The binding of polyamines and of ethidium bromide to tRNA

Translation efficiency affects the sequence-independent +1 ribosomal frameshifting by polyamines

Antizyme (AZ) interacts with ornithine decarboxylase, which catalyzes the first step of polyamine biosynthesis and recruits it to the proteasome for degradation. Synthesizing the functional AZ protein requires transition of the reading frame at the termination codon. This programmed +1 ribosomal frameshifting is induced by polyamines, but the molecular mechanism is still unknown. In this study, we explored the mechanism of polyamine-dependent +1 frameshifting using a human cell-free translation system. Unexpectedly, spermidine induced +1 frameshifting in the mutants replacing the termination codon at the shift site with a sense codon. Truncation experiments showed that +1 frameshifting occurred promiscuously in various positions of the AZ sequence. The probability of this sequence-independent +1 frameshifting increased in proportion to the length of the open reading frame. Furthermore, the +1 frameshifting was induced in some sequences other than the AZ gene in a polyamine-dependent manner. These findings suggest that polyamines have the potential to shift the reading frame in the +1 direction in any sequence. Finally, we showed that the probability of the sequence-independent +1 frameshifting by polyamines is likely inversely correlated with translation efficiency. Based on these results, we propose a model of the molecular mechanism for AZ +1 frameshifting.

Ruthenium anticancer agent KP1019 binds more tightly than NAMI-A to tRNAPhe

The ruthenium-based anticancer agent NAMI-A (ImH[trans-RuCl₄(dmso)(Im)], where Im = imidazole) has been shown to interact with RNA in vivo and in vitro. We hypothesized that the similarly structured drug KP1019 (IndH[trans-RuCl₄(Ind)₂], where Ind = indazole) binds to RNA as well. Fluorescence spectroscopy was employed to assay the interactions between either NAMI-A or KP1019 and tRNA^Phe through an intrinsic fluorophore wybutosine (Y) base and by extrinsic displacement of the intercalating agent ethidium bromide. In both the intrinsic Y-base and extrinsic ethidium bromide studies, KP1019 exhibited tighter binding to phenylalanine-specific tRNA (tRNA^Phe) than NAMI-A. In the ethidium bromide study, reducing both drugs from Ru^III to Ru^II resulted in a significant decrease in binding. Our findings suggest that the relatively large heteroaromatic indazole ligands of KP1019 intercalate in the π-stacks of tRNA^Phe within structurally complex binding pockets. In addition, NAMI-A appears to be sensitive to destabilizing electrostatic interactions with the negative phosphate backbone of tRNA^Phe. Interactions with additional tRNA molecules and other types of RNA require further evaluation to determine the role of RNA in the mechanisms of action for KP1019 and to better understand how Ru drugs fundamentally interact with biomolecules that are more structurally sophisticated than short DNA oligonucleotides. To the best of our knowledge, this is the first study to report KP1019 binding interactions with RNA.

Two stems with different characteristics and an internal loop in an RNA aptamer contribute to spermine-binding

Though polyamines (putrescine, spermidine, and spermine) bind to the specific position in RNA molecules, interaction mechanisms are poorly understood. SELEX procedure has been used to isolate high-affinity oligoribonucleotides (aptamers) from randomized RNA libraries. Selected aptamers are useful in exploring sequences and/or structures in RNAs for binding molecules. In this study, to analyze the interaction mechanism of polyamine to RNA, we selected RNA aptamers targeted for spermine. Two spermine-binding aptamers (#5 and #24) were obtained and both of them had two stem-loop structures. The 3′ stem-loop of #5 (SL_2) bound to spermine more effectively than the 5′ stem-loop of #5 did. A thermodynamic analysis by an isothermal titration calorimetry revealed that the dissociation constant of SL_2 for spermine was 27.2 μM and binding ratio was nearly 1:1. Binding assay with base-pair replaced variants showed that two stem regions and an internal loop in SL_2 were important for their spermine-binding activities. NMR analyses proposed that a terminal-side and a loop-side stem in SL_2 take a loose and a stable structure, respectively and a conformational change of SL_2 is induced by spermine. It is conclusive that two stems with different characteristics and an internal loop in SL_2 contribute to the specific spermine-binding.

