Single-molecule fluorescence imaging techniques reveal molecular mechanisms underlying deoxyribonucleic acid damage repair

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

(2022) Yujin Kang et al.   Jove-Journal of Visualized Experiments

Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway

(2021) Benjamin M. Stinson et al.   Annual Review of Biochemistry

Regeneration of PEG slide for multiple rounds of single molecule measurements

(2021) Tapas Paul et al.   BIOPHYSICAL JOURNAL

Dynamics of Ku and bacterial non-homologous end-joining characterized using single DNA molecule analysis

(2021) Robin Öz et al.   NUCLEIC ACIDS RESEARCH

Linker domain function predicts pathogenic MLH1 missense variants

(2021) James London et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single molecule microscopy reveals key physical features of repair foci in living cells

(2021) Judith Miné-Hattab et al.   eLife

Sequence-dependent cost for Z-form shapes the torsion-driven B–Z transition via close interplay of Z-DNA and DNA bubble

(2021) Sook Ho Kim et al.   NUCLEIC ACIDS RESEARCH

Single molecule analysis indicates stimulation of MUTYH by UV-DDB through enzyme turnover

(2021) Sunbok Jang et al.   NUCLEIC ACIDS RESEARCH

Regulatory R-loops as facilitators of gene expression and genome stability

(2020) Christof Niehrs et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA-dependent protein kinase promotes DNA end processing by MRN and CtIP

(2020) Rajashree A. Deshpande et al.   Science Advances

E. coli Rep helicase and RecA recombinase unwind G4 DNA and are important for resistance to G4-stabilizing ligands

(2020) Tapas Paul et al.   NUCLEIC ACIDS RESEARCH

Rad54 Drives ATP Hydrolysis-Dependent DNA Sequence Alignment during Homologous Recombination

(2020) J. Brooks Crickard et al.   CELL

Detection of OG:A Lesion Mispairs by MutY Relies on a Single His Residue and the 2-Amino Group of 8-Oxoguanine

(2020) Andrea J. Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mismatch Repair Pathway, Genome Stability and Cancer

(2020) Nives Pećina-Šlaus et al.   Frontiers in Molecular Biosciences

TonEBP recognizes R-loops and initiates m6A RNA methylation for R-loop resolution

(2020) Hyun Je Kang et al.   NUCLEIC ACIDS RESEARCH

Junction resolving enzymes use multivalency to keep the Holliday junction dynamic

(2019) Ruobo Zhou et al.   Nature Chemical Biology

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

(2019) Kathleen T. Xie et al.   SCIENCE

Eukaryotic Base Excision Repair: New Approaches Shine Light on Mechanism

(2019) William A. Beard et al.   Annual Review of Biochemistry

DNA skybridge: 3D structure producing a light sheet for high-throughput single-molecule imaging

(2019) Daehyung Kim et al.   NUCLEIC ACIDS RESEARCH

Poly(ADP-ribose) polymerase-1 antagonizes DNA resection at double-strand breaks

(2019) Marie-Christine Caron et al.   Nature Communications

Single-Molecule Electrical Detection: A Promising Route toward the Fundamental Limits of Chemistry and Life Science

(2019) Yu Li et al.   ACCOUNTS OF CHEMICAL RESEARCH

Rad52 Restrains Resection at DNA Double-Strand Break Ends in Yeast

(2019) Zhenxin Yan et al.   MOLECULAR CELL

The balancing act of R-loop biology: The good, the bad, and the ugly

(2019) Youssef A. Hegazy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

N6-methyladenosine regulates the stability of RNA:DNA hybrids in human cells

(2019) Abdulkadir Abakir et al.   NATURE GENETICS

DNA Repair: The Search for Homology

(2018) James E. Haber   BIOESSAYS

Two distinct conformational states define the interaction of human RAD51‐ATP with single‐stranded DNA

(2018) Ineke Brouwer et al.   EMBO JOURNAL

Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer

(2018) Eitan Lerner et al.   SCIENCE

DNA replication stress triggers rapid DNA replication fork breakage by Artemis and XPF

(2018) Rémy Bétous et al.   PLoS Genetics

Concurrent live imaging of DNA double-strand break repair and cell-cycle progression by CRISPR/Cas9-mediated knock-in of a tricistronic vector

(2018) Kensuke Otsuka et al.   Scientific Reports

A change of view: homologous recombination at single-molecule resolution

(2017) Kyle Kaniecki et al.   NATURE REVIEWS GENETICS

Non-homologous DNA end joining and alternative pathways to double-strand break repair

(2017) Howard H. Y. Chang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

(2017) Michael H Hauer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Recruitment of UvrBC complexes to UV-induced damage in the absence of UvrA increases cell survival

