; DNA Helicases (EC 3.6.4.-) ; UvsW protein, Bacteriophage T4 (EC 5.99.-)
    Language English
    Publishing date 2013-06-01
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2013.05.012
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  5. Article: The T4 phage UvsW protein contains both DNA unwinding and strand annealing activities.

    Nelson, Scott W / Benkovic, Stephen J

    The Journal of biological chemistry

    2006  Volume 282, Issue 1, Page(s) 407–416

    Abstract: UvsW protein belongs to the SF2 helicase family and is one of three helicases found in T4 phage. UvsW governs the transition from origin-dependent to origin-independent replication through the dissociation of R-loops located at the T4 origins of ... ...

    Abstract UvsW protein belongs to the SF2 helicase family and is one of three helicases found in T4 phage. UvsW governs the transition from origin-dependent to origin-independent replication through the dissociation of R-loops located at the T4 origins of replication. Additionally, in vivo evidence indicates that UvsW plays a role in recombination-dependent replication and/or DNA repair. Here, the biochemical properties of UvsW helicase are described. UvsW is a 3' to 5' helicase that unwinds a wide variety of substrates, including those resembling stalled replication forks and recombination intermediates. UvsW also contains a potent single-strand DNA annealing activity that is enhanced by ATP hydrolysis but does not require it. The annealing activity is inhibited by the non-hydrolysable ATP analog (adenosine 5'-O-(thiotriphosphate)), T4 single-stranded DNA-binding protein (gp32), or a small 8.8-kDa polypeptide (UvsW.1). Fluorescence resonance energy transfer experiments indicate that UvsW and UvsW.1 form a complex, suggesting that the UvsW helicase may exist as a heterodimer in vivo. Fusion of UvsW and UvsW.1 results in a 68-kDa protein having nearly identical properties as the UvsW-UvsW.1 complex, indicating that the binding locus of UvsW.1 is close to the C terminus of UvsW. The biochemical properties of UvsW are similar to the RecQ protein family and suggest that the annealing activity of these helicases may also be modulated by protein-protein interactions. The dual activities of UvsW are well suited for the DNA repair pathways described for leading strand lesion bypass and synthesis-dependent strand annealing.
    MeSH term(s) Adenosine Triphosphate/chemistry ; Bacteriophage T4/chemistry ; Base Sequence ; Cloning, Molecular ; DNA Helicases/chemistry ; DNA Helicases/physiology ; DNA Repair ; Fluorescence Resonance Energy Transfer ; Hydrolysis ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Denaturation ; Protein Structure, Tertiary ; Recombination, Genetic ; Viral Proteins/chemistry ; Viral Proteins/physiology
    Chemical Substances Viral Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; DNA Helicases (EC 3.6.4.-) ; UvsW protein, Bacteriophage T4 (EC 5.99.-)
    Language English
    Publishing date 2006-11-08
    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.M608153200
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  6. Article ; Online: Processive and unidirectional translocation of monomeric UvsW helicase on single-stranded DNA.

    Nelson, Scott W / Perumal, Senthil K / Benkovic, Stephen J

    Biochemistry

    2009  Volume 48, Issue 5, Page(s) 1036–1046

    Abstract: UvsW protein from bacteriophage T4 controls the transition from origin-dependent to origin-independent initiation of replication through the unwinding of R-loops bound to the T4 origins of replication. UvsW has also been implicated through genetic and ... ...

