Porphyrins and porphines bind strongly and specifically to tRNA, precursor tRNA and to M1 RNA and inhibit the ribonuclease P ribozyme reaction

Yoshiaki Hori, Maria C. Rogert, Terumichi Tanaka, Yo Kikuchi, Elena V. Bichenkova, Amanda N. Wilton, Abdul Gbaj, Kenneth T. Douglas*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)


Porphyrins and porphines strongly inhibit the action of the RNA subunit of the Escherichia coli ribonuclease P (M1 RNA). Meso-tetrakis(N-methyl-pyridyl) porphine followed linear competitive kinetics with pre-tRNAGly1 from E. coli as variable substrate (Ki 0.960 μM). Protoporphyrin IX showed linear competitive inhibition versus pre-tRNAGly1 from E. coli (Ki 1.90 μM). Inhibition by meso-tetrakis[4-(trimethylammonio) phenyl]porphine versus pre-tRNAGly1 from E. coli followed non-competitive kinetics (Ki 4.1 μM). The porphyrins bound directly to E. coli tRNAVal, E. coli pre-tRNAGly1 and M1 RNA and dissociation constants for the 1:1 complexes were determined using fluorescence spectroscopy. Dissociation constants (μM) against E. coli tRNAVal and E. coli pre-tRNAGly were: meso-tetrakis(N- methyl-pyridyl)porphine 1.21 and 0.170; meso-tetrakis[4-(trimethylammonio) phenyl]porphine, 0.107 and 0.293; protoporphyrin IX, 0.138 and 0.0819. For M1 RNA, dissociation constants were 32.8 nM for meso-tetrakis(N-methyl-pyridyl) porphine and 59.8 nM for meso-tetrakis[4-(trimethylammonio)phenyl]porphine and excitation and emission spectra indicate a binding mode with strong π-stacking of the porphine nucleus and base pairs in a rigid low-polarity environment. Part of the inhibition of ribonuclease P is from interaction with the pre-tRNA substrate, resulting from porphyrin binding to the D-loop/T-loop region which interfaces with M1 RNA during catalysis, and part from the porphyrin binding to the M1 RNA component.

Original languageEnglish
Pages (from-to)47-55
Number of pages9
JournalBiochimica et Biophysica Acta - Gene Structure and Expression
Issue number1
Publication statusPublished - 2005 Jul 25
Externally publishedYes


  • Fluorescence binding studies
  • Inhibition kinetics
  • Ribozyme inhibitors
  • Transfer RNA

ASJC Scopus subject areas

  • Biochemistry
  • Genetics
  • Structural Biology
  • Biophysics


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