TY - JOUR
T1 - Porphyrins and porphines bind strongly and specifically to tRNA, precursor tRNA and to M1 RNA and inhibit the ribonuclease P ribozyme reaction
AU - Hori, Yoshiaki
AU - Rogert, Maria C.
AU - Tanaka, Terumichi
AU - Kikuchi, Yo
AU - Bichenkova, Elena V.
AU - Wilton, Amanda N.
AU - Gbaj, Abdul
AU - Douglas, Kenneth T.
PY - 2005/7/25
Y1 - 2005/7/25
N2 - 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.
AB - 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.
KW - Fluorescence binding studies
KW - Inhibition kinetics
KW - Ribozyme inhibitors
KW - Transfer RNA
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U2 - 10.1016/j.bbaexp.2005.06.003
DO - 10.1016/j.bbaexp.2005.06.003
M3 - Article
C2 - 16005529
AN - SCOPUS:22444432810
VL - 1730
SP - 47
EP - 55
JO - Biochimica et Biophysica Acta - Gene Structure and Expression
JF - Biochimica et Biophysica Acta - Gene Structure and Expression
SN - 0167-4781
IS - 1
ER -