    Abstract UvsW protein from bacteriophage T4 controls the transition from origin-dependent to origin-independent initiation of replication through the unwinding of R-loops bound to the T4 origins of replication. UvsW has also been implicated through genetic and biochemical experiments to play a role in DNA repair processes such as replication fork regression and Holliday junction branch migration. UvsW is capable of unwinding a wide variety of substrates, many of which contain only duplex DNA without single-stranded regions. Based on this observation, it has been suggested that UvsW is a dsDNA translocase. In this work we examine the ability of UvsW to translocate on ssDNA. Kinetic analysis indicates that the rate of ATP hydrolysis is strongly dependent on the length of the ssDNA lattice, whereas the K(M)-DNA remains relatively constant, demonstrating that UvsW translocates on ssDNA in an ATP-dependent fashion. Experiments using streptavidin blocks or poly dT sequences located at either end of the ssDNA substrate indicate that UvsW translocates in a 3' to 5' direction. Mutant competition and heparin trapping experiments reveal that UvsW is extremely processive during ATP-driven translocation with a half-life on the order of several minutes. Finally, functional assays provide evidence that UvsW is monomeric while translocating on ssDNA. The ability of UvsW to unwind DNA duplexes is likely to be mechanistically linked to its ability to processively translocate on ssDNA in a 3' to 5' unidirectional fashion.
    MeSH term(s) Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/genetics ; Bacteriophage T4/enzymology ; DNA Helicases/chemistry ; DNA Helicases/genetics ; DNA, Single-Stranded/chemistry ; DNA, Single-Stranded/genetics ; Nucleic Acid Heteroduplexes/chemistry ; Nucleic Acid Heteroduplexes/genetics ; Protein Processing, Post-Translational/genetics ; Translocation, Genetic ; Viral Proteins/chemistry ; Viral Proteins/genetics
    Chemical Substances DNA, Single-Stranded ; Nucleic Acid Heteroduplexes ; Viral Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; DNA Helicases (EC 3.6.4.-) ; UvsW protein, Bacteriophage T4 (EC 5.99.-)
    Language English
    Publishing date 2009-01-20
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/bi801792q
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  7. Article ; Online: Repetitive lagging strand DNA synthesis by the bacteriophage T4 replisome.

    Spiering, Michelle M / Nelson, Scott W / Benkovic, Stephen J

    Molecular bioSystems

    2008  Volume 4, Issue 11, Page(s) 1070–1074

    Abstract: Our studies on the T4 replisome build on the seminal work from the Alberts laboratory. They discovered essentially all the proteins that constitute the T4 replisome, isolated them, and measured their enzymatic activities. Ultimately, in brilliant ... ...

    Abstract Our studies on the T4 replisome build on the seminal work from the Alberts laboratory. They discovered essentially all the proteins that constitute the T4 replisome, isolated them, and measured their enzymatic activities. Ultimately, in brilliant experiments they reconstituted in vitro a functioning replisome and in the absence of structural information created a mosaic as to how such a machine might be assembled. Their consideration of the problem of continuous leading strand synthesis opposing discontinuous lagging strand synthesis led to their imaginative proposal of the trombone model, an illustration that graces all textbooks of biochemistry. Our subsequent work deepens their findings through experiments that focus on defining the kinetics, structural elements, and protein-protein contacts essential for replisome assembly and function. In this highlight we address when Okazaki primer synthesis is initiated and how the primer is captured by a recycling lagging strand polymerase--problems that the Alberts laboratory likewise found mysterious and significant for all replisomes.
    MeSH term(s) Bacteriophage T4/enzymology ; Bacteriophage T4/genetics ; Bacteriophage T4/metabolism ; DNA/biosynthesis ; DNA/chemistry ; DNA/metabolism ; DNA Replication ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Models, Biological ; Multienzyme Complexes/chemistry ; Multienzyme Complexes/metabolism ; Replication Origin ; Templates, Genetic
    Chemical Substances Multienzyme Complexes ; Okazaki fragments ; DNA (9007-49-2) ; DNA synthesome (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2008-11
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2188635-0
    ISSN 1742-2051 ; 1742-206X
    ISSN (online) 1742-2051
    ISSN 1742-206X
    DOI 10.1039/b812163j
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  8. Article: RNA primer handoff in bacteriophage T4 DNA replication: the role of single-stranded DNA-binding protein and polymerase accessory proteins.

    Nelson, Scott W / Kumar, Ravindra / Benkovic, Stephen J

    The Journal of biological chemistry

    2008  Volume 283, Issue 33, Page(s) 22838–22846

    Abstract: In T4 phage, coordinated leading and lagging strand DNA synthesis is carried out by an eight-protein complex termed the replisome. The control of lagging strand DNA synthesis depends on a highly dynamic replisome with several proteins entering and ... ...

