Unravelling How Single-Stranded DNA Binding Protein Coordinates DNA Metabolism Using Single-Molecule Approaches

Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA

(2022) Shikai Jin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches

(2022) Jun-Tao Guo et al.   Biomolecules

Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins

(2021) Ondrej Belan et al.   MOLECULAR CELL

Switch-like control of helicase processivity by single-stranded DNA binding protein

(2021) Barbara Stekas et al.   eLife

Unlimited Cooperativity of Betatectivirus SSB, a Novel DNA Binding Protein Related to an Atypical Group of SSBs From Protein-Primed Replicating Bacterial Viruses

(2021) Ana Lechuga et al.   Frontiers in Microbiology

Single-Molecule Insights Into the Dynamics of Replicative Helicases

(2021) Richard R. Spinks et al.   Frontiers in Molecular Biosciences

Duplex DNA engagement and RPA oppositely regulate the DNA-unwinding rate of CMG helicase

(2020) Hazal B. Kose et al.   Nature Communications

Polymerase γ efficiently replicates through many natural template barriers but stalls at the HSP1 quadruplex

(2020) Eric D Sullivan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dynamics of the Eukaryotic Replicative Helicase at Lagging-Strand Protein Barriers Support the Steric Exclusion Model

(2019) Hazal B. Kose et al.   Cell Reports

Replicative DNA polymerases promote active displacement of SSB proteins during lagging strand synthesis

(2019) Fernando Cerrón et al.   NUCLEIC ACIDS RESEARCH

Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase

(2019) Michael R. Wasserman et al.   CELL

The Many Roles of Binding Cooperativity in the Control of DNA Replication

(2019) Peter H. von Hippel et al.   BIOPHYSICAL JOURNAL

Regulation of Nearest-Neighbor Cooperative Binding of E. coli SSB Protein to DNA

(2019) Alexander G. Kozlov et al.   BIOPHYSICAL JOURNAL

Supercoiling DNA optically

(2019) Graeme A. King et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The C-terminal tail of the NEIL1 DNA glycosylase interacts with the human mitochondrial single-stranded DNA binding protein

(2018) Nidhi Sharma et al.   DNA REPAIR

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Dynamics of E. coli single stranded DNA binding (SSB) protein-DNA complexes

(2018) Edwin Antony et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Gp2.5, the multifunctional bacteriophage T7 single-stranded DNA binding protein

(2018) Alfredo J. Hernandez et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study

(2018) Björn Hellenkamp et al.   NATURE METHODS

Reconstitution of anaphase DNA bridge recognition and disjunction

(2018) Kata Sarlós et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The human mitochondrial single-stranded DNA-binding protein displays distinct kinetics and thermodynamics of DNA binding and exchange

(2017) Yufeng Qian et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Glutamate promotes SSB protein–protein Interactions via intrinsically disordered regions

(2017) Alexander G. Kozlov et al.   JOURNAL OF MOLECULAR BIOLOGY

A practical guide to studying G-quadruplex structures using single-molecule FRET

(2017) Parastoo Maleki et al.   MOLECULAR GENETICS AND GENOMICS

Dynamic stepwise opening of integron attC DNA hairpins by SSB prevents toxicity and ensures functionality

(2017) Maj Svea Grieb et al.   NUCLEIC ACIDS RESEARCH

Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers

(2017) Franziska Kriegel et al.   NUCLEIC ACIDS RESEARCH

Shuttling along DNA and directed processing of D-loops by RecQ helicase support quality control of homologous recombination

(2017) Gábor M. Harami et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hyperstretching DNA

(2017) Koen Schakenraad et al.   Nature Communications

Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34

(2017) Elina Cernooka et al.   Scientific Reports

Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements

(2016) Domenico Salerno et al.   BIOPHYSICAL JOURNAL

Role of XPD in cellular functions: To TFIIH and beyond

(2016) Bennett Van Houten et al.   DNA REPAIR

Sliding sleeves of XRCC4–XLF bridge DNA and connect fragments of broken DNA

(2016) Ineke Brouwer et al.   NATURE

MGME1 processes flaps into ligatable nicks in concert with DNA polymerase γ during mtDNA replication

