JOHN TAINER to DNA
This is a "connection" page, showing publications JOHN TAINER has written about DNA.
Connection Strength
9.058
-
EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart. Mol Cell. 2021 07 15; 81(14):2989-3006.e9.
Score: 0.442
-
Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction. Prog Biophys Mol Biol. 2019 10; 147:47-61.
Score: 0.377
-
Uncovering the secrets of protein interactions with the DNA enforcing genomic stability. Prog Biophys Mol Biol. 2017 08; 127:89-92.
Score: 0.337
-
Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nat Commun. 2017 06 27; 8:15855.
Score: 0.335
-
Bending Forks and Wagging Dogs--It's about the DNA 3' Tail. Mol Cell. 2015 Jun 18; 58(6):972-3.
Score: 0.291
-
Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair. Prog Biophys Mol Biol. 2015 Mar; 117(2-3):182-193.
Score: 0.282
-
Probing DNA by 2-OG-dependent dioxygenase. Cell. 2013 Dec 19; 155(7):1448-50.
Score: 0.262
-
P53 conformational switching for selectivity may reveal a general solution for specific DNA binding. EMBO J. 2011 Jun 01; 30(11):2099-100.
Score: 0.220
-
Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers. 2011 Aug; 95(8):559-71.
Score: 0.218
-
Alkyltransferase-like proteins: molecular switches between DNA repair pathways. Cell Mol Life Sci. 2010 Nov; 67(22):3749-62.
Score: 0.205
-
Structural dynamics in DNA damage signaling and repair. Curr Opin Struct Biol. 2010 Jun; 20(3):283-94.
Score: 0.204
-
Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering. Curr Opin Struct Biol. 2010 Feb; 20(1):128-37.
Score: 0.200
-
Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. J Biol Chem. 2010 Jan 08; 285(2):1414-23.
Score: 0.197
-
Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell. 2008 Oct 03; 135(1):97-109.
Score: 0.183
-
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys. 2007 Aug; 40(3):191-285.
Score: 0.169
-
DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy. DNA Repair (Amst). 2007 Aug 01; 6(8):1100-15.
Score: 0.166
-
The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair. DNA Repair (Amst). 2007 Apr 01; 6(4):410-28.
Score: 0.162
-
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res. 2006; 34(20):6023-33.
Score: 0.160
-
WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nat Struct Mol Biol. 2006 May; 13(5):414-22.
Score: 0.154
-
Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Mol Cell. 2006 Apr 07; 22(1):27-37.
Score: 0.154
-
Protein mimicry of DNA and pathway regulation. DNA Repair (Amst). 2005 Dec 08; 4(12):1410-20.
Score: 0.149
-
DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol. 2004 Aug; 11(8):714-20.
Score: 0.136
-
Profiling human pathogenic repeat expansion regions by synergistic and multi-level impacts on molecular connections. Hum Genet. 2023 Feb; 142(2):245-274.
Score: 0.121
-
Distinct sequence features underlie microdeletions and gross deletions in the human genome. Hum Mutat. 2022 03; 43(3):328-346.
Score: 0.115
-
Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNA bases. J Mol Biol. 2002 Jan 18; 315(3):373-84.
Score: 0.115
-
Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM. Prog Biophys Mol Biol. 2021 08; 163:74-86.
Score: 0.105
-
Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations. Proc Natl Acad Sci U S A. 2020 06 23; 117(25):14127-14138.
Score: 0.103
-
Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. Proc Natl Acad Sci U S A. 2000 May 09; 97(10):5083-8.
Score: 0.102
-
DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected]. Nature. 2000 Jan 27; 403(6768):451-6.
Score: 0.100
-
Envisioning the fourth dimension of the genetic code: the structural biology of macromolecular recognition and conformational switching in DNA repair. Cold Spring Harb Symp Quant Biol. 2000; 65:113-26.
Score: 0.100
-
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell. 1999 Aug 06; 98(3):397-408.
Score: 0.097
-
DNA repair mechanisms for the recognition and removal of damaged DNA bases. Annu Rev Biophys Biomol Struct. 1999; 28:101-28.
Score: 0.093
-
Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA. EMBO J. 1998 Sep 01; 17(17):5214-26.
Score: 0.091
-
2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol. 2017 Sep 01; 73(Pt 9):710-728.
Score: 0.085
-
What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses. Methods Enzymol. 2017; 592:417-455.
Score: 0.083
-
Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. Elife. 2017 02 23; 6.
Score: 0.082
-
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature. 1996 Nov 07; 384(6604):87-92.
Score: 0.080
-
Mechanism and Regulation of DNA-Protein Crosslink Repair by the DNA-Dependent Metalloprotease SPRTN. Mol Cell. 2016 11 17; 64(4):688-703.
Score: 0.080
-
Noncoding RNA joins Ku and DNA-PKcs for DNA-break resistance in breast cancer. Nat Struct Mol Biol. 2016 06 07; 23(6):509-10.