    Abstract In T4 phage, coordinated leading and lagging strand DNA synthesis is carried out by an eight-protein complex termed the replisome. The control of lagging strand DNA synthesis depends on a highly dynamic replisome with several proteins entering and leaving during DNA replication. Here we examine the role of single-stranded binding protein (gp32) in the repetitive cycles of lagging strand synthesis. Removal of the protein-interacting domain of gp32 results in a reduction in the number of primers synthesized and in the efficiency of primer transfer to the polymerase. We find that the primase protein is moderately processive, and this processivity depends on the presence of full-length gp32 at the replication fork. Surprisingly, we find that an increase in the efficiency of primer transfer to the clamp protein correlates with a decrease in the dissociation rate of the primase from the replisome. These findings result in a revised model of lagging strand DNA synthesis where the primase remains as part of the replisome after each successful cycle of Okazaki fragment synthesis. A delay in primer transfer results in an increased probability of the primase dissociating from the replication fork. The interplay between gp32, primase, clamp, and clamp loader dictates the rate and efficiency of primer synthesis, polymerase recycling, and primer transfer to the polymerase.
    MeSH term(s) Bacteriophage T4/enzymology ; Bacteriophage T4/genetics ; DNA Replication ; DNA, Single-Stranded/genetics ; DNA, Viral/genetics ; DNA-Binding Proteins/metabolism ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; RNA/metabolism ; Viral Proteins/genetics ; Viral Proteins/metabolism
    Chemical Substances DNA, Single-Stranded ; DNA, Viral ; DNA-Binding Proteins ; RNA primers ; Viral Proteins ; RNA (63231-63-0) ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2008-05-28
    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.M802762200
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  9. Article ; Online: Biochemical characterization of bacteriophage T4 Mre11-Rad50 complex.

    Herdendorf, Timothy J / Albrecht, Dustin W / Benkovic, Stephen J / Nelson, Scott W

    The Journal of biological chemistry

    2010  Volume 286, Issue 4, Page(s) 2382–2392

    Abstract: The Mre11-Rad50 complex (MR) from bacteriophage T4 (gp46/47) is involved in the processing of DNA double-strand breaks. Here, we describe the activities of the T4 MR complex and its modulation by proteins involved in homologous recombination. T4 Mre11 is ...

    Abstract The Mre11-Rad50 complex (MR) from bacteriophage T4 (gp46/47) is involved in the processing of DNA double-strand breaks. Here, we describe the activities of the T4 MR complex and its modulation by proteins involved in homologous recombination. T4 Mre11 is a Rad50- and Mn(2+)-dependent dsDNA exonuclease and ssDNA endonuclease. ATP hydrolysis is required for the removal of multiple nucleotides via dsDNA exonuclease activity but not for the removal of the first nucleotide or for ssDNA endonuclease activity, indicating ATP hydrolysis is only required for repetitive nucleotide removal. By itself, Rad50 is a relatively inefficient ATPase, but the presence of Mre11 and dsDNA increases ATP hydrolysis by 20-fold. The ATP hydrolysis reaction exhibits positive cooperativity with Hill coefficients ranging from 1.4 for Rad50 alone to 2.4 for the Rad50-Mre11-DNA complex. Kinetic assays suggest that approximately four nucleotides are removed per ATP hydrolyzed. Directionality assays indicate that the prevailing activity is a 3' to 5' dsDNA exonuclease, which is incompatible with the proposed role of MR in the production of 3' ssDNA ends. Interestingly, we found that in the presence of a recombination mediator protein (UvsY) and ssDNA-binding protein (gp32), Mre11 is capable of using Mg(2+) as a cofactor for its nuclease activity. Additionally, the Mg(2+)-dependent nuclease activity, activated by UvsY and gp32, results in the formation of endonuclease reaction products. These results suggest that gp32 and UvsY may alter divalent cation preference and facilitate the formation of a 3' ssDNA overhang, which is a necessary intermediate for recombination-mediated double-strand break repair.
    MeSH term(s) Adenosine Triphosphatases/genetics ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/genetics ; Adenosine Triphosphate/metabolism ; Bacteriophage T4/enzymology ; Bacteriophage T4/genetics ; DNA Breaks, Double-Stranded ; DNA, Single-Stranded/genetics ; DNA, Single-Stranded/metabolism ; DNA, Viral/genetics ; DNA, Viral/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Exodeoxyribonucleases/genetics ; Exodeoxyribonucleases/metabolism ; Hydrolysis ; Kinetics ; Multienzyme Complexes/genetics ; Multienzyme Complexes/metabolism ; Recombination, Genetic/physiology ; Viral Proteins/genetics ; Viral Proteins/metabolism
    Chemical Substances DNA, Single-Stranded ; DNA, Viral ; DNA-Binding Proteins ; Multienzyme Complexes ; Viral Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; Exodeoxyribonucleases (EC 3.1.-) ; Adenosine Triphosphatases (EC 3.6.1.-)
    Language English
    Publishing date 2010-11-15
    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.M110.178871
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