Numerical investigation of sequence dependence in homologous recognition: evidence for homology traps.

PubWeight™: 0.78‹?›

🔗 View Article (PMC 1305611)

Published in Biophys J on March 04, 2005

Authors

Renaud Fulconis1, Marie Dutreix, Jean-Louis Viovy

Author Affiliations

1: Laboratoire Physico-Chimie Curie, UMR Centre National de la Recherche Scientifique 168, Institut Curie, Orsay, France.

Articles cited by this

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science (1996) 18.53

DNA: an extensible molecule. Science (1996) 8.19

Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol Mol Biol Rev (1999) 6.92

DNA damage tolerance, mismatch repair and genome instability. Bioessays (1994) 2.23

Structure of helical RecA-DNA complexes. Complexes formed in the presence of ATP-gamma-S or ATP. J Mol Biol (1986) 2.09

RecA binding to a single double-stranded DNA molecule: a possible role of DNA conformational fluctuations. Proc Natl Acad Sci U S A (1998) 2.00

Networks of DNA and RecA protein are intermediates in homologous pairing. Biochemistry (1985) 1.75

Pairing of homologous DNA sequences by proteins: evidence for three-stranded DNA. Genes Dev (1990) 1.70

The pairing activity of stable nucleoprotein filaments made from recA protein, single-stranded DNA, and adenosine 5'-(gamma-thio)triphosphate. J Biol Chem (1985) 1.60

Differences and similarities between various tandem repeat sequences: minisatellites and microsatellites. Biochimie (1997) 1.25

No sliding during homology search by RecA protein. J Biol Chem (1998) 1.24

Stable synapsis of homologous DNA molecules mediated by the Escherichia coli RecA protein involves local exchange of DNA strands. Genes Dev (1992) 1.21

The ATPase activity of RecA is needed to push the DNA strand exchange through heterologous regions. EMBO J (1991) 1.20

Kinetic analysis of pairing and strand exchange catalyzed by RecA. Detection by fluorescence energy transfer. J Biol Chem (1997) 1.18

Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: a model for homology search in homologous genetic recombination. Proc Natl Acad Sci U S A (1998) 1.17

(GT)n repetitive tracts affect several stages of RecA-promoted recombination. J Mol Biol (1997) 1.04

A molecular model for RecA-promoted strand exchange via parallel triple-stranded helices. Biophys J (1999) 1.01

Twisting and untwisting a single DNA molecule covered by RecA protein. Biophys J (2004) 1.00

(CA/GT)(n) microsatellites affect homologous recombination during yeast meiosis. Genes Dev (2000) 0.97

Physics of RecA-mediated homologous recognition. Biophys J (2004) 0.92

RecA-mediated strand exchange traverses substitutional heterologies more easily than deletions or insertions. Nucleic Acids Res (2001) 0.90

Model of RecA-mediated homologous recognition. Phys Rev Lett (2004) 0.89

Dissociation kinetics of RecA protein-three-stranded DNA complexes reveals a low fidelity of RecA-assisted recognition of homology. J Mol Biol (1998) 0.85

RecA realigns suboptimally paired frames of DNA repeats through a process that requires ATP hydrolysis. Biochemistry (2000) 0.84

Influence of DNA sequence on the positioning of RecA monomers in RecA-DNA cofilaments. J Biol Chem (2001) 0.82

RecA mediated initial alignment of homologous DNA molecules displays apparent first order kinetics with little effect of heterology. DNA Repair (Amst) (2004) 0.78

RecA-promoted sliding of base pairs within DNA repeats: quantitative analysis by a slippage assay. Biochem Biophys Res Commun (2002) 0.77

Articles by these authors

Classification of microarray data using gene networks. BMC Bioinformatics (2007) 2.44

Microfluidic high-throughput encapsulation and hydrodynamic self-sorting of single cells. Proc Natl Acad Sci U S A (2008) 2.22

Nucleosome chiral transition under positive torsional stress in single chromatin fibers. Mol Cell (2007) 1.76

