Single-molecule views of protein movement on single-stranded DNA.

scientific article published on 23 February 2012

Single-molecule views of protein movement on single-stranded DNA. is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1146/ANNUREV-BIOPHYS-042910-155351
P932PMC publication ID3719979
P698PubMed publication ID22404684
P5875ResearchGate publication ID221690743

P50authorTaekjip HaQ7674759
Timothy M. LohmanQ7807375
P2093author name stringAlexander G Kozlov
P2860cites workSSB as an organizer/mobilizer of genome maintenance complexesQ79661973
Elastic properties of a single-stranded charged homopolymeric ribonucleotideQ80786214
Replication Protein A (RPA): The Eukaryotic SSBQ22066159
Tyrosine phosphorylation enhances RAD52-mediated annealing by modulating its DNA binding.Q24318110
RNA helicases at work: binding and rearrangingQ24603646
Active and passive mechanisms of helicasesQ24610541
The single-stranded DNA-binding protein of Escherichia coliQ24634735
Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicaseQ24642351
Direct imaging of human Rad51 nucleoprotein dynamics on individual DNA moleculesQ24654281
Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanismQ24669910
Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolutionQ24670433
Characterization of individual polynucleotide molecules using a membrane channelQ24681325
NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening forkQ27481047
Structure of the DNA binding domain of E. coli SSB bound to ssDNAQ27626150
Structure of the gene 2.5 protein, a single-stranded DNA binding protein encoded by bacteriophage T7Q27633789
UvrD helicase unwinds DNA one base pair at a time by a two-part power strokeQ27640956
Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implicationsQ27641751
Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structuresQ27650665
Single-stranded DNA-binding protein complex from Helicobacter pylori suggests an ssDNA-binding surfaceQ27654116
Rotations of the 2B Sub-domain of E. coli UvrD Helicase/Translocase Coupled to Nucleotide and DNA BindingQ27670550
Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNAQ27729794
Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolutionQ27734819
A single-stranded DNA binding protein required for mitochondrial DNA replication in S. cerevisiae is homologous to E. coli SSBQ27938802
Srs2 disassembles Rad51 filaments by a protein-protein interaction triggering ATP turnover and dissociation of Rad51 from DNA.Q27938895
Initiation of genetic recombination and recombination-dependent replicationQ28141289
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Structural transitions within human Rad51 nucleoprotein filaments.Q37293375
SSB protein diffusion on single-stranded DNA stimulates RecA filament formation.Q37435878
Stepwise translocation of nucleic acid motors.Q37671354
Imaging of single molecule diffusionQ37680828
Insight into helicase mechanism and function revealed through single-molecule approachesQ37777437
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Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary associationQ38323281
Escherichia coli single-stranded DNA binding protein is mobile on DNA: 1H NMR study of its interaction with oligo- and polynucleotidesQ38353192
Direct measurements of the stabilization of single-stranded DNA under tension by single-stranded binding proteinsQ38439985
Changes in the tension in dsDNA alter the conformation of RecA bound to dsDNA-RecA filamentsQ38855351
Single-stranded DNA binding proteins required for DNA replicationQ39740421
Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activityQ39750512
Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA.Q39899310
UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli.Q40919283
5'-Single-stranded/duplex DNA junctions are loading sites for E. coli UvrD translocaseQ41694137
An absolute method for the determination of the persistence length of native DNA from electron micrographsQ41726080
Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein.Q41844418
DNA helicase activity of PcrA is not required for the displacement of RecA protein from DNA or inhibition of RecA-mediated strand exchange.Q41908991
Processive translocation mechanism of the human Bloom's syndrome helicase along single-stranded DNA.Q41992667
A nonuniform stepping mechanism for E. coli UvrD monomer translocation along single-stranded DNAQ42030386
Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicaseQ42159743
The nature of the force-induced conformation transition of dsDNA studied by using single molecule force spectroscopyQ43153049