Molecular Recognition of tRNA with 1-Naphthyl Acetyl Spermine, Spermine, and Spermidine: A Thermodynamic, Biophysical, and Molecular Docking Investigative Approach

The role of tRNA in protein translational machinery and the influence of polyamines on the interaction of acylated and deacylated tRNA with ribosomes make polyamine-tRNA interaction conspicuous. We studied the interaction of two biogenic polyamines, spermine (SPM) and spermidine (SPD), with tRNA^Phe and compared the results to those of the analogue 1-naphthyl acetyl spermine (NASPM). The binding affinity of SPM was comparable to that of NASPM; both were higher than that of SPD. The interactions led to significant thermal stabilization of tRNA^Phe and an increase in the enthalpy of transition. All the interactions were exothermic in nature and displayed prominent enthalpy-entropy compensation behavior. The entropy-driven nature of the interaction, the structural perturbations observed, and docking results proved that the polyamines were bound in the groove of the anticodon arm of tRNA^Phe. The amine groups of polyamines were involved in extensive electrostatic, H-bonding, and van der Waals interactions with tRNA^Phe. The naphthyl group of NASPM showed an additional stacking interaction with G24 and G26 of tRNA^Phe, which was absent in others. The results demonstrate that 1-naphthyl acetyl spermine can target the same binding sites as the biogenic polyamines without substituting for the functions played by them, which may lead to exhibition of selective anticancer cytotoxicity.

The phosphate clamp: sequence selective nucleic acid binding profiles and conformational induction of endonuclease inhibition by cationic Triplatin complexes

The substitution-inert polynuclear platinum(II) complex (PPC) series, [{trans-Pt(NH3)2(NH2(CH2)nNH3)}2-μ-(trans-Pt(NH3)2(NH2(CH2)nNH2)2}](NO3)8, where n = 5 (AH78P), 6 (AH78 TriplatinNC) and 7 (AH78H), are potent non-covalent DNA binding agents where nucleic acid recognition is achieved through use of the 'phosphate clamp' where the square-planar tetra-am(m)ine Pt(II) coordination units all form bidentate N-O-N complexes through hydrogen bonding with phosphate oxygens. The modular nature of PPC-DNA interactions results in high affinity for calf thymus DNA (Kapp ∼5 × 10(7) M(-1)). The phosphate clamp-DNA interactions result in condensation of superhelical and B-DNA, displacement of intercalated ethidium bromide and facilitate cooperative binding of Hoechst 33258 at the minor groove. The effect of linker chain length on DNA conformational changes was examined and the pentane-bridged complex, AH78P, was optimal for condensing DNA with results in the nanomolar region. Analysis of binding affinity and conformational changes for sequence-specific oligonucleotides by ITC, dialysis, ICP-MS, CD and 2D-(1)H NMR experiments indicate that two limiting modes of phosphate clamp binding can be distinguished through their conformational changes and strongly suggest that DNA condensation is driven by minor-groove spanning. Triplatin-DNA binding prevents endonuclease activity by type II restriction enzymes BamHI, EcoRI and SalI, and inhibition was confirmed through the development of an on-chip microfluidic protocol.

Probing the interaction of spermine and 1-naphthyl acetyl spermine with DNA polynucleotides: a comparative biophysical and thermodynamic investigation

