Specific contacts between the Escherichia coli RNA polymerase (nucleosidetriphosphate:RNA nucleotidyl-transferase, EC184.108.40.206) and the phosphates and purine bases of the A3 promoter of phage T7 cluster into three regions located approximately 10, 16, and 35 base pairs before RNA initiation site. Two of these contain nucleotide sequences that are fairly conserved among many promoters, known as the "Pribnow box" and "-35 region" homologies; the third, just upstream from the Pribnow box, is not conserved. The polymerase binds preferentially to the coding strand and for the most part touches only one face of the DNA helix.
The specificity of different classes of ethylating agents toward various sites of HeLa cell DNA in vitro and in vivo
Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state
Analysis of DNA-protein interactions: from nitrocellulose filter binding assays to microarray studies
Thermodynamic and molecular analysis of the AbrB-binding sites within the phyC-region of Bacillus amyloliquefaciens FZB45
Temperature dependence of the rate constants of the Escherichia coli RNA polymerase-lambda PR promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening
Promoter recognition by Escherichia coli RNA polymerase. Influence of DNA structure in the spacer separating the -10 and -35 regions
Interaction of Escherichia coli RNA polymerase with DNA in an elongation complex arrested at a specific psoralen crosslink site
FLP recombinase of the 2 microns circle plasmid of Saccharomyces cerevisiae bends its DNA target. Isolation of FLP mutants defective in DNA bending
Yeast HAP1 activator competes with the factor RC2 for binding to the upstream activation site UAS1 of the CYC1 gene
Single-stranded DNA-protein binding in the procyclic acidic repetitive protein (PARP) promoter of Trypanosoma brucei
A novel transcriptional regulatory factor that binds to the polyoma virus enhancer in a developmental stage-specific manner
The interaction between Bacillus subtilis sigma-A (sigma A) factor and RNA polymerase with promoters
Transcription factor RFX1 helps control the promoter of the mouse ribosomal protein-encoding gene rpL30 by binding to its alpha element
An H3 coding region regulatory element is common to all four nucleosomal classes of mouse histone-encoding genes
Separate mechanisms are involved in rifampicin upmodulated and downmodulated gene expression in Salmonella Typhimurium
On the inhibition of the RNA polymerase-catalysed synthesis of RNA by daunomycin. Interference of the inhibitor with elongation and pre-longation steps
Interaction of the atypical prokaryotic transcription activator FlhD2C2 with early promoters of the flagellar gene hierarchy
The DNA-binding domain of the gene regulatory protein AreA extends beyond the minimal zinc-finger region conserved between GATA proteins
Vitamin D receptor interactions with positive and negative DNA response elements: an interference footprint comparison
Contacts between hormone receptor and DNA double helix within a glucocorticoid regulatory element of mouse mammary tumor virus
Hydroxyl radical "footprinting": high-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein
"Ultraviolet footprinting" accurately maps sequence-specific contacts and DNA kinking in the EcoRI endonuclease-DNA complex
An element downstream of the cap site is required for transcription of the gene encoding mouse ribosomal protein L32
T-cell nuclei contain a protein that binds upstream of the murine granulocyte-macrophage colony-stimulating factor gene
Alkylation interference identifies essential DNA contacts for sequence-specific binding of the eukaryotic transcription factor C/EBP
Functional borders, genetic fine structure, and distance requirements of cis elements mediating light responsiveness of the parsley chalcone synthase promoter
Functional dissection of a mouse ribosomal protein promoter: significance of the polypyrimidine initiator and an element in the TATA-box region
Hydroxyl radical footprint analysis of human immunodeficiency virus reverse transcriptase-template.primer complexes
An amplification-promoting sequence from mouse genomic DNA: interaction with a trans-acting factor that also affects gene expression
Transposase makes critical contacts with, and is stimulated by, single-stranded DNA at the P element termini in vitro
The effect of the delta subunit on the interaction of Bacillus subtilis RNA polymerase with bases in a SP82 early gene promoter
Alkyl phosphotriester modified oligodeoxyribonucleotides. V. Synthesis and absolute configuration of Rp and Sp diastereomers of an ethyl phosphotriester (Et) modified EcoRI recognition sequence, d[GGAA(Et)TTCC]. A synthetic approach to regio- and stereospecific ethylation-interference studies
