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  1. Article ; Online: Mismatch repair: Choreographing accurate strand excision.

    Fishel, Richard

    Current biology : CB

    2020  Volume 31, Issue 6, Page(s) R293–R296

    Abstract: State-of-the-art genetic and cellular studies uniquely implicate the S. cerevisiae Pms1 endonuclease (human PMS2) and ExoI as the major components that produce and/or maintain the strand-specific nicks that precisely direct mismatch repair. ...

    Abstract State-of-the-art genetic and cellular studies uniquely implicate the S. cerevisiae Pms1 endonuclease (human PMS2) and ExoI as the major components that produce and/or maintain the strand-specific nicks that precisely direct mismatch repair.
    MeSH term(s) DNA Mismatch Repair ; Humans ; MutL Proteins ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances PMS1 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; MutL Proteins (EC 3.6.1.3)
    Language English
    Publishing date 2020-07-08
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 1071731-6
    ISSN 1879-0445 ; 0960-9822
    ISSN (online) 1879-0445
    ISSN 0960-9822
    DOI 10.1016/j.cub.2021.02.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 3208: Show issues Location:
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  2. Article ; Online: Mismatch repair.

    Fishel, Richard

    The Journal of biological chemistry

    2015  Volume 290, Issue 44, Page(s) 26395–26403

    Abstract: Highly conserved MutS homologs (MSH) and MutL homologs (MLH/PMS) are the fundamental components of mismatch repair (MMR). After decades of debate, it appears clear that the MSH proteins initiate MMR by recognizing a mismatch and forming multiple ... ...

    Abstract Highly conserved MutS homologs (MSH) and MutL homologs (MLH/PMS) are the fundamental components of mismatch repair (MMR). After decades of debate, it appears clear that the MSH proteins initiate MMR by recognizing a mismatch and forming multiple extremely stable ATP-bound sliding clamps that diffuse without hydrolysis along the adjacent DNA. The function(s) of MLH/PMS proteins is less clear, although they too bind ATP and are targeted to MMR by MSH sliding clamps. Structural analysis combined with recent real-time single molecule and cellular imaging technologies are providing new and detailed insight into the thermal-driven motions that animate the complete MMR mechanism.
    MeSH term(s) Adenosine Triphosphate/genetics ; Adenosine Triphosphate/metabolism ; Animals ; DNA/genetics ; DNA/metabolism ; DNA Mismatch Repair/physiology ; DNA Repair Enzymes/genetics ; DNA Repair Enzymes/metabolism ; Humans ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism
    Chemical Substances Nuclear Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; DNA Repair Enzymes (EC 6.5.1.-)
    Language English
    Publishing date 2015-09-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.R115.660142
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: DNA strand breaks and gaps target retroviral intasome binding and integration.

    Senavirathne, Gayan / London, James / Gardner, Anne / Fishel, Richard / Yoder, Kristine E

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 7072

    Abstract: Retrovirus integration into a host genome is essential for productive infections. The integration strand transfer reaction is catalyzed by a nucleoprotein complex (Intasome) containing the viral integrase (IN) and the reverse transcribed (RT) copy DNA ( ... ...

    Abstract Retrovirus integration into a host genome is essential for productive infections. The integration strand transfer reaction is catalyzed by a nucleoprotein complex (Intasome) containing the viral integrase (IN) and the reverse transcribed (RT) copy DNA (cDNA). Previous studies suggested that DNA target-site recognition limits intasome integration. Using single molecule Förster resonance energy transfer (smFRET), we show prototype foamy virus (PFV) intasomes specifically bind to DNA strand breaks and gaps. These break and gap DNA discontinuities mimic oxidative base excision repair (BER) lesion-processing intermediates that have been shown to affect retrovirus integration in vivo. The increased DNA binding events targeted strand transfer to the break/gap site without inducing substantial intasome conformational changes. The major oxidative BER substrate 8-oxo-guanine as well as a G/T mismatch or +T nucleotide insertion that typically introduce a bend or localized flexibility into the DNA, did not increase intasome binding or targeted integration. These results identify DNA breaks or gaps as modulators of dynamic intasome-target DNA interactions that encourage site-directed integration.
    MeSH term(s) DNA, Viral/metabolism ; Integrases/metabolism ; Retroviridae/genetics ; Retroviridae/metabolism ; Spumavirus/genetics ; Spumavirus/metabolism ; DNA, Complementary ; Virus Integration
    Chemical Substances DNA, Viral ; Integrases (EC 2.7.7.-) ; DNA, Complementary
    Language English
    Publishing date 2023-11-03
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42641-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Strategies for Targeting Retroviral Integration for Safer Gene Therapy: Advances and Challenges.

    Yoder, Kristine E / Rabe, Anthony J / Fishel, Richard / Larue, Ross C

    Frontiers in molecular biosciences

    2021  Volume 8, Page(s) 662331

    Abstract: Retroviruses are obligate intracellular parasites that must integrate a copy of the viral genome into the host DNA. The integration reaction is performed by the viral enzyme integrase in complex with the two ends of the viral cDNA genome and yields an ... ...

