Theoretical exploration of netropsin binding to tRNA(Phe)

RNase activity of a DNA minor groove binder with a minimalist catalytic motif from RNase A

Imidazole and compounds containing imidazole residues have been shown to cleave RNA in an RNase A-mimicking manner. Di-imidazole lexitropsin is a compound which is derived from the polyamide drugs distamycin and netropsin essentially by the replacement of two pyrrole heterocycles with N-methyl-imidazole residues. This enables it to bind to the minor groove of B-DNA in a sequence-specific manner. We demonstrate here that this lexitropsin derivative has RNA cleavage activity, as tested on model RNAs. Optimal cleavage conditions and cleavage specificity resemble those known from other imidazole conjugates and are thus consistent with an RNase A type cleavage mechanism. The optimum concentration of the compound for cleavage is similar to previously investigated imidazole-based RNase mimics. As a whole new class of chemical compounds capable of interacting with nucleic acids through extensive hydrogen bonding, these imidazole containing compounds constitute promising scaffolds and ligands, for the construction of novel RNase mimics with high affinity.

Synthetic inhibitors of the processing of pretransfer RNA by the ribonuclease P ribozyme: enzyme inhibitors which act by binding to substrate

2,2'-p-Phenylene bis[6-(4-methyl-1-piperazinyl)]benzimidazole, 2,2'-bis(3,5-dihydroxyphenyl)-6,6'-bis benzimidazole, and 2,2'-bis(4-hydroxyphenyl)-6,6'-bis benzimidazole are shown by UV-visible and fluorescence spectrophotometry to be strong ligands for tRNA, giving simple, hyperbolic binding isotherms with apparent dissociation constants in the micromolar range. Hydroxyl radical footprinting indicates that they may bind in the D and T loops. On the basis of this tRNA recognition as a rationale, they were tested as inhibitors of the processing of precursor tRNAs by the RNA subunit of Escherichia coli RNase P (M1 RNA). Preliminary studies show that inhibition of the processing of Drosophila tRNA precursor molecules by phosphodiester bond cleavage, releasing the extraneous 5'-portion of RNA and the mature tRNA molecule, was dependent on both the structure of the inhibitor and the structure of the particular tRNA precursor substrate for tRNA(Ala), tRNA(Val), and tRNA(His). In more detailed followup using the tRNA(His) precursor as the substrate, experiments to determine the concentration dependence of the reaction showed that inhibition took time to reach its maximum extent. I(50) values (concentrations for 50% inhibition) were between 5.3 and 20.8 microM, making these compounds among the strongest known inhibitors of this ribozyme, and the first inhibitors of it not based on natural products. These compounds effect their inhibition by binding to the substrate of the enzyme reaction, making them examples of an unusual class of enzyme inhibitors. They provide novel, small-molecule, inhibitor frameworks for this endoribonuclease ribozyme.

Characterization of DNA-directed RNA polymerases in isolated macronuclei of the ciliated protozoan Tetrahymena thermophila. Effects of purified ornithine decarboxylase and amine compounds

The possible regulatory interactions of purified ornithine decarboxylase with DNA-directed RNA polymerases in isolated macronuclei from the ciliated protozoan Tetrahymena thermophila were studied. It has been found that highly purified ODC (specific activity 10.2 mumols CO2 x h-1 x mg-1), even at activities of 37,500 nmol CO2 x h-1 per ml failed to alter RNA polymerase activity in the in vitro transcription assay in the presence or absence of the substrate L-ornithine at 20mM. The naturally occurring di- and polyamines putrescine, spermidine, and spermine stimulated in-vitro-transcription in isolated macronuclei more at optimal Mg2+/Mn(2+)-concentrations than at suboptimal concentrations, suggesting that polyamines act via a mechanism which is distinct from that of the inorganic cations. Of the monovalent amine compounds tested, (NH4)+ at high concentrations between 40 and 50mM slightly stimulated activity whereas the onset of stimulation by the organic amine compounds, piperidine and cyclohexylamine, was inversely related to the hydrophobicity of each particular compound. In the series of divalent amines, the correct distance between the N-atoms appeared to be very important since ethylenediamine and piperazine did not stimulate significantly but did inhibit at concentrations above 5 mM. 1,3-Diaminopropane stimulated slightly but inhibited above 10 mM, whereas the 1,4-diamino compounds putrescine and 1,4-diaminocyclohexane (DAC) were equally potent stimulators with the more hydrophobic one, DAC, reaching the maximum at lower concentrations than putrescine. For the trivalent amines, the influence of correct spacing seems not to be as important: N-(2-aminoethyl)piperazine stimulated very similar to spermidine.(ABSTRACT TRUNCATED AT 250 WORDS)

Polyamine effects on DNA-directed RNA polymerases in the ciliate Tetrahymena thermophila. In vivo- and in vitro-experiments suggesting highly specific regulative interactions