(2016) Jay P. Uhler et al.   NUCLEIC ACIDS RESEARCH

Chemo-mechanical pushing of proteins along single-stranded DNA

(2016) Joshua E. Sokoloski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mitochondrial Single-stranded DNA-binding Proteins Stimulate the Activity of DNA Polymerase γ by Organization of the Template DNA

(2015) Grzegorz L. Ciesielski et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Intrinsically Disordered C-Terminal Tails of E . coli Single-Stranded DNA Binding Protein Regulate Cooperative Binding to Single-Stranded DNA

(2015) Alexander G. Kozlov et al.   JOURNAL OF MOLECULAR BIOLOGY

Nanopore Analysis of Single-Stranded Binding Protein Interactions with DNA

(2015) Michael M. Marshall et al.   LANGMUIR

Mapping the interactions of the single-stranded DNA binding protein of bacteriophage T4 (gp32) with DNA lattices at single nucleotide resolution: gp32 monomer binding

(2015) Davis Jose et al.   NUCLEIC ACIDS RESEARCH

Regulation of yeast DNA polymerase δ-mediated strand displacement synthesis by 5′-flaps

(2015) Katrina N. Koc et al.   NUCLEIC ACIDS RESEARCH

Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach

(2015) Michael J. Morten et al.   NUCLEIC ACIDS RESEARCH

Double-stranded DNA translocase activity of transcription factor TFIIH and the mechanism of RNA polymerase II open complex formation

(2015) James Fishburn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The exonuclease activity of DNA polymerase γ is required for ligation during mitochondrial DNA replication

(2015) Bertil Macao et al.   Nature Communications

The HRDC domain of E. coli RecQ helicase controls single-stranded DNA translocation and double-stranded DNA unwinding rates without affecting mechanoenzymatic coupling

(2015) Gábor M. Harami et al.   Scientific Reports

Cooperative base pair melting by helicase and polymerase positioned one nucleotide from each other

(2015) Divya Nandakumar et al.   eLife

Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways

(2015) Sukrit Suksombat et al.   eLife

Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function

(2015) Jason C Bell et al.   eLife

Linear mtDNA fragments and unusual mtDNA rearrangements associated with pathological deficiency of MGME1 exonuclease

(2014) Thomas J. Nicholls et al.   HUMAN MOLECULAR GENETICS

Ultrafast Redistribution of E. coli SSB along Long Single-Stranded DNA via Intersegment Transfer

(2014) Kyung Suk Lee et al.   JOURNAL OF MOLECULAR BIOLOGY

Single-molecule studies of polymerase dynamics and stoichiometry at the bacteriophage T7 replication machinery

(2014) H. J. Geertsema 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

In TFIIH, XPD Helicase Is Exclusively Devoted to DNA Repair

(2014) Jochen Kuper et al.   PLOS BIOLOGY

In Vivo Occupancy of Mitochondrial Single-Stranded DNA Binding Protein Supports the Strand Displacement Mode of DNA Replication

(2014) Javier Miralles Fusté et al.   PLoS Genetics

A toolbox for generating single-stranded DNA in optical tweezers experiments

(2013) Andrea Candelli et al.   BIOPOLYMERS

PriC-mediated DNA Replication Restart Requires PriC Complex Formation with the Single-stranded DNA-binding Protein

(2013) Sarah R. Wessel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Interaction of T4 UvsW Helicase and Single-Stranded DNA Binding Protein gp32 through Its Carboxy-Terminal Acidic Tail

(2013) Senthil K. Perumal et al.   JOURNAL OF MOLECULAR BIOLOGY

Exonuclease of human DNA polymerase gamma disengages its strand displacement function