The interaction of spermine and its analogue, 1-naphthyl acetyl spermine with four double stranded DNA polynucleotides has been studied to understand the structural and thermodynamic basis of the binding. The efficacy and specificity of DNA binding of this analogue has not yet been revealed. The energetics of the interaction was studied by isothermal titration calorimetry and differential scanning calorimetry. Circular dichroism spectroscopy, UV-thermal melting and ethidium bromide displacement assay have been employed to characterize the association. Circular dichroism studies showed that 1-naphthyl acetyl spermine caused a stronger structural perturbation in the polynucleotides. Among the adenine-thymine polynucleotides the alternating polynucleotide was more preferred by naphthyl acetyl spermine compared to the preference of spermine for the homo sequence. The higher melting stabilization revealed by the optical melting and differential scanning calorimetry results suggested that the binding of 1-naphthyl acetyl spermine increased the melting temperature and the total standard molar enthalpy of the transition of adenine-thymine polynucleotides. Microcalorimetry results revealed that unlike spermine the binding of 1-naphthyl acetyl spermine was endothermic. The interaction was characterized by total enthalpy-entropy compensation and high standard molar heat capacity values. There are differences in the mode of association of 1-naphthyl acetyl spermine and spermine. 1-naphthyl acetyl spermine binds with an enhanced affinity with the adenine-thymine hetero polynucleotide. Thus, the result suggests the importance of polyamine analogues and their ability to interfere with normal polyamine interactions.

Binding of the biogenic polyamines to deoxyribonucleic acids of varying base composition: base specificity and the associated energetics of the interaction

Background

The thermodynamics of the base pair specificity of the binding of the polyamines spermine, spermidine, putrescine, and cadaverine with three genomic DNAs Clostridium perfringens, 27% GC, Escherichia coli, 50% GC and Micrococcus lysodeikticus, 72% GC have been studied using titration calorimetry and the data supplemented with melting studies, ethidium displacement and circular dichroism spectroscopy results.

Methodology/Principal Findings

Isothermal titration calorimetry, differential scanning calorimetry, optical melting studies, ethidium displacement, circular dichroism spectroscopy are the various techniques employed to characterize the interaction of four polyamines, spermine, spermidine, putersine and cadaverine with the DNAs. Polyamines bound stronger with AT rich DNA compared to the GC rich DNA and the binding varied depending on the charge on the polyamine as spermine>spermidine >putrescine>cadaverine. Thermodynamics of the interaction revealed that the binding was entropy driven with small enthalpy contribution. The binding was influenced by salt concentration suggesting the contribution from electrostatic forces to the Gibbs energy of binding to be the dominant contributor. Each system studied exhibited enthalpy-entropy compensation. The negative heat capacity changes suggested a role for hydrophobic interactions which may arise due to the non polar interactions between DNA and polyamines.

Conclusion/Significance

From a thermodynamic analysis, the AT base specificity of polyamines to DNAs has been elucidated for the first time and supplemented by structural studies.

RNA binding small molecules: Studies on t-RNA binding by cytotoxic plant alkaloids berberine, palmatine and the comparison to ethidium

The interaction of two natural protoberberine plant alkaloids berberine and palmatine with t-RNA(phe) was studied using various biophysical techniques and the data was compared with the binding of the classical DNA intercalator, ethidium. The results of optical thermal melting, differential scanning calorimetry and circular dichroism characterized the native cloverleaf structure of t-RNA under the conditions of the study. The strong binding of the alkaloids and ethidium to t-RNA was revealed from the absorption and fluorescence studies. The salt dependence of the binding constants enabled the dissection of the binding free energy to electrostatic and non-electrostatic contributions. This analysis revealed a surprisingly large favourable component of the non-electrostatic contribution to the binding of these charged alkaloids and ethidium to t-RNA. Isothermal titration calorimetric studies revealed that the binding of both the alkaloids is driven by a moderately favourable enthalpy decrease and a moderately favourable entropy increase while that of ethidium is driven by a large favourable enthalpy decrease. Taken together, the results suggest that the binding of these alkaloid molecules on the t-RNA structure appears to be mostly by partial intercalation while ethidium intercalates to the t-RNA. These results reveal the molecular aspects on the interaction of these alkaloids to t-RNA.

