Published in J Mol Biol on November 14, 2003
Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. Proc Natl Acad Sci U S A (2006) 1.75
Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping. Proc Natl Acad Sci U S A (2007) 1.31
Ligand-induced conformational changes and conformational dynamics in the solution structure of the lactose repressor protein. J Mol Biol (2007) 1.20
Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro. Proc Natl Acad Sci U S A (2011) 1.18
Single-molecule spectroscopic determination of lac repressor-DNA loop conformation. Biophys J (2005) 1.14
Disruption of protein-mediated DNA looping by tension in the substrate DNA. Biophys J (2005) 1.09
DNA trajectory in the Gal repressosome. Genes Dev (2004) 1.08
The antiparallel loops in gal DNA. Nucleic Acids Res (2008) 1.02
Tetramer opening in LacI-mediated DNA looping. Proc Natl Acad Sci U S A (2009) 0.99
Interplay of protein and DNA structure revealed in simulations of the lac operon. PLoS One (2013) 0.97
Dividing a supercoiled DNA molecule into two independent topological domains. Proc Natl Acad Sci U S A (2011) 0.97
Galactose repressor mediated intersegmental chromosomal connections in Escherichia coli. Proc Natl Acad Sci U S A (2012) 0.92
Structural insights into the role of architectural proteins in DNA looping deduced from computer simulations. Biochem Soc Trans (2013) 0.83
Weak operator binding enhances simulated lac repressor-mediated DNA looping. Biopolymers (2013) 0.83
The replication of plastid minicircles involves rolling circle intermediates. Nucleic Acids Res (2009) 0.82
Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR. Nucleic Acids Res (2008) 0.80
Do femtonewton forces affect genetic function? A review. J Biol Phys (2006) 0.79
Molecular Mechanisms of Transcription Initiation at gal Promoters and their Multi-Level Regulation by GalR, CRP and DNA Loop. Biomolecules (2015) 0.75
The transcriptional regulator GalR self-assembles to form highly regular tubular structures. Sci Rep (2016) 0.75
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol (2008) 10.10
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature (2010) 6.87
Switches in bacteriophage lambda development. Annu Rev Genet (2005) 3.24
CpG islands recruit a histone H3 lysine 36 demethylase. Mol Cell (2010) 2.86
Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium. Infect Immun (2002) 2.52
A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. J Mol Biol (2007) 2.46
Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials. Ultramicroscopy (2003) 2.01
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res (2010) 1.87
Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats. J Mol Biol (2003) 1.87
Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res (2012) 1.77
Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding. J Biol Chem (2005) 1.76
On the role of Cro in lambda prophage induction. Proc Natl Acad Sci U S A (2005) 1.65
Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc Natl Acad Sci U S A (2003) 1.63
Clostridium taeniosporum spore ribbon-like appendage structure, composition and genes. Mol Microbiol (2007) 1.58
Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy. J Biomol NMR (2003) 1.53
Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor. Nucleic Acids Res (2009) 1.49
Selective requirements for histone H3 and H4 N termini in p300-dependent transcriptional activation from chromatin. Mol Cell (2002) 1.44
The p53 tumor suppressor network is a key responder to microenvironmental components of chronic inflammatory stress. Cancer Res (2005) 1.42
Toward a live microbial microbicide for HIV: commensal bacteria secreting an HIV fusion inhibitor peptide. Proc Natl Acad Sci U S A (2005) 1.39
Atomic force microscopy studies provide direct evidence for dimerization of the HIV restriction factor APOBEC3G. J Biol Chem (2010) 1.38
Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA. J Biosci (2002) 1.37
High-sensitivity bacterial detection using biotin-tagged phage and quantum-dot nanocomplexes. Proc Natl Acad Sci U S A (2006) 1.36
A gamut of loops: meandering DNA. Trends Biochem Sci (2005) 1.33
Efficient degradation and expression prioritization with small RNAs. Phys Biol (2007) 1.33
Simplified models of biological networks. Annu Rev Biophys (2010) 1.33
Escherichia coli K1's capsule is a barrier to bacteriophage T7. Appl Environ Microbiol (2005) 1.31
Nanoliter multiplex PCR arrays on a SlipChip. Anal Chem (2010) 1.30
Dynamics of nucleosomes revealed by time-lapse atomic force microscopy. Biochemistry (2009) 1.30
Single-molecule atomic force microscopy force spectroscopy study of Aβ-40 interactions. Biochemistry (2011) 1.30
Axiom of determining transcription start points by RNA polymerase in Escherichia coli. Mol Microbiol (2004) 1.27
Bacteriophage infection is targeted to cellular poles. Mol Microbiol (2008) 1.25
Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct (2011) 1.25
Three-stage regulation of the amphibolic gal operon: from repressosome to GalR-free DNA. J Mol Biol (2006) 1.25
Signal integration in the galactose network of Escherichia coli. Mol Microbiol (2007) 1.25
Recognition of the tumor suppressor protein p53 and other protein targets by the calcium-binding protein S100B. Biochim Biophys Acta (2006) 1.24
Nucleosome positioning in human HOX gene clusters. Genome Res (2008) 1.23
Dynamic features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci U S A (2009) 1.23
Protein interactions and misfolding analyzed by AFM force spectroscopy. J Mol Biol (2005) 1.23
Specific binding of poly(ADP-ribose) polymerase-1 to cruciform hairpins. J Mol Biol (2005) 1.22
In vitro repression of the gal promoters by GalR and HU depends on the proper helical phasing of the two operators. J Biol Chem (2001) 1.22
A mutant spacer sequence between -35 and -10 elements makes the Plac promoter hyperactive and cAMP receptor protein-independent. Proc Natl Acad Sci U S A (2004) 1.22
Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding. EMBO J (2002) 1.21
A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res (2005) 1.21
Genetic flexibility of regulatory networks. Proc Natl Acad Sci U S A (2010) 1.20
Nucleoid remodeling by an altered HU protein: reorganization of the transcription program. Proc Natl Acad Sci U S A (2005) 1.20
Forcing nonamyloidogenic beta-synuclein to fibrillate. Biochemistry (2005) 1.19
Multilevel autoregulation of λ repressor protein CI by DNA looping in vitro. Proc Natl Acad Sci U S A (2011) 1.18
Spiral structure of Escherichia coli HUalphabeta provides foundation for DNA supercoiling. Proc Natl Acad Sci U S A (2007) 1.18
Assembly of single chromatin fibers depends on the tension in the DNA molecule: magnetic tweezers study. Proc Natl Acad Sci U S A (2003) 1.18
Dynamics of nucleosomes assessed with time-lapse high-speed atomic force microscopy. Biochemistry (2011) 1.18
The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev (2013) 1.16
DNA strand arrangement within the SfiI-DNA complex: atomic force microscopy analysis. Biochemistry (2006) 1.16
alpha-Synuclein misfolding: single molecule AFM force spectroscopy study. J Mol Biol (2008) 1.16
Effect of varying the supercoiling of DNA on transcription and its regulation. Biochemistry (2003) 1.12
Nanomedicine and protein misfolding diseases. Nanomedicine (2005) 1.11
Combinatorics of feedback in cellular uptake and metabolism of small molecules. Proc Natl Acad Sci U S A (2007) 1.11
Holliday junction dynamics and branch migration: single-molecule analysis. Proc Natl Acad Sci U S A (2005) 1.10
Early stages for Parkinson's development: alpha-synuclein misfolding and aggregation. J Neuroimmune Pharmacol (2008) 1.09
Cellular stress created by intermediary metabolite imbalances. Proc Natl Acad Sci U S A (2009) 1.09
Effects of nitration on the structure and aggregation of alpha-synuclein. Brain Res Mol Brain Res (2005) 1.09
Mitogen-activated protein kinase phosphatase 2: a novel transcription target of p53 in apoptosis. Cancer Res (2006) 1.08
DNA trajectory in the Gal repressosome. Genes Dev (2004) 1.08
Protein-DNA hydrophobic recognition in the minor groove is facilitated by sugar switching. J Mol Biol (2004) 1.08
nuScore: a web-interface for nucleosome positioning predictions. Bioinformatics (2008) 1.08
Mapping nucleosome locations on the 208-12 by AFM provides clear evidence for cooperativity in array occupation. Biochemistry (2002) 1.07
Probing Interactions within the synaptic DNA-SfiI complex by AFM force spectroscopy. J Mol Biol (2006) 1.07
Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet (2012) 1.04
Why do phage play dice? J Virol (2009) 1.03
Molecular mechanism underlying RAG1/RAG2 synaptic complex formation. J Biol Chem (2009) 1.03
Supercoiling-induced DNA bending. Biochemistry (2004) 1.03
Effect of spermidine on misfolding and interactions of alpha-synuclein. PLoS One (2012) 1.03
Direct visualization of the EcoRII-DNA triple synaptic complex by atomic force microscopy. Biochemistry (2007) 1.02
Right-handed DNA supercoiling by an octameric form of histone-like protein HU: modulation of cellular transcription. J Biol Chem (2006) 1.02
The antiparallel loops in gal DNA. Nucleic Acids Res (2008) 1.02
Effect of DNA supercoiling on the geometry of holliday junctions. Biochemistry (2006) 1.02
DNA recombination: holliday junctions dynamics and branch migration. J Biol Chem (2003) 1.01
The role of histone H4 biotinylation in the structure of nucleosomes. PLoS One (2011) 1.01
Molecular mechanism of misfolding and aggregation of Aβ(13-23). J Phys Chem B (2013) 1.01
Identification of host receptor and receptor-binding module of a newly sequenced T5-like phage EPS7. FEMS Microbiol Lett (2008) 1.00
Nanoscale structure and dynamics of ABOBEC3G complexes with single-stranded DNA. Biochemistry (2012) 1.00
Nanoprobing of α-synuclein misfolding and aggregation with atomic force microscopy. Nanomedicine (2010) 1.00
p53 binding to nucleosomal DNA depends on the rotational positioning of DNA response element. J Biol Chem (2009) 0.99
Distinctive sequence patterns in metazoan and yeast nucleosomes: implications for linker histone binding to AT-rich and methylated DNA. Nucleic Acids Res (2009) 0.99
Mechanistic evaluation of the pros and cons of digital RT-LAMP for HIV-1 viral load quantification on a microfluidic device and improved efficiency via a two-step digital protocol. Anal Chem (2013) 0.99
Genetic instability favoring transversions associated with ErbB2-induced mammary tumorigenesis. Proc Natl Acad Sci U S A (2002) 0.99
DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme. Nucleic Acids Res (2010) 0.99
Mica functionalization for imaging of DNA and protein-DNA complexes with atomic force microscopy. Methods Mol Biol (2013) 0.98
Interaction of the Zalpha domain of human ADAR1 with a negatively supercoiled plasmid visualized by atomic force microscopy. Nucleic Acids Res (2004) 0.98
DNA topology and geometry in Flp and Cre recombination. J Mol Biol (2006) 0.98
GalR represses galP1 by inhibiting the rate-determining open complex formation through RNA polymerase contact: a GalR negative control mutant. J Mol Biol (2004) 0.98