Structural plasticity of single chromatin fibers revealed by torsional manipulation. Nat Struct Mol Biol (2006) 1.74

Self-assembled magnetic matrices for DNA separation chips. Science (2002) 1.59

Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays. Proc Natl Acad Sci U S A (2010) 1.54

Droplet fusion by alternating current (AC) field electrocoalescence in microchannels. Electrophoresis (2005) 1.47

Colorectal cancer metastasis: the DNA repair inhibitor Dbait increases sensitivity to hyperthermia and improves efficacy of radiofrequency ablation. Radiology (2013) 1.45

Microfluidic: an innovative tool for efficient cell sorting. Methods (2012) 1.26

Small-molecule drugs mimicking DNA damage: a new strategy for sensitizing tumors to radiotherapy. Clin Cancer Res (2009) 1.25

Quantitative microfluidic separation of DNA in self-assembled magnetic matrixes. Anal Chem (2004) 1.19

Hyperactivation of DNA-PK by double-strand break mimicking molecules disorganizes DNA damage response. PLoS One (2009) 1.18

Automated microdroplet platform for sample manipulation and polymerase chain reaction. Anal Chem (2006) 1.17

Real-time measurements of the nucleation, growth and dissociation of single Rad51-DNA nucleoprotein filaments. Nucleic Acids Res (2007) 1.14

Therapeutic approach of human peritoneal carcinomatosis with Dbait in combination with capnoperitoneum: proof of concept. Surg Endosc (2011) 1.14

Heat shock protein 90α (Hsp90α) is phosphorylated in response to DNA damage and accumulates in repair foci. J Biol Chem (2012) 1.10

Axon diodes for the reconstruction of oriented neuronal networks in microfluidic chambers. Lab Chip (2011) 1.08

EMMA, a cost- and time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in 1,525 patients. Hum Mutat (2011) 1.08

Mechanism of RecA-mediated homologous recombination revisited by single molecule nanomanipulation. EMBO J (2006) 1.02

Contamination-free continuous flow microfluidic polymerase chain reaction for quantitative and clinical applications. Anal Chem (2005) 1.01

Twisting and untwisting a single DNA molecule covered by RecA protein. Biophys J (2004) 1.00

Wallerian-like degeneration of central neurons after synchronized and geometrically registered mass axotomy in a three-compartmental microfluidic chip. Neurotox Res (2010) 1.00

Use of self assembled magnetic beads for on-chip protein digestion. Lab Chip (2005) 0.99

Surface treatment and characterization: perspectives to electrophoresis and lab-on-chips. Electrophoresis (2006) 0.99

Right-handed nucleosome: myth or reality? Cell (2009) 0.97

A low-cost, label-free DNA detection method in lab-on-chip format based on electrohydrodynamic instabilities, with application to long-range PCR. Lab Chip (2012) 0.96

Direct observation of twisting steps during Rad51 polymerization on DNA. Proc Natl Acad Sci U S A (2009) 0.96

Electrohydrodynamically induced aggregation during constant and pulsed field capillary electrophoresis of DNA. Biopolymers (1999) 0.93

Non-markovian transport of DNA in microfluidic post arrays. Phys Rev Lett (2005) 0.90

Spi-1/PU.1 oncogene accelerates DNA replication fork elongation and promotes genetic instability in the absence of DNA breakage. Cancer Res (2010) 0.90

Model of RecA-mediated homologous recognition. Phys Rev Lett (2004) 0.89

NAD+ acts on mitochondrial SirT3 to prevent axonal caspase activation and axonal degeneration. FASEB J (2013) 0.89

Lamination-based rapid prototyping of microfluidic devices using flexible thermoplastic substrates. Electrophoresis (2007) 0.89

Linker histones incorporation maintains chromatin fiber plasticity. Biophys J (2011) 0.89

Development of a magnetic immunosorbent for on-chip preconcentration of amyloid β isoforms: Representatives of Alzheimer's disease biomarkers. Biomicrofluidics (2012) 0.88