tRNA(Phe) binds aminoglycoside antibiotics

Aminoglycoside antibiotics have recently been found to bind to a variety of unrelated RNA molecules, including sequences that are important for retroviral replication. We report the binding of neomycin B, kanamycin A, and Neo-Neo (a synthetic neomycin-neomycin dimer) to tRNA(Phe). Using thermal denaturation studies, fluorescence spectroscopy, Pb2+-mediated tRNA(Phe) cleavage, and gel mobility shift assays, we have established that aminoglycosides interact with yeast tRNA(Phe) and are likely to induce a conformational change. Thermal denaturation studies revealed that aminoglycosides have a substantial stabilizing effect on tRNA(Phe) secondary and tertiary structures, much greater than the stabilization effect of spermine, an unstructured polyamine. Aminoglycoside-induced inhibition of Pb2+-mediated tRNA(Phe) cleavage yielded IC50 values of: 5 microM for Neo-Neo, 100 microM for neomycin B, > 1 mM for kanamycin A, and > 10 mM for spermine. Enzymatic and chemical footprinting indicate that the anticodon stem as well as the junction of the TpsiC and D loops are preferred aminoglycoside binding sites.

S-adenosyl-L-methionine decarboxylase of Acanthamoeba castellanii (Neff): purification and properties

S-Adenosyl-L-methionine decarboxylase (AdoMetDC) has been purified to near homogeneity from the Neff strain of Acanthamoeba castellanii. The holoenzyme molecular mass is 88.8 kDa, including two copies each of a 32.8 kDa alpha-subunit and a 10-15 kDa beta-subunit. The alpha-subunit contains the active site. It has an N-terminal pyruvoyl group, and the first 19 amino acids are 63 and 74% identical with comparable sequences from yeast and mammals, respectively. The apparent Km for S-adenosylmethionine (AdoMet) in the presence of 2 mM putrescine was 30.0 microM. The enzyme was stimulated 2-fold by putrescine, but was unaffected by spermidine. It was inhibited by the following anti-metabolites, listed with their Ki values: Berenil (0.17 microM), pentamidine (19.4 microM), propamidine (334 microM), hydroxystilbamidine (357 microM), methylglyoxal bis(guanylhydrazone) (604 microM) and ethidium bromide (1.3 mM). Activity of the enzyme fell to undetectable levels during cell differentiation (encystment).

Differential effects of spermine and its analogues on the structures of polynucleotides complexed with ethidium bromide

The interactions of spermine and polyamine analogues with synthetic polynucleotides of various base sequences complexed with ethidium bromide (EB) were investigated using measurements of fluorescence intensity and steady-state fluorescence polarization. Spermine and polyamine analogues displaced some but not all of the EB bound to poly(dA-dT).poly(dA-dT) or poly(dG-dC).poly(dG-dC), suggesting that polyamines may stabilize these polynucleotides in a conformation with reduced affinity for EB. Modifications of the aliphatic backbone of spermine have pronounced effects on its ability to displace EB from poly(dA-dT).poly(dA-dT) but not from poly-(dG-dC).poly(dG-dC). Spermine and some but not all of the polyamine analogues caused fluorescence depolarization when they interacted with the complex of EB and poly(dA-dT).poly-(dA-dT). Neither spermine nor any of the analogues, however, induced fluorescence depolarization in the complex of EB with poly(dG-dC).poly(dG-dC) or poly(dA).poly(dT). This suggests that spermine and some spermine analogues induce structural changes specific to alternating A-T sequences.

Interactions between natural polyamines and tRNA: an 15N NMR analysis

15N NMR spectroscopy was used to explore the interactions between natural polyamines and Escherichia coli tRNA. It was found that when tRNA is added to solutions of 15N-labeled spermine or spermidine, there is a considerable decrease in the relative heights of the -NH(2+)--resonances with respect to the signals arising from the -NH3+ groups. The presence of tRNA was also found to reduce the longitudinal relaxation times T1 of the nitrogens, mainly those of the -NH(2+)- groups. The longitudinal relaxation times of the nitrogens were used to characterize the temperature dependence of the binding, and they allowed us to calculate the activation energies that determine the correlation times of amino groups in the presence of tRNA. Both the thermodynamic and the relaxation results indicate that (i) spermine binds more strongly to tRNA than spermidine does and (ii) within each of these molecules the -NH(2+)- groups bind more strongly to tRNA than the more electropositive -NH3+ moieties. This specificity suggests that the interaction between polyamines and tRNA cannot be described exclusively in terms of electrostatic forces and that other interactions (most likely, hydrogen bonding) are very important for establishing the polyamine-tRNA link. Some of the factors that may conspire against the binding of -NH3+ groups to tRNA are briefly discussed.

