The site-specific cleavage of double-stranded (ds) RNA is a conserved early step in bacterial ribosomal RNA (rRNA) maturation that is carried out by ribonuclease III. Studies on the RNase III mechanism of dsRNA cleavage have focused mainly on the enzymes from mesophiles such as Escherichia coli. In contrast, little is known of the RNA processing pathways and the functions of associated ribonucleases in the hyperthermophiles. Therefore, structural and biochemical studies of proteins from hyperthermophilic bacteria are providing essential insight on the sources of biomolecular thermostability, and how enzymes function at high temperatures. The biochemical behavior of RNase III of the hyperthermophilic bacterium Thermotoga maritima is analyzed using purified recombinant enzyme and the cognate pre-ribosomal RNAs as substrates. The T. maritima genome encodes a ~5,000 nucleotide (nt) transcript, expressed from the single ribosomal RNA (rRNA) operon. RNase III processing sites are expected to form through base-pairing of complementary sequences that flank the 16S and 23S rRNAs. The Thermotoga pre-16S and pre-23S processing stems are synthesized in the form of small hairpins, and are efficiently and site-specifically cleaved by Tm-RNase III at sites consistent with an in vivo role of the enzyme in producing the immediate precursors to the mature rRNAs. T. maritima (Tm)-RNase III activity is dependent upon divalent metal ion, with Mg^2+ as the preferred species, at concentrations >= 1 mM. Mn^2+, Co^2+ and Ni^2+ also support activity, but with reduced efficiency. The enzyme activity is also supported by salt (Na^+, K^+, or NH4^+) in the 50-80 mM range, with an optimal pH of ~8. Catalytic activity exhibits a broad temperature maximum of ~40-70 deg C, with significant activity retained at 95 deg C. Comparison of the Charged-versus-Polar (C-vP) bias of the protein side chains indicates that Tm-RNase III thermostability is due to large C-vP bias. Analysis of pre-23S substrate variants reveals a dependence of reactivity on the base-pair (bp) sequence in the proximal box (pb), a site of protein contact that functions as a positive determinant of recognition of E. coli (Ec)-RNase III substrates. The pb sequence dependence of reactivity is similar to that observed with the Ec-RNase III pb. Moreover, Tm-RNase III cleaves an Ec-RNase III substrate with identical specificity, and is inhibited by pb antideterminants that also inhibit Ec-Rnase III. These studies reveal the conservation acrosss a broad phylogenetic distance of substrate reactivity epitopes, both the positive and negative determinants, among bacterial RNase III substrates. / Chemistry

Ribonuclease III is a highly-conserved bacterial enzyme that cleaves double-stranded (ds) RNA structures, and participates in diverse RNA maturation and decay pathways. Essential insight on the RNase III mechanism of dsRNA cleavage has been provided by crystallographic studies of the enzyme from the hyperthermophilic bacterium, Aquifex aeolicus. However, those crystals involved complexes containing either cleaved RNA, or a mutant RNase III that is catalytically inactive. In addition, neither the biochemical properties of A. aeolicus (Aa)-RNase III, nor the reactivity epitopes of its cognate substrates are known. The goal of this project is to use Aa-RNase III, for which there is atomic-level structural information, to determine how RNase III recognizes its substrates and selects the target site. I first purified recombinant Aa-RNase III and defined the conditions that support its optimal in vitro catalytic activity. The catalytic activity of purified recombinant Aa-RNase III exhibits a temperature optimum of 70-85°C, a pH optimum of 8.0, and with either Mg2+ or Mn2+ supports efficient catalysis. Cognate substrates for Aa-RNase III were identified and their reactivity epitopes were characterized, including the specific bp sequence elements that determine processing reactivity and selectivity. Small RNA hairpins, based on the double-stranded structures associated with the Aquifex 16S and 23S rRNA precursors, are cleaved in vitro at sites that are consistent with production of the immediate precursors to the mature rRNAs. Third, the role of the dsRBD in scissile bond selection was examined by a mutational analysis of the conserved interactions of RNA binding motif 1 (RBM1) with the substrate proximal box (pb). The individual contributions towards substrate recognition were determined for conserved amino acid side chains in the RBM1. It also was shown that the dsRBD plays key dual roles in both binding energy and selectivity, through RBM1 responsiveness to proximal box bp sequence. The dsRBD is specifically responsive to an antideterminant (AD) bp in pb position 2. The relative structural rigidity of both dsRNA and dsRBD rationalizes the strong effect of an inhibitory bp at pb position 2: disruption of one RBM1 side chain interaction can effectively disrupt the other RBM1 side chain interactions. Finally, a cis-acting model was developed for subunit involvement in substrate recognition by RNase III. Structurally asymmetric mutant heterodimers of Escherichia coli (Ec)-RNase III were constructed, and asymmetric substrates were employed to reveal how RNase III can bind and deliver hairpin substrates to the active site cleft in a pathway that requires specific binding configurations of both enzyme and substrate. / Chemistry

<p>This thesis contains two parts.</p><p>In the first part, general and versatile palladium-mediated ¹¹C-C bond forming reactions for use in the production of radiotracers for Positron Emission Tomography (PET) were explored. Two complimentarty approaches were investigated: the coupling of [¹¹C]methyl iodide with a vinyl stannane and the reaction of a [¹¹C]methylated stannane with various organohalides. The former approach resulted in an improved, fully automated method for the synthesis of the potential cell proliferation tracer 1-(2’-deoxy-2’-fluoro-β-D-arabinofuranosyl)-[<i>methyl</i>-¹¹C]- thymine. The tracer was obtained in an isolated decay-corrected radiochemical yield of 28% at 25 min after end of radionuclide production. </p><p>In the latter approach, a [¹¹C]methylated tricyclic stannane (5-[¹¹C]methyl-1-aza- 5-stannabicyclo[3.3.3]undecane) was synthesised in 47% decay-corrected radiochemical yield, starting from [¹¹C]methyl iodide. This stannane was successfully employed in palladium-mediated coupling reactions with aryl, heteroaryl and vinyl halides.</p><p>In the second part, effects of the osmolytes glycine betaine, trimethylamine <i>N</i>-oxide (TMAO) and urea on Ribonuclease A (RNase A) were investigated using Nuclear Magnetic Resonance (NMR) spectroscopy. