title: Single-stranded DNA aptamers for functional probing of bacterial RNA polymerase.
abstract: Bacterial RNA polymerase (RNAP) is the main regulatory hub of gene transcription. During transcription, RNAP interacts with the DNA template, RNA product, nucleotide substrates, metal cofactors, and regulatory molecules that bind to distinct RNAP sites to modulate its activity. RNAP is also inhibited by several known antibiotics and is a promising target for development of novel antibacterial compounds. Despite great progress in structural analysis of RNAP in recent years, many details of RNAP interactions with nucleic acids, regulatory molecules and antibiotics remain insufficiently understood. Aptamers that target various epitopes on the RNAP molecule represent a useful tool for functional analysis of transcription. Here, we describe protocols for selection of highly specific aptamers to different components of RNAP and their applications for analysis of RNAP-ligand interactions and RNAP inhibition.
authors: Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., Moscow, 123182, Russia.
authors: Danil
authors: D
authors: Pupov
authors: Andrey
authors: A
authors: Kulbachinskiy
mesh_terms: D052157:Aptamers, Nucleotide / Q000235:genetics*; D001419:Bacteria / Q000201:enzymology*; D020029:Base Pairing; D001483:Base Sequence; D004277:DNA, Single-Stranded / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D015336:Molecular Probe Techniques; D015335:Molecular Probes / Q000235:genetics*; D008969:Molecular Sequence Data; D015394:Molecular Structure
chemical_list: D052157:Aptamers, Nucleotide; D004277:DNA, Single-Stranded; D015335:Molecular Probes; D012321:DNA-Directed RNA Polymerases