Cadaverine, an Essential Diamine for the Normal Root Development of Germinating Soybean (Glycine max) Seeds

When the polyamine content of soybean (Glycine max) seeds was examined during the early stages of germination, the major polyamine in the cotyledons was found to be spermidine, followed by spermine; while very low concentrations of cadaverine were found. In the embryonic axes, however, cadaverine was the main polyamine and its content markedly increased 24 hours after the start of germination. When the germination of the seeds was performed in the presence of 1 millimolar alpha-difluoromethylornithine (DFMO), a marked decrease in the cadaverine content was found, while the other polyamines were not affected. This decrease of the cadaverine content was already noticeable after the first hours of germination. In the presence of DFMO, a pronounced elongation in the roots of the seedlings and a marked decrease in the appearance of secondary roots as compared with controls, was observed. This abnormal rooting of the seedlings caused by DFMO was almost completely reverted by the addition of 1 millimolar cadaverine. The latter also increased the appearance of secondary roots in the seedlings. The decrease in the cadaverine content produced by DFMO could be traced to a strong inhibition of lysine decarboxylase. A temporal correlation between the increase in cadaverine content and the increase in lysine decarboxylase activity was found. Both reached a maximum at the second day of germination. The activity of diamine oxidase, the cadaverine degrading enzyme, started to increase at the third day and reached a maximum between the fourth and fifth day of germination. DFMO increased the activity of diamine oxidase by about 25%. Hence, the large decrease in cadaverine content produced by DFMO has to be attributed to the in vivo suppression of lysine decarboxylase activity. Ornithine decarboxylase activity was also suppressed by DFMO, but putrescine and spermidine contents were not affected, except in the meristematic tissues. The obtained results suggest an important role for cadaverine in the normal rooting process of soybean seedlings.

Eflornithine for the treatment of Pneumocystis carinii pneumonia in patients with the acquired immunodeficiency syndrome: a preliminary review

Pneumocystis carinii pneumonia (PCP) is the most common opportunistic infection in patients with acquired immunodeficiency syndrome (AIDS). Eflornithine is an antiprotozoal agent active against P. carinii. It acts by inhibiting ornithine decarboxylase, an enzyme that is essential for cellular function. The drug is initially administered intravenously, followed by oral therapy. Eflornithine has been used on a compassionate basis in AIDS patients with PCP who were intolerant of or unresponsive to traditional agents. Overall, the response rate has been about 35%; however, conclusions are difficult to make since patients had different stages of disease and received treatment for varying periods of time. Side effects include depression of bone marrow function, diarrhea, hearing loss, seizures, alterations in liver function tests, and rash. While the need for safer and more efficacious antipneumocystis drugs grows, widespread use of seemingly promising agents should be based on well-conducted clinical trials.

Controlled degradation of yeast tRNAPhe by spleen phosphodiesterase in the presence of ethidium bromide

Degradation of yeast tRNAPhe with spleen phosphodiesterase in the presence of ethidium bromide has been studied. It was found that in the presence of the intercalating dye, the digestion is halted after a limited number of nucleotides is removed. Possible explanations of the observed phenomenon in connection with tRNA-ethidium bromide complex formation are discussed.

Self-catalyzed cyclization of the intervening sequence RNA of Tetrahymena: inhibition by intercalating dyes

The intervening sequence (IVS) excised from the pre-rRNA of Tetrahymena undergoes a self-catalyzed cleavage-ligation reaction to form a covalently closed circular RNA. This cyclization reaction is kinetically inhibited by ethidium bromide (50% inhibition at 22 +/- 14 microM, greater than 99% inhibition at 53 +/- 16 microM for a 20 minute reaction). The dye does not alter the sites of the cyclization reaction, but it does increase the relative amount of reaction at a minor site 19 nucleotides from the 5' end of the IVS. The reversibility of the inhibition and the relative inhibitory strength of acridine orange, ethidium and proflavine suggest that inhibition is due to intercalation of the dye in functionally important secondary or tertiary structures of the IVS. The concentration of dye required to inhibit cyclization is much higher than expected from the known binding constants of such dyes to tRNA. At high Mg2+ to Na+ ratios, conditions which should stabilize RNA structure, a subpopulation of the IVS RNA molecules is resistant to ethidium inhibition, even at 200 microM ethidium. These data are interpreted as reflecting two conformational isomers of the IVS that differ in their reactivity and in their sensitivity to dye binding.