(2013) Quan He et al.   MITOCHONDRION

STED nanoscopy combined with optical tweezers reveals protein dynamics on densely covered DNA

(2013) Iddo Heller et al.   NATURE METHODS

Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA

(2013) Jichuan Zhang et al.   NUCLEIC ACIDS RESEARCH

Structural mechanisms of PriA-mediated DNA replication restart

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

Rescuing Stalled or Damaged Replication Forks

(2013) J. T. P. Yeeles et al.   Cold Spring Harbor Perspectives in Biology

Structural features of the single-stranded DNA-binding protein MoSub1 fromMagnaporthe oryzae

(2012) Jinguang Huang et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Single-Molecule Views of Protein Movement on Single-Stranded DNA

(2012) Taekjip Ha et al.   Annual Review of Biophysics

Specificity of Binding of Single-Stranded DNA-Binding Protein to Its Target

(2012) Luda S. Shlyakhtenko et al.   BIOCHEMISTRY

Superfamily 2 helicases

(2012) Alicia et al.   Frontiers in Bioscience-Landmark

The PriA Replication Restart Protein Blocks Replicase Access Prior to Helicase Assembly and Directs Template Specificity through Its ATPase Activity

(2012) Carol M. Manhart et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Electrostatics of Nucleic Acid Folding under Conformational Constraint

(2012) Peter C. Anthony et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Direct imaging of RecA nucleation and growth on single molecules of SSB-coated ssDNA

(2012) Jason C. Bell et al.   NATURE

Replication–transcription conflicts in bacteria

(2012) Houra Merrikh et al.   NATURE REVIEWS MICROBIOLOGY

Collaborative coupling between polymerase and helicase for leading-strand synthesis

(2012) Maria Manosas et al.   NUCLEIC ACIDS RESEARCH

Mechanism of strand displacement synthesis by DNA replicative polymerases

(2012) Maria Manosas et al.   NUCLEIC ACIDS RESEARCH

Non-specific binding of Na + and Mg 2+ to RNA determined by force spectroscopy methods

(2012) C. V. Bizarro et al.   NUCLEIC ACIDS RESEARCH

Direct Observation of Stalled Fork Restart via Fork Regression in the T4 Replication System

(2012) M. Manosas et al.   SCIENCE

SSB Functions as a Sliding Platform that Migrates on DNA via Reptation

(2011) Ruobo Zhou et al.   CELL

Selective Bypass of a Lagging Strand Roadblock by the Eukaryotic Replicative DNA Helicase

(2011) Yu V. Fu et al.   CELL

Iron–sulphur clusters in nucleic acid processing enzymes

(2011) Malcolm F White et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

A history of TFIIH: Two decades of molecular biology on a pivotal transcription/repair factor

(2011) Jean-Marc Egly et al.   DNA REPAIR

XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase

(2011) Jill O. Fuss et al.   DNA REPAIR

Imaging of nucleic acids with atomic force microscopy

(2011) Yuri L. Lyubchenko et al.   METHODS

Combining optical trapping, fluorescence microscopy and micro-fluidics for single molecule studies of DNA–protein interactions

(2011) Andrea Candelli et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Phylogenetic and Complementation Analysis of a Single-Stranded DNA Binding Protein Family from Lactococcal Phages Indicates a Non-Bacterial Origin

(2011) Agnieszka K. Szczepankowska et al.   PLoS One

Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR

(2011) Y. Takayama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Molecule Studies of the Replisome

(2010) Antoine M. van Oijen et al.   Annual Review of Biophysics

Binding Specificity ofEscherichia coliSingle-Stranded DNA Binding Protein for the χ Subunit of DNA pol III Holoenzyme and PriA Helicase

(2010) Alexander G. Kozlov et al.   BIOCHEMISTRY

FtsK DNA Translocase: The Fast Motor That Knows Where It's Going

(2010) Estelle Crozat et al.   CHEMBIOCHEM

SF1 and SF2 helicases: family matters

(2010) Margaret E Fairman-Williams et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Timing, Coordination, and Rhythm: Acrobatics at the DNA Replication Fork

(2010) Samir M. Hamdan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Two Modes of Interaction of the Single-stranded DNA-binding Protein of Bacteriophage T7 with the DNA Polymerase-Thioredoxin Complex

(2010) Sharmistha Ghosh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulation of Single-stranded DNA Binding by the C Termini of Escherichia coli Single-stranded DNA-binding (SSB) Protein

(2010) Alexander G. Kozlov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MMXD, a TFIIH-Independent XPD-MMS19 Protein Complex Involved in Chromosome Segregation

(2010) Shinsuke Ito et al.   MOLECULAR CELL

Active and passive mechanisms of helicases

(2010) Maria Manosas et al.   NUCLEIC ACIDS RESEARCH

Torsional regulation of hRPA-induced unwinding of double-stranded DNA

(2010) Iwijn De Vlaminck et al.   NUCLEIC ACIDS RESEARCH

Quantitative Modeling and Optimization of Magnetic Tweezers

(2009) Jan Lipfert et al.   BIOPHYSICAL JOURNAL

Structural Insight into Processive Human Mitochondrial DNA Synthesis and Disease-Related Polymerase Mutations

(2009) Young-Sam Lee et al.   CELL

Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli

(2009) N. Handa et al.   GENES & DEVELOPMENT

Single Molecule Analysis of a Red Fluorescent RecA Protein Reveals a Defect in Nucleoprotein Filament Nucleation That Relates to Its Reduced Biological Functions

(2009) Naofumi Handa et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

C-terminal Phenylalanine of Bacteriophage T7 Single-stranded DNA-binding Protein Is Essential for Strand Displacement Synthesis by T7 DNA Polymerase at a Nick in DNA

(2009) Sharmistha Ghosh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Strand Displacement by DNA Polymerase III Occurs through a τ-ψ-χ Link to Single-stranded DNA-binding Protein Coating the Lagging Strand Template

(2009) Quan Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single-Stranded DNA-Binding Protein Complex from Helicobacter pylori Suggests an ssDNA-Binding Surface

(2009) Kun-Wei Chan et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2009) Masayoshi Honda et al.   MOLECULAR CELL

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

(2009) Rahul Roy et al.   NATURE

Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome

(2009) Maria Manosas et al.   Nature Chemical Biology

Real-time single-molecule observation of rolling-circle DNA replication

(2009) Nathan A. Tanner et al.   NUCLEIC ACIDS RESEARCH

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

XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations

(2008) Li Fan et al.   CELL

RecQ helicases: guardian angels of the DNA replication fork

(2008) Csanád Z. Bachrati et al.   CHROMOSOMA

SSB as an Organizer/Mobilizer of Genome Maintenance Complexes

(2008) Robert D. Shereda et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Ferroplasma acidarmanus RPA2 Facilitates Efficient Unwinding of Forked DNA Substrates by Monomers of FacXPD Helicase

(2008) Robert A. Pugh et al.   JOURNAL OF MOLECULAR BIOLOGY

Human DNA2 Is a Mitochondrial Nuclease/Helicase for Efficient Processing of DNA Replication and Repair Intermediates

(2008) Li Zheng 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

Non-hexameric DNA helicases and translocases: mechanisms and regulation

(2008) Timothy M. Lohman et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-molecule studies of fork dynamics in Escherichia coli DNA replication

(2008) Nathan A Tanner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNA

(2008) L. Shokri et al.   NUCLEIC ACIDS RESEARCH

Single Strand Binding Proteins Increase the Processivity of DNA Unwinding by the Hepatitis C Virus Helicase

(2007) Vaishnavi Rajagopal et al.   JOURNAL OF MOLECULAR BIOLOGY