(2017) Luke Springall et al.   NUCLEIC ACIDS RESEARCH

A mitosis-specific and R loop–driven ATR pathway promotes faithful chromosome segregation

(2017) Lilian Kabeche et al.   SCIENCE

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

(2017) Michael H Hauer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Yeast Srs2 Helicase Promotes Redistribution of Single-Stranded DNA-Bound RPA and Rad52 in Homologous Recombination Regulation

(2017) Luisina De Tullio et al.   Cell Reports

Dissociation of Rad51 Presynaptic Complexes and Heteroduplex DNA Joints by Tandem Assemblies of Srs2

(2017) Kyle Kaniecki et al.   Cell Reports

Mechanism and regulation of DNA end resection in eukaryotes

(2016) Lorraine S. Symington   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

The DNA fibre technique – tracking helicases at work

(2016) Jadwiga Nieminuszczy et al.   METHODS

Single-Molecule Imaging Reveals that Rad4 Employs a Dynamic DNA Damage Recognition Process

(2016) Muwen Kong et al.   MOLECULAR CELL

A Polar and Nucleotide-Dependent Mechanism of Action for RAD51 Paralogs in RAD51 Filament Remodeling

(2016) Martin R.G. Taylor et al.   MOLECULAR CELL

The Fanconi anaemia pathway: new players and new functions

(2016) Raphael Ceccaldi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Distinct binding of BRCA2 BRC repeats to RAD51 generates differential DNA damage sensitivity

(2016) Gouri Chatterjee et al.   NUCLEIC ACIDS RESEARCH

Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions

(2016) Maxwell W. Brown et al.   Nature Communications

Coordinated nuclease activities counteract Ku at single-ended DNA double-strand breaks

(2016) Pauline Chanut et al.   Nature Communications

A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement

(2016) Sona Valuchova et al.   Scientific Reports

Promotion of RAD51-Mediated Homologous DNA Pairing by the RAD51AP1-UAF1 Complex

(2016) Fengshan Liang et al.   Cell Reports

DNA Sequence Alignment by Microhomology Sampling during Homologous Recombination

(2015) Zhi Qi et al.   CELL

Base triplet stepping by the Rad51/RecA family of recombinases

(2015) J. Y. Lee et al.   SCIENCE

Optical Tweezers Analysis of DNA–Protein Complexes

(2014) Iddo Heller et al.   CHEMICAL REVIEWS

Base excision repair: A critical player in many games

(2014) Susan S. Wallace   DNA REPAIR

Single-Molecule Imaging of FtsK Translocation Reveals Mechanistic Features of Protein-Protein Collisions on DNA

(2014) Ja Yil Lee et al.   MOLECULAR CELL

Understanding nucleotide excision repair and its roles in cancer and ageing

(2014) Jurgen A. Marteijn et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates

(2014) H. Ghodke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization and quantification of nascent RAD51 filament formation at single-monomer resolution

(2014) Andrea Candelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein induced fluorescence enhancement (PIFE) for probing protein–nucleic acid interactions

(2013) Helen Hwang et al.   CHEMICAL SOCIETY REVIEWS

Replication Dynamics: Biases and Robustness of DNA Fiber Analysis

(2013) Hervé Técher et al.   JOURNAL OF MOLECULAR BIOLOGY

Real-time single-molecule imaging reveals a direct interaction between UvrC and UvrB on DNA tightropes

(2013) Craig D. Hughes et al.   NUCLEIC ACIDS RESEARCH

Visualization of local DNA unwinding by Mre11/Rad50/Nbs1 using single-molecule FRET

(2013) B. Cannon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule views on homologous recombination

(2013) Andrea Candelli et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Nucleotide Excision Repair in Eukaryotes

(2013) O. D. Scharer   Cold Spring Harbor Perspectives in Biology

Srs2 prevents Rad51 filament formation by repetitive motion on DNA

(2013) Yupeng Qiu et al.   Nature Communications

Single-Stranded DNA Curtains for Real-Time Single-Molecule Visualization of Protein–Nucleic Acid Interactions

(2012) Bryan Gibb et al.   ANALYTICAL CHEMISTRY

Recent Advances in Magnetic Tweezers

(2012) Iwijn De Vlaminck et al.   Annual Review of Biophysics

Measuring intermolecular rupture forces with a combined TIRF-optical trap microscope and DNA curtains

(2012) Ja Yil Lee et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

From yeast to mammals: Recent advances in genetic control of homologous recombination

(2012) Yoav Karpenshif et al.   DNA REPAIR

Analysis of DNA replication profiles in budding yeast and mammalian cells using DNA combing