Self-catalyzed cyclization of the intervening sequence RNA of Tetrahymena: inhibition by methidiumpropyl.EDTA and localization of the major dye binding sites

The intervening sequence (IVS) excised from the rRNA precursor of Tetrahymena thermophila is converted to a covalently closed circular RNA in the absence of proteins in vitro. This self-catalyzed cyclization reaction is inhibited by the intercalating dye methidiumpropyl.EDTA (MPE; R.P. Hertzberg and P.B. Dervan (1982) J. Am. Chem. Soc. 104, 313-315). The MPE binding sites have been localized by mapping the sites of MPE.Fe(II) cleavage of the IVS RNA. There are three major binding sites within the 414 nucleotide IVS RNA. Two of these sites coincide with the A.B and 9L.2 pairings. These are structural elements that are conserved in all group I introns and are implicated as being functionally important for splicing. We propose that interaction of MPE with these sites is responsible for dye inhibition of cyclization. The reactions of MPE.Fe(II) with an RNA of known structure, tRNAPhe, and with the IVS RNA were studied as a function of temperature, ionic strength and ethidium concentration. Based on the comparison of the reaction with these two RNAs, we conclude that the dye is a very useful probe for structural regions of large RNAs, while it provides more limited structural information about the small, compact tRNA molecule.

The binding of spermine to polynucleotides and complementary oligonucleotides at near physiological ionic strength

The binding of [14C] spermine to polynucleotides has been studied by equilibrium dialysis and the data analysed by Scatchard plots. The binding of spermine to poly(A) shows a binding site for 1 spermine/140 nucleotides when measured in 0.2M NaCl at 5 degrees C. Poly(C) also has a similar sites; on the other hand poly(U) and poly(G) each have a binding site for 1 spermine/12 nucleotides. The addition of complementary di- or trinucleotides to either poly(A) or poly(U) affects their ability to bind spermine, in particular the high affinity site on poly(A) is no longer detectable. The effect of spermine, spermidine and putrescine on the binding of polynucleotides to complementary di- and trinucleotides was also studied. Spermine markedly increased the binding of both ApA and of ApApA to poly(U) whereas spermidine and putrescine had very little effect. In contrast spermine had little effect on the binding of either UpU or UpUpU to poly(A). These results suggest that spermine binding to oligo- and polynucleotides is dependent on the particular nucleotide combination involved and that spermine may therefore be able to act selectively within cells.

Proton exchange rates in transfer RNA as a function of spermidine and magnesium

Solvent exchange rates of selected protons were measured by NMR saturation recovery for E. coli tRNAVal, E. colifMet and yeast tRNAPhe, at temperatures from 20 to 40 degrees C, in the presence of 0.12M Na+ and various levels of added spermidine. tRNAVal was also studied with added Mg++. The exchange rates in zero spermidine and Mg++ indicate early melting of the U8 A14 interaction, in accord with thermodynamic melting studies. Exchange rates for secondary protons suggest early melting of the T stem in tRNAfMet and the acceptor stem in tRNAPhe, in contradiction with melting transition assignments from thermodynamic work. Addition of 10 spermidines per tRNA stabilizes the secondary and tertiary interactions more effectively than added Na+, but less so than Mg++. Added spermidine has the curious effect of increasing the exchange rate of the psi 55 N1 proton, while protecting the psi 55 N3 proton from exchange in all three tRNA's. Added Mg++ has the same effect on tRNAVal.