Score: 0.078
-
Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining. Nucleic Acids Res. 2015 Aug 18; 43(14):7021-31.
Score: 0.073
-
Emerging critical roles of Fe-S clusters in DNA replication and repair. Biochim Biophys Acta. 2015 Jun; 1853(6):1253-71.
Score: 0.071
-
Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair (Amst). 2014 May; 17:110-20.
Score: 0.067
-
ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling. EMBO J. 2014 Mar 03; 33(5):482-500.
Score: 0.066
-
Super-resolution in solution X-ray scattering and its applications to structural systems biology. Annu Rev Biophys. 2013; 42:415-41.
Score: 0.062
-
XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair. Biochem Cell Biol. 2013 Feb; 91(1):31-41.
Score: 0.062
-
Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes. J Biol Chem. 2013 Mar 22; 288(12):8445-8455.
Score: 0.062
-
Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability. Proc Natl Acad Sci U S A. 2012 May 29; 109(22):8528-33.
Score: 0.059
-
Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase. Nucleic Acids Res. 2012 Jul; 40(13):6070-81.
Score: 0.058
-
Flap endonucleases pass 5'-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5'-ends. Nucleic Acids Res. 2012 May; 40(10):4507-19.
Score: 0.058
-
DNA charge transport as a first step in coordinating the detection of lesions by repair proteins. Proc Natl Acad Sci U S A. 2012 Feb 07; 109(6):1856-61.
Score: 0.057
-
The wonders of flap endonucleases: structure, function, mechanism and regulation. Subcell Biochem. 2012; 62:301-26.
Score: 0.057
-
Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases. Trends Biochem Sci. 2012 Feb; 37(2):74-84.
Score: 0.057
-
ATP-stimulated, DNA-mediated redox signaling by XPD, a DNA repair and transcription helicase. J Am Chem Soc. 2011 Oct 19; 133(41):16378-81.
Score: 0.056
-
XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair. J Biol Chem. 2011 Sep 16; 286(37):32638-50.
Score: 0.055
-
XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair (Amst). 2011 Jul 15; 10(7):697-713.
Score: 0.055
-
Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell. 2011 Apr 15; 145(2):198-211.
Score: 0.054
-
Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA-bound states. Biochemistry. 2010 Jul 27; 49(29):6165-76.
Score: 0.052
-
Structural basis of O6-alkylguanine recognition by a bacterial alkyltransferase-like DNA repair protein. J Biol Chem. 2010 Apr 30; 285(18):13736-41.
Score: 0.050
-
Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair. J Mol Biol. 2010 Apr 02; 397(3):647-63.
Score: 0.050
-
Amyotrophic lateral sclerosis. Adv Exp Med Biol. 2010; 685:9-20.
Score: 0.050
-
Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase. Nucleic Acids Res. 2009 Oct; 37(18):6161-73.
Score: 0.048
-
Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Nature. 2009 Jun 11; 459(7248):808-13.
Score: 0.048
-
Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair. Nat Struct Mol Biol. 2009 Feb; 16(2):138-43.
Score: 0.047
-
Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template. Biochem Cell Biol. 2007 Aug; 85(4):509-20.
Score: 0.042
-
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A. 2007 Jan 30; 104(5):1465-70.
Score: 0.041
-
A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell. 2006 Oct 20; 24(2):279-91.
Score: 0.040
-
A novel processive mechanism for DNA synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial DNA polymerase. J Mol Biol. 2006 May 19; 358(5):1229-43.
Score: 0.038
-
Structure and function of the double-strand break repair machinery. DNA Repair (Amst). 2004 Aug-Sep; 3(8-9):863-73.
Score: 0.034
-
Interaction interface of human flap endonuclease-1 with its DNA substrates. J Biol Chem. 2004 Jun 04; 279(23):24394-402.
Score: 0.033
-
GRB2 stabilizes RAD51 at reversed replication forks suppressing genomic instability and innate immunity against cancer. Nat Commun. 2024 Mar 08; 15(1):2132.
Score: 0.033
-
Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell. 2004 Jan 09; 116(1):39-50.
Score: 0.033
-
Dynamics of the DYNLL1-MRE11 complex regulate DNA end resection and recruitment of Shieldin to DSBs. Nat Struct Mol Biol. 2023 10; 30(10):1456-1467.
Score: 0.032
-
Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. EMBO J. 2003 Sep 01; 22(17):4566-76.
Score: 0.032
-
Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases. Nat Commun. 2023 05 13; 14(1):2758.
Score: 0.031
-
A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair. Nucleic Acids Res. 2023 02 22; 51(3):1019-1033.
Score: 0.031
-
Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair. Proc Natl Acad Sci U S A. 2022 08 23; 119(34):e2207408119.
Score: 0.030
-
Monitoring Nuclease Activity by X-Ray Scattering Interferometry Using Gold Nanoparticle-Conjugated DNA. Methods Mol Biol. 2022; 2444:183-205.