(2012) Julien N. Bianco et al.   METHODS

How RecBCD Enzyme and Chi Promote DNA Break Repair and Recombination: a Molecular Biologist's View

(2012) G. R. Smith   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Mechanism of Homology Recognition in DNA Recombination from Dual-Molecule Experiments

(2012) Iwijn De Vlaminck et al.   MOLECULAR CELL

Quantitative Live Cell Imaging Reveals a Gradual Shift between DNA Repair Mechanisms and a Maximal Use of HR in Mid S Phase

(2012) Ketki Karanam et al.   MOLECULAR CELL

Single-molecule imaging of DNA curtains reveals mechanisms of KOPS sequence targeting by the DNA translocase FtsK

(2012) J. Y. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Double-Strand Break Repair-Independent Role for BRCA2 in Blocking Stalled Replication Fork Degradation by MRE11

(2011) Katharina Schlacher et al.   CELL

Conformational trapping of Mismatch Recognition Complex MSH2/MSH3 on repair-resistant DNA loops

(2011) W. H. Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity

(2011) H. Hwang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule Four-Color FRET

(2010) Jinwoo Lee  et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

PcrA Helicase Dismantles RecA Filaments by Reeling in DNA in Uniform Steps

(2010) Jeehae Park et al.   CELL

Making the best of the loose ends: Mre11/Rad50 complexes and Sae2 promote DNA double-strand break resection

(2010) Tanya T. Paull   DNA REPAIR

Collaborative Dynamic DNA Scanning by Nucleotide Excision Repair Proteins Investigated by Single- Molecule Imaging of Quantum-Dot-Labeled Proteins

(2010) Neil M. Kad et al.   MOLECULAR CELL

Exo1 Competes with Repair Synthesis, Converts NER Intermediates to Long ssDNA Gaps, and Promotes Checkpoint Activation

(2010) Michele Giannattasio et al.   MOLECULAR CELL

Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase

(2010) Ilya J. Finkelstein et al.   NATURE

Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments

(2010) Jan Lipfert et al.   NATURE METHODS

Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52–ssDNA complexes

(2010) Jill M. Grimme et al.   NUCLEIC ACIDS RESEARCH

Minute negative superhelicity is sufficient to induce the B-Z transition in the presence of low tension

(2010) M. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UV-DDB: A molecular machine linking DNA repair with ubiquitination

(2009) Kaoru Sugasawa   DNA REPAIR

BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation

(2009) Jaya G Yodh et al.   EMBO JOURNAL

Nanofabricated Racks of Aligned and Anchored DNA Substrates for Single-Molecule Imaging

(2009) Jason Gorman et al.   LANGMUIR

Single-Molecule Analysis Reveals Differential Effect of ssDNA-Binding Proteins on DNA Translocation by XPD Helicase

(2009) Masayoshi Honda et al.   MOLECULAR CELL

Srs2 Disassembles Rad51 Filaments by a Protein-Protein Interaction Triggering ATP Turnover and Dissociation of Rad51 from DNA

(2009) Edwin Antony et al.   MOLECULAR CELL

The DNA-damage response in human biology and disease

(2009) Stephen P. Jackson et al.   NATURE

SSB protein diffusion on single-stranded DNA stimulates RecA filament formation

(2009) Rahul Roy et al.   NATURE

Dynamics of RecA filaments on single-stranded DNA

(2009) Marijn T. J. van Loenhout et al.   NUCLEIC ACIDS RESEARCH

Rad52 promotes second-end DNA capture in double-stranded break repair to form complement-stabilized joint molecules

(2009) A. V. Nimonkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct observation of twisting steps during Rad51 polymerization on DNA

(2009) H. Arata et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Live cell microscopy analysis of radiation-induced DNA double-strand break motion

(2009) B. Jakob et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA molecules

(2009) J. Hilario et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent Advances in Optical Tweezers

(2008) Jeffrey R. Moffitt et al.   Annual Review of Biochemistry

Advances in Single-Molecule Fluorescence Methods for Molecular Biology

(2008) Chirlmin Joo et al.   Annual Review of Biochemistry

Structure of the DNA Repair Helicase XPD

(2008) Huanting Liu et al.   CELL

RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks

(2008) M. S. Dillingham et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Homologous Recombination in Real Time: DNA Strand Exchange by RecA

(2008) Thijn van der Heijden et al.   MOLECULAR CELL

Mechanism of homologous recombination from the RecA–ssDNA/dsDNA structures

(2008) Zhucheng Chen et al.   NATURE

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

(2008) Keir C Neuman et al.   NATURE METHODS

Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexes

(2008) E. Rothenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Repair of UV damage in bacteria

(2007) Nora Goosen et al.   DNA REPAIR