Semiphenomenological model for the dispersion of DNA during electrophoresis in a microfluidic array of posts. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.88

Motion of single long DNA molecules through arrays of magnetic columns. Electrophoresis (2005) 0.88

Design, modeling and characterization of microfluidic architectures for high flow rate, small footprint microfluidic systems. Lab Chip (2011) 0.88

A "dry and wet hybrid" lithography technique for multilevel replication templates: Applications to microfluidic neuron culture and two-phase global mixing. Biomicrofluidics (2011) 0.88

Kinesin KIFC1 actively transports bare double-stranded DNA. Nucleic Acids Res (2013) 0.87

Pharmacokinetics and Toxicity in Rats and Monkeys of coDbait: A Therapeutic Double-stranded DNA Oligonucleotide Conjugated to Cholesterol. Mol Ther Nucleic Acids (2012) 0.87

Preclinical study of the DNA repair inhibitor Dbait in combination with chemotherapy in colorectal cancer. J Gastroenterol (2011) 0.87

High-throughput simultaneous detection of point mutations and large-scale rearrangements by CE. Electrophoresis (2007) 0.87

Measurement of the surface concentration for bioassay kinetics in microchannels. Anal Chem (2005) 0.87

Compaction kinetics on single DNAs: purified nucleosome reconstitution systems versus crude extract. Biophys J (2005) 0.87

Impact of ionizing radiation on the life cycle of Saccharomyces cerevisiae Ty1 retrotransposon. Yeast (2005) 0.86

Inferring biological networks with output kernel trees. BMC Bioinformatics (2007) 0.86

Stimulation of D-loop formation by polypurine/polypyrimidine sequences. Nucleic Acids Res (2003) 0.85

Sieving mechanisms in polymeric matrices. Electrophoresis (2003) 0.85

Self-assembled magnetic nanowires made irreversible by polymer bridging. Langmuir (2005) 0.84

Inhibition of DNA damage repair by artificial activation of PARP with siDNA. Nucleic Acids Res (2013) 0.84

Microchip electrophoresis profiling of Aβ peptides in the cerebrospinal fluid of patients with Alzheimer's disease. Anal Chem (2010) 0.84

On-chip tryptic digest with direct coupling to ESI-MS using magnetic particles. Electrophoresis (2008) 0.83

Synapto-protective drugs evaluation in reconstructed neuronal network. PLoS One (2013) 0.83

Programmable magnetic tweezers and droplet microfluidic device for high-throughput nanoliter multi-step assays. Angew Chem Int Ed Engl (2012) 0.83

ATM germline mutations in women with familial breast cancer and a relative with haematological malignancy. Breast Cancer Res Treat (2009) 0.83

The in vivo radiosensitizing effect of gold nanoparticles based MRI contrast agents. Small (2014) 0.83

Fabrication of thermoplastics chips through lamination based techniques. Lab Chip (2012) 0.82

Utilization of newly developed immobilized enzyme reactors for preparation and study of immunoglobulin G fragments. J Chromatogr B Analyt Technol Biomed Life Sci (2004) 0.82

Poly(N,N-dimethylacrylamide)-grafted polyacrylamide: a self-coating copolymer for sieving separation of native proteins by CE. Electrophoresis (2006) 0.82

Controlled proteolysis of normal and pathological prion protein in a microfluidic chip. Lab Chip (2008) 0.81

In-capillary non-covalent labeling of insulin and one gastrointestinal peptide for their analyses by capillary electrophoresis with laser-induced fluorescence detection. J Chromatogr A (2005) 0.80

Distribution and radiosensitizing effect of cholesterol-coupled Dbait molecule in rat model of glioblastoma. PLoS One (2012) 0.80

β-amyloid induces a dying-back process and remote trans-synaptic alterations in a microfluidic-based reconstructed neuronal network. Acta Neuropathol Commun (2014) 0.80

New family of fluorinated polymer chips for droplet and organic solvent microfluidics. Lab Chip (2010) 0.80

Enhanced mismatch mutation analysis: simultaneous detection of point mutations and large scale rearrangements by capillary electrophoresis, application to BRCA1 and BRCA2. Methods Mol Biol (2010) 0.79

Functionalized magnetic micro- and nanoparticles: optimization and application to micro-chip tryptic digestion. Electrophoresis (2006) 0.79

FISH in chips: turning microfluidic fluorescence in situ hybridization into a quantitative and clinically reliable molecular diagnosis tool. Lab Chip (2015) 0.79

High purity microfluidic sorting and analysis of circulating tumor cells: towards routine mutation detection. Lab Chip (2015) 0.79

DNA-PK target identification reveals novel links between DNA repair signaling and cytoskeletal regulation. PLoS One (2013) 0.79

Epitope mapping of allergen ovalbumin using biofunctionalized magnetic beads packed in microfluidic channels The first step towards epitope-based vaccines. J Chromatogr A (2008) 0.79

Probing Rad51-DNA interactions by changing DNA twist. Nucleic Acids Res (2012) 0.78

Methods toward in vivo measurement of zebrafish epithelial and deep cell proliferation. Comput Methods Programs Biomed (2009) 0.78

Comb-like copolymers as self-coating, low-viscosity and high-resolution matrices for DNA sequencing. Electrophoresis (2002) 0.78

Soft microflow sensors. Lab Chip (2009) 0.77

DNA-PKcs plays role in cancer metastasis through regulation of secreted proteins involved in migration and invasion. Cell Cycle (2015) 0.77

Magneto-immunocapture with on-bead fluorescent labeling of amyloid-β peptides: towards a microfluidized-bed-based operation. Analyst (2015) 0.77

A high-throughput mutation detection method based on heteroduplex analysis using graft copolymer matrixes: application to Brca1 and Brca2 analysis. Anal Chem (2004) 0.76

Application of an improved magnetic immunosorbent in an Ephesia chip designed for circulating tumor cell capture. Electrophoresis (2013) 0.76

Tyrosinase gene correction using fluorescent oligonucleotides. Pigment Cell Res (2003) 0.76

Albumin-coated monodisperse magnetic poly(glycidyl methacrylate) microspheres with immobilized antibodies: application to the capture of epithelial cancer cells. J Biomed Mater Res A (2012) 0.76

New non-covalent strategies for stable surface treatment of thermoplastic chips. Lab Chip (2013) 0.76

Optimizing the design of oligonucleotides for homology directed gene targeting. PLoS One (2011) 0.75

Immunoaffinity reactors for prion protein qualitative analysis. Proteomics (2005) 0.75

Microchip electrophoresis, with respect to "profiling of Aβ peptides in the cerebrospinal fluid of patients with Alzheimer's disease". Methods Mol Biol (2012) 0.75

Asymmetric axonal edge guidance: a new paradigm for building oriented neuronal networks. Lab Chip (2016) 0.75

Magnetic proteinase K reactor as a new tool for reproducible limited protein digestion. Bioconjug Chem (2008) 0.75

Separation of time scales in one-dimensional directed nucleation-growth processes. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.75

Bioaffinity magnetic reactor for peptide digestion followed by analysis using bottom-up shotgun proteomics strategy. J Sep Sci (2008) 0.75

Evaluation of microchip material and surface treatment options for IEF of allergenic milk proteins on microchips. Electrophoresis (2009) 0.75

Improving sensitivity of electrophoretic heteroduplex analysis using nucleosides as additives: Application to the breast cancer predisposition gene BRCA2. Electrophoresis (2006) 0.75

Magnetic fluidized bed for solid phase extraction in microfluidic systems. Lab Chip (2017) 0.75

Versatile method for electroosmotic flow measurements in microchip electrophoresis. J Chromatogr A (2008) 0.75

[Homologous recombination and gene targeting]. C R Biol (2003) 0.75

10th anniversary issue: France. Lab Chip (2011) 0.75