Proximity relationship between the active site of Escherichia coli RNA polymerase and rifampicin binding domain: a resonance energy-transfer study.
AuthorsKumar KP, Reddy PS, Chatterji D
JournalBiochemistry
PubMed ID1510938
'Escherichia coli RNA polymerase has two subsites, i and i + 1, for the binding of the first two substrates, and the first phosphodiester bond is formed between them during the initiation of transcription. Various studies have shown earlier that the inhibitor rifampicin has little effect, if any, on the ... More
Synthesis and characterization of stacked and quenched uridine nucleotide fluorophores.
AuthorsDhar G, Bhaduri A
JournalJ Biol Chem
PubMed ID10329647
'Intramolecular aromatic interactions in aqueous solution often lead to stacked conformation for model organic molecules. This designing principle was used to develop stacked and folded uridine nucleotide analogs that showed highly quenched fluoroscence in aqueous solution by attaching the fluorophore 1-aminonaphthalene-5-sulfonate (AmNS) to the terminal phosphate via a phosphoramidate bond. ... More
Proximity between nucleotide/dinucleotide and metal ion binding sites in DNA-dependent RNA polymerase from Escherichia coli.
AuthorsTyagi SC, Wu FY
JournalBiochemistry
PubMed ID1321660
'In order to understand translocation in transcription, it is important to develop a continuous functional assay for RNA polymerase (RNAP) activity in vitro. Fluorescent derivatives of ATP, UTP, UpA, and CpA with aminonaphthalene-5-sulfonic acid (AmNS) attached to the nucleotide triphosphates via a gamma-phosphoramidate bond or to the dinucleotide monophosphates via ... More
Fluorescent nucleotide triphosphate substrates for snake venom phosphodiesterase.
AuthorsPollack SE, Auld DS
JournalAnal Biochem
PubMed ID6299131
Transcription of giant DNA complexed with cationic nanoparticles as a simple model of chromatin.
AuthorsZinchenko AA, Luckel F, Yoshikawa K
JournalBiophys J
PubMed ID17142281
We prepared complexes of giant double-stranded DNA with cationic nanoparticles of 10-40 nm in diameter as an artificial model of chromatin and characterized the properties of changes in their higher-order conformation. We measured the changes in transcriptional activity that accompanied the DNA conformational transitions. Complete inhibition was found at excess ... More
High-throughput screening of RNA polymerase inhibitors using a fluorescent UTP analog.
AuthorsBhat J, Rane R, Solapure SM, Sarkar D, Sharma U, Harish MN, Lamb S, Plant D, Alcock P, Peters S, Barde S, Roy RK
JournalJ Biomol Screen
PubMed ID17021309
RNA polymerase (RNAP) is a well-validated target for the development of antibacterial and antituberculosis agents. Because the purification of large quantities of native RNA polymerase from pathogenic mycobacteria is hazardous and cumbersome, the primary screening was carried out using Escherichia coli RNAP. The authors have developed a high-throughput screening (HTS) ... More
Fluorescence resonance energy transfer studies on the proximity relationship between the intrinsic metal ion and substrate binding sites of Escherichia coli RNA polymerase.
AuthorsWu FY, Tyagi SC
JournalJ Biol Chem
PubMed ID3308870
DNA-dependent RNA polymerase from Escherichia coli contains 2 mol of zinc/mol of holoenzyme (alpha 2 beta beta' sigma) with one zinc each in the beta and beta' subunits. A new method to substitute selectively the zinc in the beta subunit was developed by the inactivation of RNA polymerase with 0.25 ... More
Evidence for a pyrimidine-nucleotide-specific initiation site (the i site) on Escherichia coli RNA polymerase. Proximity relationship with the inhibitor binding domain.
AuthorsReddy PS, Chatterji D
JournalEur J Biochem
PubMed ID7957189
Escherichia coli RNA polymerase has two sites, the i and i + 1, for the binding of the first two substrates. The i site is template- and Mg(2+)-independent and purine-nucleotide-specific, whereas the i + 1 site is template- and Mg(2+)-dependent and shows no nucleotide preference. The specificity of the i ... More