    Abstract Retroviruses are obligate intracellular parasites that must integrate a copy of the viral genome into the host DNA. The integration reaction is performed by the viral enzyme integrase in complex with the two ends of the viral cDNA genome and yields an integrated provirus. Retroviral vector particles are attractive gene therapy delivery tools due to their stable integration. However, some retroviral integration events may dysregulate host oncogenes leading to cancer in gene therapy patients. Multiple strategies to target retroviral integration, particularly to genetic safe harbors, have been tested with limited success. Attempts to target integration may be limited by the multimerization of integrase or the presence of host co-factors for integration. Several retroviral integration complexes have evolved a mechanism of tethering to chromatin via a host protein. Integration host co-factors bind chromatin, anchoring the complex and allowing integration. The tethering factor allows for both close proximity to the target DNA and specificity of targeting. Each retrovirus appears to have distinct preferences for DNA sequence and chromatin features at the integration site. Tethering factors determine the preference for chromatin features, but do not affect the subtle sequence preference at the integration site. The sequence preference is likely intrinsic to the integrase protein. New developments may uncouple the requirement for a tethering factor and increase the ability to redirect retroviral integration.
    Language English
    Publishing date 2021-05-12
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.662331
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Evolutionary advantage of a dissociative search mechanism in DNA mismatch repair.

    Crocker, Kyle / London, James / Medina, Andrés / Fishel, Richard / Bundschuh, Ralf

    Physical review. E

    2021  Volume 103, Issue 5-1, Page(s) 52404

    Abstract: Protein complexes involved in DNA mismatch repair diffuse along dsDNA as sliding clamps in order to locate a hemimethylated incision site. They have been observed to use a dissociative mechanism, in which two proteins, while continuously remaining ... ...

    Abstract Protein complexes involved in DNA mismatch repair diffuse along dsDNA as sliding clamps in order to locate a hemimethylated incision site. They have been observed to use a dissociative mechanism, in which two proteins, while continuously remaining attached to the DNA, sometimes associate into a single complex sliding on the DNA and sometimes dissociate into two independently sliding proteins. Here, we study the probability that these complexes locate a given target site via a semi-analytic, Monte Carlo calculation that tracks the association and dissociation of the sliding complexes. We compare such probabilities to those obtained using a nondissociative diffusive scan in the space of physically realistic diffusion constants, hemimethylated site distances, and total search times to determine the regions in which dissociative searching is more or less efficient than nondissociative searching. We conclude that the dissociative search mechanism is advantageous in the majority of the physically realistic parameter space, suggesting that the dissociative search mechanism confers an evolutionary advantage.
    MeSH term(s) DNA Mismatch Repair ; Diffusion
    Language English
    Publishing date 2021-07-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.103.052404
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: MutS functions as a clamp loader by positioning MutL on the DNA during mismatch repair.

    Yang, Xiao-Wen / Han, Xiao-Peng / Han, Chong / London, James / Fishel, Richard / Liu, Jiaquan

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 5808

    Abstract: Highly conserved MutS and MutL homologs operate as protein dimers in mismatch repair (MMR). MutS recognizes mismatched nucleotides forming ATP-bound sliding clamps, which subsequently load MutL sliding clamps that coordinate MMR excision. Several MMR ... ...

    Abstract Highly conserved MutS and MutL homologs operate as protein dimers in mismatch repair (MMR). MutS recognizes mismatched nucleotides forming ATP-bound sliding clamps, which subsequently load MutL sliding clamps that coordinate MMR excision. Several MMR models envision static MutS-MutL complexes bound to mismatched DNA via a positively charged cleft (PCC) located on the MutL N-terminal domains (NTD). We show MutL-DNA binding is undetectable in physiological conditions. Instead, MutS sliding clamps exploit the PCC to position a MutL NTD on the DNA backbone, likely enabling diffusion-mediated wrapping of the remaining MutL domains around the DNA. The resulting MutL sliding clamp enhances MutH endonuclease and UvrD helicase activities on the DNA, which also engage the PCC during strand-specific incision/excision. These MutS clamp-loader progressions are significantly different from the replication clamp-loaders that attach the polymerase processivity factors β-clamp/PCNA to DNA, highlighting the breadth of mechanisms for stably linking crucial genome maintenance proteins onto DNA.
    MeSH term(s) Adenosine Triphosphate/metabolism ; DNA/metabolism ; DNA Mismatch Repair ; DNA Repair ; Endonucleases/metabolism ; Escherichia coli Proteins/metabolism ; MutL Proteins/genetics ; MutL Proteins/metabolism ; MutS DNA Mismatch-Binding Protein/genetics ; Nucleotides ; Proliferating Cell Nuclear Antigen/metabolism
    Chemical Substances Escherichia coli Proteins ; Nucleotides ; Proliferating Cell Nuclear Antigen ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; Endonucleases (EC 3.1.-) ; MutL Proteins (EC 3.6.1.3) ; MutS DNA Mismatch-Binding Protein (EC 3.6.1.3)
    Language English
    Publishing date 2022-10-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-33479-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book: Archaic occupations at White Bend