Interaction between E. coli RNA polymerase and the tetR promoter from pSC101: homologies and differences with other E. coli promoter systems from close contact point studies
Purification of intercalator-released p67, a polypeptide that interacts specifically with the c-fos serum response element
A second RNA-polymerase can bind specifically to the bla promoter of Tn3, repressing transcription initiation
An intermediate in the phage lambda site-specific recombination reaction is revealed by phosphorothioate substitution in DNA
Two target sites for protein binding in the promoter region of a cell cycle regulated human H1 histone gene
A characterization of the elements comprising the promoter of the mouse ribosomal protein gene RPS16
The 43 residue DNA binding domain of gamma delta resolvase binds adjacent major and minor grooves of DNA
Astrocytes and glioblastoma cells express novel octamer-DNA binding proteins distinct from the ubiquitous Oct-1 and B cell type Oct-2 proteins
The T----C substitution at -198 of the A gamma-globin gene associated with the British form of HPFH generates overlapping recognition sites for two DNA-binding proteins
The transcription factor LF-A1 interacts with a bipartite recognition sequence in the promoter regions of several liver-specific genes
Binding site selection analysis of protein-DNA interactions via solid phase sequencing of oligonucleotide mixtures
Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme
Two distinct, sequence-specific DNA-binding proteins interact independently with the major replication pause region of sea urchin mtDNA
Recognition of specific nucleotide bases and cooperative DNA binding by the trans-acting nitrogen regulatory protein NIT2 of Neurospora crassa
Single-step piperidine elution, cleavage, and recovery of premodified DNA electrotransferred on NA-45 membrane from mobility-shift gels
In vivo footprinting of the IRF-1 promoter: inducible occupation of a GAS element next to a persistent structural alteration of the DNA
Minor groove contacts are essential for an interaction of the human cytomegalovirus IE2 protein with its DNA target
Fine structure analyses of the Drosophila and Saccharomyces heat shock factor--heat shock element interactions
Adipocyte-specific transcription factor ARF6 is a heterodimeric complex of two nuclear hormone receptors, PPAR gamma and RXR alpha
The coding sequences of mouse H2A and H3 histone genes contains a conserved seven nucleotide element that interacts with nuclear factors and is necessary for normal expression
The beta recombinase of plasmid pSM19035 binds to two adjacent sites, making different contacts at each of them
A new interference footprinting method for analysing simultaneously protein contacts to phosphate and guanine residues on DNA
In the TTF-1 homeodomain the contribution of several amino acids to DNA recognition depends on the bound sequence
Identification of a second conserved element within the coding sequence of a mouse H3 histone gene that interacts with nuclear factors and is necessary for normal expression
Binding of NF1 to the MMTV promoter in nucleosomes: influence of rotational phasing, translational positioning and histone H1
A versatile in vivo footprinting technique using 1,10-phenanthroline-copper complex to study important cellular processes
Alterations in two conserved regions of promoter sequence lead to altered rates of polymerase binding and levels of gene expression
Effects of mutations at tyrosine 66 and asparagine 123 in the active site pocket of Escherichia coli uracil DNA glycosylase on uracil excision from synthetic DNA oligomers: evidence for the occurrence of long-range interactions between the enzyme and substrate
Differences in replication of a DNA template containing an ethyl phosphotriester by T4 DNA polymerase and Escherichia coli DNA polymerase I
High mobility group A2 protein and its derivatives bind a specific region of the promoter of DNA repair gene ERCC1 and modulate its activity
Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor
Electron microscopic analysis of the interaction of Escherichia coli RNA polymerase with alkylated T7 DNA
The 'CC.Ar.GG' box. A protein-binding site common to transcription-regulatory regions of the cardiac actin, c-fos and interleukin-2 receptor genes
Characterization of the nuclear proteins binding the CACCC element of a glucocorticoid-responsive enhancer in the tyrosine aminotransferase gene
Rag-1 mutations associated with B-cell-negative scid dissociate the nicking and transesterification steps of V(D)J recombination
Vitamin D receptor interactions with the rat parathyroid hormone gene: synergistic effects between two negative vitamin D response elements
Investigation of the mechanisms of DNA binding of the human G/T glycosylase using designed inhibitors
Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase alpha subunit
Biochemical identification of base and phosphate contacts between Fis and a high-affinity DNA binding site
Sa-Lrp from Sulfolobus acidocaldarius is a versatile, glutamine-responsive, and architectural transcriptional regulator
Proteins binding to the liver-specific pyruvate kinase gene promoter. A unique combination of known factors
Functional analysis of wild=type and altered tryptophan operon promoters of Salmonella typhimurium in Escherichia coli
Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression
Isolation and characterization of the diastereoisomers of a series of phosphate-ethylated dinucleoside monophosphates
Gene regulation at the right operator (OR) of bacteriophage lambda. II. OR1, OR2, and OR3: their roles in mediating the effects of repressor and cro
Binding of RNA polymerase and the catabolite gene activator protein within the cat promoter in Escherichia coli
Specific interactions between the IclR repressor of the acetate operon of Escherichia coli and its operator
Transcriptional activation at adjacent operators in the divergent-overlapping ilvY and ilvC promoters of Escherichia coli
Enhancer binding protein (EBP1) makes base and backbone contacts over one complete turn of the DNA double helix
Chemical footprinting of the interaction between left-handed Z-DNA and anti-Z-DNA antibodies by diethylpyrocarbonate carbethoxylation
Transcriptional inhibition of the bacteriophage T7 early promoter region by oligonucleotide triple helix formation
Stable binding of Drosophila heat shock factor to head-to-head and tail-to-tail repeats of a conserved 5 bp recognition unit
A novel cis element mediating ligand-independent activation by c-ErbA: implications for hormonal regulation
The thyroid hormone receptor binds with opposite transcriptional effects to a common sequence motif in thyroid hormone and estrogen response elements
Transcriptional activity of the Rous sarcoma virus long terminal repeat correlates with binding of a factor to an upstream CCAAT box in vitro
The DNA-binding domain of HPV-16 E2 protein interaction with the viral enhancer: protein-induced DNA bending and role of the nonconserved core sequence in binding site affinity
Multiple sets of adjacent mu E1 and oct-1 binding sites upstream of the pseudorabies virus immediate-early gene promoter
Effect of alkylation with N-methyl-N-nitrosourea and N-ethyl-N-nitrosourea on the secondary structure of DNA
Abasic site binding by the human apurinic endonuclease, Ape, and determination of the DNA contact sites
Transition-state destabilization reveals how human DNA polymerase β proceeds across the chemically unstable lesion N7-methylguanine
Cobalt-bleomycins and deoxyribonucleic acid: sequence-dependent interactions, action spectrum for nicking, and indifference to oxygen
Changes in the DNA structure of the lac UV5 promoter during formation of an open complex with Escherichia coli RNA polymerase
Fine mapping of DNA single-stranded regions using base-specific chemical probes: study of an open complex formed between RNA polymerase and the lac UV5 promoter
Transcriptional switching by the metalloregulatory MerR protein: initial characterization of DNA and mercury (II) binding activities
Binding of tachyplesin I to DNA revealed by footprinting analysis: significant contribution of secondary structure to DNA binding and implication for biological action
Application of phosphate-backbone-modified oligonucleotides in the studies on EcoRI endonuclease mechanism of action
Template-directed interference footprinting of cytosine contacts in a protein-DNA complex: potent interference by 5-aza-2'-deoxycytidine
The arginine repressor of Escherichia coli K-12 makes direct contacts to minor and major groove determinants of the operators
Thermodynamic and alkylation interference analysis of the lac repressor-operator substituted with the analogue 7-deazaguanine
Identification of phosphate groups involved in metal binding and tertiary interactions in the core of the Neurospora VS ribozyme
Bend induced by the phage phi 29 transcriptional activator in the viral late promoter is required for activation
Interaction between the replication origin and the initiator protein of the filamentous phage f1. Binding occurs in two steps
Characterization of UEF-4, a DNA-binding protein required for transcriptional synergism between two AP-1 sites in the human urokinase enhancer.
DNA distortion and base flipping by the EcoRV DNA methyltransferase. A study using interference at dA and T bases and modified deoxynucleosides.
Increased gamma-globin expression in a nondeletion HPFH mediated by an erythroid-specific DNA-binding factor
Ethylation interference and X-ray crystallography identify similar interactions between 434 repressor and operator
Bacteriophage lambda protein cII binds promoters on the opposite face of the DNA helix from RNA polymerase
Regulation of xylose utilization in Bacillus licheniformis: Xyl repressor-xyl-operator interaction studied by DNA modification protection and interference
Purification and functional characterization of the KdgR protein, a major repressor of pectinolysis genes of Erwinia chrysanthemi
A factor known to bind to endogenous Ig heavy chain enhancer only in lymphocytes is a ubiquitously active transcription factor
Quantitation of DNA adduct of thymidylyl(3'-5')thymidine methyl phosphotriester by liquid chromatography/negative electrospray tandem mass spectrometry
Multiple factors interacting at the GATA sites of the gonadotropin-releasing hormone neuron-specific enhancer regulate gene expression
Distinct organization of DNA complexes of various HMGI/Y family proteins and their modulation upon mitotic phosphorylation
Integration host factor (IHF) modulates the expression of the pyrimidine-specific promoter of the carAB operons of Escherichia coli K12 and Salmonella typhimurium LT2
The roles of specific template nucleosides in the formation of stable transcription complexes by Escherichia coli RNA polymerase
A three-protein-DNA complex on a B cell-specific domain of the immunoglobulin mu heavy chain gene enhancer.
Regulation of expression within a gene family. The case of the rat gammaB- and gammaD-crystallin promoters.
Characterization of the closed complex intermediate formed during transcription initiation by Escherichia coli RNA polymerase.
T4 endonuclease V protects the DNA strand opposite a thymine dimer from cleavage by the footprinting reagents DNase I and 1,10-phenanthroline-copper.
Zinc fingers 1-7 of EVI1 fail to bind to the GATA motif by itself but require the core site GACAAGATA for binding.
Structural studies of lacUV5-RNA polymerase interactions in vitro. Ethylation interference and missing nucleoside analysis
Leucine-responsive regulatory protein-DNA interactions in the leader region of the ilvGMEDA operon of Escherichia coli.
Purification and characterization of UEF3, a novel factor involved in the regulation of the urokinase and other AP-1 controlled promoters.
Computer modeling of three-dimensional structure of DNA-packaging RNA (pRNA) monomer, dimer, and hexamer of Phi29 DNA packaging motor.
Architectural accommodation in the complex of four p53 DNA binding domain peptides with the p21/waf1/cip1 DNA response element.
Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters
Structural determinants for substrate binding and catalysis by the structure-specific endonuclease XPG.
High specificity and tight spatial restriction of self-biotinylation by DNA and RNA G-Quadruplexes complexed in vitro and in vivo with Heme
The plasmid vectors, pBS2ndd and pBS3ndd, for versatile cloning with low background in Escherichia coli
Architecture of high mobility group protein I-C.DNA complex and its perturbation upon phosphorylation by Cdc2 kinase
Exonuclease-mediated ELISA-like assay for detecting DNA-binding activity of transcription factors: measurement of activated NF-kappaB
Quantitation of lower levels of the DNA adduct of thymidylyl(3'-5')thymidine methyl phosphotriester by liquid chromatography/negative atmospheric pressure chemical ionization tandem mass spectrometry
DNA-Binding and Transcription Activation by Unphosphorylated Response Regulator AgrR From Cupriavidus metallidurans Involved in Silver Resistance
Site-specific interactions of JBP with base and sugar moieties in duplex J-DNA. Evidence for both major and minor groove contacts
Substrate recognition and induced DNA deformation by transposase at the target-capture stage of Tn10 transposition
Identification of functional domains in the self-cleaving Neurospora VS ribozyme using damage selection
Binding of phage phi29 protein p4 to the early A2c promoter: recruitment of a repressor by the RNA polymerase
Developmental competence of the gut endoderm: genetic potentiation by GATA and HNF3/fork head proteins
Characterization of the small subunit of the terminase enzyme of the Bacillus subtilis bacteriophage SPP1
Alkylating agent and chromatin structure determine sequence context-dependent formation of alkylpurines
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
Evolution of Pluripotency
Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.
Lipidomics & Rhinovirus Infection
Lipidomics can be used to examine the lipid species involved with pathogenic conditions, such as viral associated inflammation. Discovered the latest research on Lipidomics & Rhinovirus Infection.
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Chronic Fatigue Syndrome
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Alzheimer's Disease: MS4A
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STING Receptor Agonists
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Laryngeal Neoplasms occur in the Larynx and are typically associated with smoking and alcohol consumption. Discover the latest research on Laryngeal Neoplasms here.
Cell Atlas Along the Gut-Brain Axis
Profiling cells along the gut-brain axis at the single cell level will provide unique information for each cell type, a three-dimensional map of how cell types work together to form tissues, and insights into how changes in the map underlie health and disease of the GI system and its crosstalk with the brain. Disocver the latest research on single cell analysis of the gut-brain axis here.