Mechanism of RecA-mediated homologous recombination revisited by single molecule nanomanipulation.Q43248578
Reversible unfolding of single RNA molecules by mechanical forceQ43590684
Quantitative analysis of the kinetics of end-dependent disassembly of RecA filaments from ssDNA.Q44082228
Kinetic mechanism of direct transfer of Escherichia coli SSB tetramers between single-stranded DNA moleculesQ44148069
Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicaseQ44175920
Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorderQ44264525
Salt dependent binding of T4 gene 32 protein to single and double-stranded DNA: single molecule force spectroscopy measurementsQ44823457
Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: the effect of the 3' arm and the stability of the dsDNA on the unwinding activity of the Escherichia coli DnaB helicaseQ45069464
Homologous recombination in real time: DNA strand exchange by RecA.Q46579775
Repetitive shuttling of a motor protein on DNA.Q46776457
Demonstration of unidirectional single-stranded DNA translocation by PcrA helicase: measurement of step size and translocation speedQ47249752
Kinetic measurement of the step size of DNA unwinding by Escherichia coli UvrD helicaseQ47315601
Mechanical measurement of single-molecule binding rates: kinetics of DNA helix-destabilization by T4 gene 32 proteinQ47737307
Direct observation of multiple pathways of single-stranded DNA stretching.Q49526400
MCM forked substrate specificity involves dynamic interaction with the 5'-tail.Q50664621
Nonlinear low-force elasticity of single-stranded DNA molecules.Q51849738
Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration.Q52673770
A motor that makes its own track: helicase unwinding of DNA.Q53848563
Observation of a single-beam gradient force optical trap for dielectric particlesQ54197257
Bacillus stearothermophilus PcrA monomer is a single-stranded DNA translocase but not a processive helicase in vitro.Q54437963
Effects of Escherichia coli SSB protein on the single-stranded DNA-dependent ATPase activity of Escherichia coli RecA protein. Evidence that SSB protein facilitates the binding of RecA protein to regions of secondary structure within single-strandedQ54768170
Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibilityQ57367231
Helix-Coil Kinetics of Individual Polyadenylic Acid Molecules in a Protein ChannelQ57905440
χ-Sequence recognition and DNA translocation by single RecBCD helicase/nuclease moleculesQ59098644
Binding mode transitions of Escherichia coli single strand binding protein-single-stranded DNA complexes. Cation, anion, pH, and binding density effectsQ68130424
Escherichia coli single-strand binding protein forms multiple, distinct complexes with single-stranded DNAQ68927238
Visualization of SSB-ssDNA complexes active in the assembly of stable RecA-DNA filamentsQ70415897
Measurement of lactose repressor-mediated loop formation and breakdown in single DNA moleculesQ72417475
No sliding during homology search by RecA proteinQ77545299
Stretching single stranded DNA, a model polyelectrolyteQ78671406
Single molecule force spectroscopy of salt-dependent bacteriophage T7 gene 2.5 protein binding to single-stranded DNAQ79271219
Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolismQ28245231
VirE2: a unique ssDNA-compacting molecular machineQ28472239
Single-molecule analysis reveals the kinetics and physiological relevance of MutL-ssDNA bindingQ28476139
OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequencesQ29620102
Structure and mechanism of helicases and nucleic acid translocasesQ29620151
Saccharomyces cerevisiae replication protein A binds to single-stranded DNA in multiple salt-dependent modesQ30441264
How directional translocation is regulated in a DNA helicase motorQ30480704
Impediment of E. coli UvrD by DNA-destabilizing force reveals a strained-inchworm mechanism of DNA unwindingQ30485195
Dynamics of RecA filaments on single-stranded DNAQ30488763
Single-molecule analysis reveals differential effect of ssDNA-binding proteins on DNA translocation by XPD helicaseQ30491608
Direct observation of twisting steps during Rad51 polymerization on DNA.Q30491797
Torsional regulation of hRPA-induced unwinding of double-stranded DNA.Q30495260
Visualizing helicases unwinding DNA at the single molecule levelQ30495681
Single-molecule analysis reveals three phases of DNA degradation by an exonucleaseQ30500295
Electrokinetic trapping at the one nanometer limit.Q30500817
High-resolution, single-molecule measurements of biomolecular motionQ30501806
Single-molecule assay reveals strand switching and enhanced processivity of UvrDQ30579543
Forward and reverse motion of single RecBCD molecules on DNA.Q30751649
Processive translocation and DNA unwinding by individual RecBCD enzyme moleculesQ30980458
Polymerization and mechanical properties of single RecA-DNA filamentsQ31395922
Biocompatible force sensor with optical readout and dimensions of 6 nm3.Q33223781
Extreme conformational diversity in human telomeric DNAQ33229923
Microsecond dynamics of protein-DNA interactions: direct observation of the wrapping/unwrapping kinetics of single-stranded DNA around the E. coli SSB tetramerQ33242508
Polymer properties of polythymine as revealed by translational diffusionQ33285129
Counting RAD51 proteins disassembling from nucleoprotein filaments under tension.Q33390361
ILPR G-quadruplexes formed in seconds demonstrate high mechanical stabilities.Q33401032
Human Rad52 binds and wraps single-stranded DNA and mediates annealing via two hRad52-ssDNA complexesQ33524756
Single-molecule TPM studies on the conversion of human telomeric DNAQ33795604
Single-molecule studies of the effect of template tension on T7 DNA polymerase activity.Q33893261
Structure and function of hexameric helicases.Q34019405
PcrA helicase dismantles RecA filaments by reeling in DNA in uniform stepsQ34144302
Probing single-stranded DNA conformational flexibility using fluorescence spectroscopyQ34185396
The elasticity of a single supercoiled DNA moleculeQ34374724
Studies on the structure and dynamics of the human telomeric G quadruplex by single-molecule fluorescence resonance energy transferQ34382392
Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor.Q34387536
DNA primase acts as a molecular brake in DNA replicationQ34490702
Analysis of single-molecule FRET trajectories using hidden Markov modelingQ34536849
Real-time observation of RecA filament dynamics with single monomer resolution.Q34556173
Direct observation of individual RecA filaments assembling on single DNA moleculesQ34567581
Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpinsQ34597333
Non-hexameric DNA helicases and translocases: mechanisms and regulationQ34770065
Do-it-yourself guide: how to use the modern single-molecule toolkitQ34782759
High-throughput single-molecule optofluidic analysisQ34788307
The RecA/RAD51 protein drives migration of Holliday junctions via polymerization on DNA.Q34835783
Biochemistry of eukaryotic homologous recombinationQ34925302
Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivityQ34937813
SSB functions as a sliding platform that migrates on DNA via reptation.Q35162915
Steric exclusion and wrapping of the excluded DNA strand occurs along discrete external binding paths during MCM helicase unwinding.Q35174785
Real-time observation of strand exchange reaction with high spatiotemporal resolutionQ35186210
Escherichia coli DNA helicases: mechanisms of DNA unwindingQ35225286
Replication by a single DNA polymerase of a stretched single-stranded DNAQ35364666
Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocaseQ35590981
From RPA to BRCA2: lessons from single-stranded DNA binding by the OB-foldQ35753202
Fueling protein DNA interactions inside porous nanocontainers.Q35921608
Kinetics of conformational fluctuations in DNA hairpin-loopsQ36206384
Structure and mechanism of Escherichia coli RecA ATPaseQ36272177
Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like unitsQ36313556
Real-time measurements of the nucleation, growth and dissociation of single Rad51-DNA nucleoprotein filamentsQ36328990
Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicaseQ36392919
Measurement of the salt-dependent stabilization of partially open DNA by Escherichia coli SSB proteinQ36471394
RecA binding to a single double-stranded DNA molecule: a possible role of DNA conformational fluctuationsQ36523051
Kinetics and thermodynamics of salt-dependent T7 gene 2.5 protein binding to single- and double-stranded DNAQ36909335
Human Rad52-mediated homology search and annealing occurs by continuous interactions between overlapping nucleoprotein complexesQ37068558
Single-molecule four-color FRET.Q37071039
BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiationQ37105584
Single-molecule detection of folding and unfolding of the G-quadruplex aptamer in a nanopore nanocavity.Q37108469
Advances in single-molecule fluorescence methods for molecular biologyQ37138480
P304page(s)295-319
P577publication date2012-02-23
P1433published inAnnual Review of BiophysicsQ4034062
P1476titleSingle-molecule views of protein movement on single-stranded DNA.
P478volume41

Reverse relations

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