Antisense oligoribonucleotides and RNase P. A great potential

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

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-tRNA(Gly1) from E. coli as variable substrate (Ki 0.960 microM). Protoporphyrin IX showed linear competitive inhibition versus pre-tRNA(Gly1) from E. coli (Ki 1.90 microM). Inhibition by meso-tetrakis[4-(trimethylammonio)phenyl]porphine versus pre-tRNA(Gly1) from E. coli followed non-competitive kinetics (Ki 4.1 microM). 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 (microM) 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 pi-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.

Targeted cleavage of RNA molecules by human RNase P using minimized external guide sequences

The endoribonuclease RNase P processes tRNA-like structures that are assembled out of two separate strands. In these bimolecular constructs, one of the strands is cleaved by the enzyme, and the other one is called the external guide sequence (EGS). A number of EGS with different mutations and deletions were tested for the ability to induce cleavage with human RNase P. Different domains of the original tRNAtyr-like structure were deleted or modified. The anticodon stem and loop and the variable loop could be deleted without a detrimental effect on recognition by RNase P. Modifications in the lengths of T stem and aminoacyl acceptor stem led to a decrease in the relative amount of cleavage, whereas modifications of the D stem were more permissible. Single nucleotide deletions in the T loop reduced cleavage to different extents, depending on the position. Values for the Kd of complex formation of bimolecular constructs with annealing arms of varying lengths ranged from 0.2 nM to 28 nM. A cleavage rate of 1 min(-1) was measured for both the bimolecular target-EGS complex and tRNA precursor.

Further characterization of human RNase MRP/RNase P and related autoantibodies

We characterized a panel of human RNase MRP/RNase P autoantibodies by immunoprecipitation, immunodepletion, immunoaffinity purification and immunoblotting. We report on the protein spectrum that is recognized by RNase MRP/RNase P autoantibodies. We also describe another, related patient serum that based on these assays does not immunoprecipitate RNase P/MRP/Th40. This autoantibody 'KC', however, coimmunoprecipitates the RNase MRP/RNase P associated RNAs from HeLa and La9 cell extracts as shown by nuclease protection experiments.