    Fishel, Richard L

    Helton, Falling Springs, and Hemphill horizons of the Lamoine Valley, Hancock County, Illinois

    (Illinois State Archaeological Survey research reports ; 29)

    2013  

    Author's details edited by Richard L. Fishel; with contributions by Richard L. Fishel, Michael F. Kolb, Steven R. Kuehn, David J. Nolan, and Mary L. Simon
    Series title Illinois State Archaeological Survey research reports ; 29
    Keywords Excavations (Archaeology) ; Indians of North America/Implements/Antiquities ; Indians of North America/Antiquities ; Hancock County (Ill.) ; White Bend Site (Ill.)
    Language English
    Size xiii, 201 pages, illustrations, maps (mostly color), 28 cm
    Publisher Illinois State Archaeological Survey
    Publishing place Champaign, Illinois
    Document type Book
    Note Includes bibliographical references (pages 191-201)
    ISBN 9781930487291 ; 1930487290
    Database Former special subject collection: coastal and deep sea fishing

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  8. Book: Woodland habitations in the interior of Western Illinois

    Fishel, Richard L

    a view from White bend

    (Illinois State Archaeological Survey research reports ; 30)

    2013  

    Author's details ed. by Richard L. Fishel
    Series title Illinois State Archaeological Survey research reports ; 30
    Keywords Excavations (Archaeology) ; Indians of North America/Implements ; Indians of North America/Antiquities ; Hancock County (Ill.) ; White Bend Site (Ill.)
    Language English
    Size XX, 348 S, Ill., Kt
    Publisher Illinois State Archaeological Survey
    Publishing place Champaign
    Document type Book
    Note Includes bibliographical references
    ISBN 9781930487307 ; 1930487304
    Database Former special subject collection: coastal and deep sea fishing

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  9. Article ; Online: Enhanced gene targeting to evaluate Lynch syndrome alterations.

    Fishel, Richard / Heinen, Christopher D

    Proceedings of the National Academy of Sciences of the United States of America

    2016  Volume 113, Issue 15, Page(s) 3918–3920

    MeSH term(s) Colorectal Neoplasms, Hereditary Nonpolyposis/genetics ; Gene Targeting ; Germ-Line Mutation ; Humans ; MutS Homolog 2 Protein/genetics
    Chemical Substances MutS Homolog 2 Protein (EC 3.6.1.3)
    Language English
    Publishing date 2016-04-12
    Publishing country United States
    Document type Editorial ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1602650113
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Linker domain function predicts pathogenic MLH1 missense variants.

    London, James / Martín-López, Juana / Yang, Inho / Liu, Jiaquan / Lee, Jong-Bong / Fishel, Richard

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 9

    Abstract: The pathogenic consequences of 369 unique human HsMLH1 missense variants has been hampered by the lack of a detailed function in mismatch repair (MMR). Here single-molecule images show that HsMSH2-HsMSH6 provides a platform for HsMLH1-HsPMS2 to form a ... ...

    Abstract The pathogenic consequences of 369 unique human HsMLH1 missense variants has been hampered by the lack of a detailed function in mismatch repair (MMR). Here single-molecule images show that HsMSH2-HsMSH6 provides a platform for HsMLH1-HsPMS2 to form a stable sliding clamp on mismatched DNA. The mechanics of sliding clamp progression solves a significant operational puzzle in MMR and provides explicit predictions for the distribution of clinically relevant HsMLH1 missense mutations.
    MeSH term(s) Binding Sites ; Colorectal Neoplasms, Hereditary Nonpolyposis/genetics ; Colorectal Neoplasms, Hereditary Nonpolyposis/metabolism ; Colorectal Neoplasms, Hereditary Nonpolyposis/pathology ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Damage ; DNA Mismatch Repair ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Humans ; Models, Molecular ; MutL Protein Homolog 1/chemistry ; MutL Protein Homolog 1/genetics ; MutL Protein Homolog 1/metabolism ; MutS Homolog 2 Protein/chemistry ; MutS Homolog 2 Protein/genetics ; MutS Homolog 2 Protein/metabolism ; Mutation, Missense ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs
    Chemical Substances DNA-Binding Proteins ; G-T mismatch-binding protein ; MLH1 protein, human ; DNA (9007-49-2) ; MSH2 protein, human (EC 3.6.1.3) ; MutL Protein Homolog 1 (EC 3.6.1.3) ; MutS Homolog 2 Protein (EC 3.6.1.3)
    Language English
    Publishing date 2021-02-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2019215118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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