Ornithine decarboxylase may be a multifunctional protein

Ornithine decarboxylase may undergo posttranslational modifications which alter its function. Both transamidation of glutamine residues in the enzyme catalyzed by TGase and phosphorylation of serine and threonine residues catalyzed by a polyamine-stimulated protein kinase have been demonstrated. Data are presented which suggest that these modifications result in translocation of the modified protein to the nucleolus where it regulates the activity of RNA polymerase I to transcribe rDNA, the only active nucleolar genes. Transamidation of specific proteins with primary amines catalyzed by intracellular TGase may be an important posttranslational modification, capable of altering genetic transcription. The rapid half-life of ODC (10-15 min) may be related to rapid posttranslational modification with loss of enzymatic activity rather than to protein degradation.

Binding of spermine to tRNATyr stabilizes the conformation of the anticodon loop and creates strong binding sites for divalent cations

Electron spin resonance (ESR) spectra of yeast tRNATyr. spin-labelled in the isopentenyladenosine residue adjacent to the anticodon, were measured as a function of temperature at various spermine/tRNA ratios. The critical temperature, at which a change in the activation energy for spin-label motion takes place, changes abruptly by almost 10 degrees C upon the addition of the fifth spermine molecule/tRNATyr molecule, indicating a marked stabilization of the anticodon region. Scatchard plots for Mn2+ binding to tRNATyr in the presence of spermine do not follow theoretically predicted curves for electrostatic type of interaction, assuming that four negative charges on tRNA are neutralized by each spermine molecule. It was estimated that two to three new binding sites for divalent cations are created upon the binding of spermine to tRNATyr.

Bleomycin-induced life prolongation of mice infected with Trypanosoma brucei brucei EATRO 110

The antitumour antibiotic bleomycin, supplied as commercial BlenoxaneR (a mixture of bleomycinic acids), at 7 or 14 mg/kg prolonged life greater than 30 days beyond death of controls without relapse or sign of trypanosomes in the peripheral blood of mice infected with Trypanosoma b. brucei EATRO 110. Control mice died in three to four days. The purified A2 and B2 bleomycin congeners were also active at this dose. Spermidine, spermine and hirudonine (1,8-diamidinospermidine) but not putrescine, co-administered with drug, annulled the curative effects of these compounds, as signalled by appearance of trypanosomes in the blood and death of the animals.

Polyamine metabolism: a potential therapeutic target in trypanosomes

alpha-Difluoromethylornithine (RMI 71,782), a specific irreversible inhibitor of the first step in polyamine biosynthesis, that is, the formation of putrescine from ornithine by ornithine decarboxylase, cures mice infected with a virulent, rodent-passaged strain of Trypanosoma brucei brucei. This parasite is closely related to the trypanosomes that cause human sleeping sickness. The drug, which is remarkably nontoxic, was effective when administered in drinking water or by intubation. The ability of the compound to inhibit ornithine decarboxylase in vitro was demonstrated by the reduced amounts of putrescine synthesized from tritiated ornithine in Trypanosoma brucei suspensions. These observations direct attention to polyamine metabolism as a target for chemotherapy of parasitic diseases.

Use of polynucleotide/polyacrylamide-gel electrophoresis as a sensitive technique for the detection and comparison of ribonuclease activities

A technique is described in which the incorporation of a polynucleotide substrate into the matrix of a polyacrylamide gel allows the use of electrophoresis for the detection of polycationic ribonuclease activity rather than simply the presence of protein. Because use is made of the catalytic properties of ribonucleases, polynucleotide/polyacrylamide-gel electrophoresis is apparoximately 10(5) times more sensitive for the detection of these enzymes than conventional gel electrophoresis with the use of protein-staining dyes. Initial studies showed that the poor migration, in the gels, of highly charged polycationic ribonucleases in the presence of negatively charged synthetic polynucleotides could be overcome by high concentrations of spermine. The positively charged polyamine, by neutralizing the polyanionic polynucleotide, enabled these basic enzymes to migrate considerable distances in the gel. Electrophoresis of the RNAases under conditions of low pH, and incubation of the gel at neutral pH followed by staining for polynucleotide, resulted in coloured gels containing clear bands that define regions of enzyme activity. Alterations in spermine concentration or substrate identity caused changes in the positions of these bands, suggesting a dynamic interaction among the enzyme, polyamine and polynucleotide. Because of the advantages, in terms of selectivity and sensitivity of polynucleotide/polyacrylamide-gel electrophoresis, this technique was used to demonstrate the nuclease homogenity of three purified bovine muscle enzymes, and to compare these enzymes with each other, as well as with bovine pancreatic ribonuclease A.