Stimulation of growth in resting cultures of the ciliated protozoan Tetrahymena thermophila stimulated putrescine formation in a manner coordinated to transcription and partly to DNA-polymerisation. The stimulation of polyamine biosynthesis involved increased formation of the precursor L-ornithine from L-arginine as well as stimulation of the regulative key enzyme ornithine decarboxylase. In order to characterize the interrelationships between polyamines and transcription, which were suggested by these in vivo-assays, in vitro-assays were performed employing isolated pure macronuclei from Tetrahymena thermophila. The results obtained were: i) The diamine putrescine and the polyamines spermidine and spermine stimulated the incorporation of [4-14C]UTP into RNA time- and concentration dependently. This stimulation was not due to changes in the ionic strength nor to substitution for divalent cations (e.g. Mg2+ or Mn2+). The di- and polyamines did not alter the Km of RNA polymerases for the substrates, e.g. UTP. ii) Purified yeast-RNA, when added to the in vitro transcription system at concentrations capable of stimulating purified ornithine decarboxylase from Tetrahymena inhibited the RNA polymerases. The inhibitory effect of RNA on the polymerases was partly antagonized by spermidine and spermine but not by putrescine whereas the residual polymerase activity was stimulated by all three bases. iii) The stimulating effects of the di- and polyamines were synergistic but not absolutely additive, suggesting different targets for their actions. iv) Stimulation of RNA polymerases by putrescine, spermidine, or spermine after inhibition of particular enzymes by alpha-amanitin allowed to distinguish the effects on the three polymerases (I, II, and III): putrescine was not specific for any of the polymerases; spermidine was most active stimulating polymerase I and spermine was most active stimulating polymerase II, less active stimulating polymerase I but strongly inhibitory to polymerase III. v) The results obtained in the previous experiments were confirmed by electrophoretic analysis of the products formed in the in vitro transcription assays which furthermore showed that the differences between the experiments with or without polyamines were most pronounced if partly denatured calf thymus DNA was present in the assay mixture. This finding and the inhibition by RNA suggest that the factor influenced most by the polyamines is the binding of the RNA polymerases to the DNA target.

Theoretical studies on the interaction of proteins and nucleic acid. II. The binding of alpha-helix to B-DNA

Interactions between B-DNA and homopolymeric alpha-helices of glycine, alanine, serine, asparagine and aspartic acid have been studied theoretically. The complexation energy has been minimised taking into account the interactions between DNA and the polypeptides as well as the internal energy of the alpha-helix and the interaction energy of counterions with the complex. The results obtained indicate the important role of strong hydrogen bonds between the peptide side chains and nucleic acid phosphate groups, these bonds being much stronger than specific interactions with the base-pairs. The formation of these structural bonds depends on the size of the alpha-helix, which in turn determines whether bridging across the major groove is possible. The steric role of the methyl group of thymine in orienting the peptide helix and the role of DNA screening cations in complex stabilization are also significant.

Theoretical studies on the interaction of proteins and nucleic acids. I. The binding of beta-pleated sheets to A- and B-DNA

A theoretical investigation of the interaction between a beta-ribbon consisting of two glycine hexapeptides and DNA in its A and B conformations is presented. A refined semi-empirical energy formula and a sophisticated energy minimization technique are used to optimize the complex, taking into account the DNA-beta-ribbon interaction, the full flexibility of the oligopeptide chains and of the positions of the DNA screening counterions. A considerable flexibility of the beta-ribbon is demonstrated, which allows the polypeptide fragment to interact comfortably with both forms of DNA considered and with different base-pair sequences. The results are discussed in connection with the general problem of DNA-protein recognition.

Netropsin specifically recognizes one of the two conformationally equivalent strands of poly(dA).poly(dT). One dimensional NMR study at 500 MHz involving NOE transfer between netropsin and DNA protons

Recent observations that the heteronomous structural model for poly(dA).poly(dT) is not found in solution and that in this DNA, the two strands are conformationally equivalent (J. Biomole. Str. Dyns. 2, 1057 (1985], has added a new dimension to the structural dynamics of DNA-netropsin complex. Does the antibiotic somehow distinguish between the two strands and specifically interact with only one of the conformationally equivalent strands? Model-building studies suggest that netropsin can either bind to the dA-strand in the minor groove such that H-bonds are formed between the imino protons N4-H, N6-H, N8-H of netropsin and N3 atoms of A or can bind to the dT-strand in the minor groove and form H-bonds between the imino-protons N4-H, N6-H, N8-H of netropsin and O2 atoms of T. If netropsin binds to the dA-strand, AH2 atoms of poly(dA).poly(dT) would be in closer proximity to the imino protons N4-H, N6-H, N8-H and pyrrole ring protons C5-H, C11-H of netropsin than they would be, if netropsin binds to the dT-strand. In order to distinguish these possibilities experiments were conducted which involved NOE energy transfer between netropsin and DNA protons in the drug-DNA complex. Difference NOE spectra of netropsin-poly(dA).poly(dT) complex in which AH2 was irradiated indicate that dominant NOEs were observed at the imino and pyrrole ring protons of netropsin. When the netropsin pyrrole ring protons were irradiated, the magnetization transfer was at AH2 of DNA. These observations suggest that netropsin binds to the dA-strand of poly(dA).poly(dT) even though dA/dT strands are conformationally equivalent.