title: Proximity between nucleotide/dinucleotide and metal ion binding sites in DNA-dependent RNA polymerase from Escherichia coli.
abstract: 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 a 5'-secondary amine linkage were synthesized [Tyagi, S.C., & Wu, F.Y.-H. (1987) J. Biol. Chem. 262, 10684-10688]. The fluorescent emission spectra of (5'-AmNS)UpA, (5'-AmNS)CpA, (gamma-AmNS)ATP, and (gamma-AmNS)UTP overlap the absorption spectrum of co-substituted RNA polymerase (Co-RNAP) and ensure fluorescence resonance energy transfer (FRET) between the fluorescent analog and Co(II) in Co-RNAP. The binding constants at a single site for (gamma-AmNS)ATP, (gamma-AmNS)UTP, (5'-AmNS)UpA, and (5'-AmNS)CpA were observed to be 7.11, 5.26, 0.52, and 0.61 microM, respectively, in Co-RNAP and 5.70, 3.42, 0.12, and 0.21 microM, respectively, in Zn-RNAP. (8-AmTEMPO)ATP, with the spin probe AmTEMPO attached to the C-8 position at ATP [Tyagi, S.C. (1991) J. Biol. Chem. 266, 17936-17940], and Mn(3'-OCH3)UTP were synthesized. Mn-(II)-substituted RNA polymerase (Mn-RNAP) is prepared. The single site binding constants for (8-Am-TEMPO)ATP and Mn(3'-OCH3)UTP were 3.58 and 2.35 microM in Zn-RNAP and 5.77 and 3.43 microM in Mn-RNAP, respectively. These results indicate that dinucleotides bind much more tightly than mononucleotides to RNAP and that the binding constants are roughly the same for both Co- and Zn-substituted RNAP.(ABSTRACT TRUNCATED AT 250 WORDS)
authors.affiliation: Department of Biochemistry and Cell Biology, State University of New York, Stony Brook 11794-5215.
authors.forename: S C
authors.initials: SC
authors.lastname: Tyagi
authors.forename: F Y
authors.initials: FY
authors.lastname: Wu
mesh_terms: D001665:Binding Sites; D002413:Cations, Divalent; D012321:DNA-Directed RNA Polymerases / Q000648:ultrastructure*; D004578:Electron Spin Resonance Spectroscopy; D004926:Escherichia coli / Q000201:enzymology*; D007700:Kinetics; D008670:Metals; D009711:Nucleotides / Q000378:metabolism; D009841:Oligonucleotides / Q000378:metabolism; D013050:Spectrometry, Fluorescence; D014158:Transcription, Genetic
chemical_list: D002413:Cations, Divalent; D008670:Metals; D009711:Nucleotides; D009841:Oligonucleotides; D012321:DNA-Directed RNA Polymerases