Direct physical measurements on substituted agarose gels: evidence for intercalation of gel-bound ethidium into transfer RNA

The cation of the salt ethidium bromide (3,8-diamino-5-ethyl-6-phenylphenanthridinium bromide) has been covalently linked to an agarose matrix through an intermediate 3,3'-diaminodipropylaminosuccinyl spacer arm. Partition binding and visible absorption spectral measurements on the gel were used to monitor the binding of transfer RNA to the covalently bound ethidium group. Direct fluorescence measurements of the formation of the gel-bound complex indicate that this binding involves the intercalation of the ethidium groups into the tRNA molecule. Dissociation of the ethidium-tRNA complex was monitored as a function of sodium chloride concentration by both direct solution spectral measurement of the released tRNA and by fluorescence quenching measurements of the dissociation of the intercalation complex. The derivatized gel has been shown to be capable of the fractionation of tRNA species by elution with a positive salt gradient under column flow conditions.

The interactions between nucleic acids and polyamines. I. High resolution carbon-13 and hydrogen-1 nuclear magnetic resonance studies of spermidine and 5'-AMP

In 0.5 M solution at pH 7.6, interaction of spermidine and 5'-AMP is demonstrated by downfield proton NMR shifts. Shifts of ribose and adenine protons support a model in which triprotonated spermidine engages the phosphate anion with the C-3 diamine segment in a conformation to maximize interaction and the C-4 amino segment extended to interact with adenine N-7 (base anti, 2' endo, g'g' and gg nucleoside conformation). Changes in carbon-13 chemical shifts fro ribose C-5' (downfield), C-2' C-3', and C-4' (upfield) and for adenine C-6 and C-8 (upfield) support this model. In 0.006 M solution no significant changes in proton shifts and therefore no evidence for interaction was found. Spermidine and 5' -UMP (0.006 M) showed interaction at pH 10.5 (small upfield shifts in the proton nmr) interpreted as changing conformation by solvent interaction. In 0.00l M 3'-UMP at pH 10.5 small downfield proton shifts induced by spermidine are attributed to interactions with phosphate anion.

Spermine stabilizes the conformation of tRNAPhe in crystals

Crystals from yeast tRNAPhe were dissolved and compared with tRNAPhe that had not been srystallized. A number of differences were found regarding the interaction with ethidium bromide, the melting point and the circular dichroic signal. These differences were assigned to the presence of spermine in the dissolved crystals indicating a transient stabilization of the conformation of tRNAPhe, probably as a tRNAPhe-spermine complex, after dissolving.

Allosteric interpretation of Mg2+ binding to the denaturable Escherichia coli tRNAGlu2+

The Mg2+ binding properties of the denaturable tRNAGlu2 from E. coli in 0.1 M Na+, pH7, are characterized by equilibrium dialysis. At 34 degrees C, where the native and denatured conformers are in equilibrium, Mg2+ binding is cooperative. By trapping the tRNA completely in the native conformation at 4 degrees C it is shown that native tRNAGlu2 possesses one strong binding site, K1 = 7.5 x 10(4) M-1 and approximately 36 weak sites with K2 = 8.3 x 10(2) M-1. A significantly lower affinity for the denatured conformer is indicated. We show that Mg2+ effects an allosteric transition from the low affinity denatured conformational state to the high affinity native state and develop the appropriate equations to fit the Mg2+ binding data with physically meaningful parameters. Our results also suggest the previously reported cooperative cation binding to tRNA arises from a cation induced conformational change to the native tRNA conformation and does not reflect the inherent Mg2+ binding properties of the native conformer.