Score: 0.029
-
Translesion polymerase eta both facilitates DNA replication and promotes increased human genetic variation at common fragile sites. Proc Natl Acad Sci U S A. 2021 11 30; 118(48).
Score: 0.028
-
Structural biochemistry and interaction architecture of the DNA double-strand break repair Mre11 nuclease and Rad50-ATPase. Cell. 2001 May 18; 105(4):473-85.
Score: 0.027
-
DNA damage recognition and repair pathway coordination revealed by the structural biochemistry of DNA repair enzymes. Prog Nucleic Acid Res Mol Biol. 2001; 68:315-47.
Score: 0.027
-
Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease. Prog Biophys Mol Biol. 2021 08; 163:87-108.
Score: 0.026
-
Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair. DNA Repair (Amst). 2020 12; 96:102972.
Score: 0.026
-
Dancing with the elephants: envisioning the structural biology of DNA repair pathways. Mutat Res. 2000 Aug 30; 460(3-4):139-41.
Score: 0.026
-
Lessons learned from structural results on uracil-DNA glycosylase. Mutat Res. 2000 Aug 30; 460(3-4):183-99.
Score: 0.026
-
Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding. EMBO J. 2000 Apr 03; 19(7):1719-30.
Score: 0.025
-
SLX4IP acts with SLX4 and XPF-ERCC1 to promote interstrand crosslink repair. Nucleic Acids Res. 2019 11 04; 47(19):10181-10201.
Score: 0.025
-
Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nat Struct Mol Biol. 2019 06; 26(6):397-406.
Score: 0.024
-
Mutation of an active site residue in Escherichia coli uracil-DNA glycosylase: effect on DNA binding, uracil inhibition and catalysis. Biochemistry. 1999 Apr 13; 38(15):4834-45.
Score: 0.024
-
MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Nat Struct Biol. 1998 Dec; 5(12):1058-64.
Score: 0.023
-
Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Cell. 1998 Oct 02; 95(1):135-46.
Score: 0.023
-
Dissection of DNA double-strand-break repair using novel single-molecule forceps. Nat Struct Mol Biol. 2018 06; 25(6):482-487.
Score: 0.022
-
HU multimerization shift controls nucleoid compaction. Sci Adv. 2016 07; 2(7):e1600650.
Score: 0.020
-
Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase. EMBO J. 1996 Jul 01; 15(13):3442-7.
Score: 0.020
-
Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA. Cell. 1995 Sep 08; 82(5):701-8.
Score: 0.018
-
Structure and function of Escherichia coli endonuclease III. Ann N Y Acad Sci. 1994 Jul 29; 726:215-22.
Score: 0.017
-
Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res. 2014 Jan; 42(2):906-17.
Score: 0.016
-
Eukaryotic class II cyclobutane pyrimidine dimer photolyase structure reveals basis for improved ultraviolet tolerance in plants. J Biol Chem. 2012 Apr 06; 287(15):12060-9.
Score: 0.014
-
Neutralizing mutations of carboxylates that bind metal 2 in T5 flap endonuclease result in an enzyme that still requires two metal ions. J Biol Chem. 2011 Sep 02; 286(35):30878-30887.
Score: 0.014
-
Substrate recognition and catalysis by flap endonucleases and related enzymes. Biochem Soc Trans. 2010 Apr; 38(2):433-7.
Score: 0.013
-
Selenocysteine's mechanism of incorporation and evolution revealed in cDNAs of three glutathione peroxidases. Protein Eng. 1988 Sep; 2(3):239-46.
Score: 0.011
-
Three metal ions participate in the reaction catalyzed by T5 flap endonuclease. J Biol Chem. 2008 Oct 17; 283(42):28741-6.
Score: 0.011
-
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol. 2008 May; 15(5):515-22.
Score: 0.011
-
Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease. J Mol Biol. 2007 Aug 03; 371(1):34-48.
Score: 0.010
-
The C-terminal domain of yeast PCNA is required for physical and functional interactions with Cdc9 DNA ligase. Nucleic Acids Res. 2007; 35(5):1624-37.
Score: 0.010
-
Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase. J Biol Chem. 2004 Nov 05; 279(45):46930-9.
Score: 0.009
-
Structural and functional analysis of Mre11-3. Nucleic Acids Res. 2004; 32(6):1886-93.
Score: 0.008
-
Mre11 and Rad50 from Pyrococcus furiosus: cloning and biochemical characterization reveal an evolutionarily conserved multiprotein machine. J Bacteriol. 2000 Nov; 182(21):6036-41.
Score: 0.007
-
The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. EMBO J. 1997 Nov 03; 16(21):6548-58.
Score: 0.005
-
Evolution of CuZn superoxide dismutase and the Greek key beta-barrel structural motif. Proteins. 1989; 5(4):322-36.
Score: 0.003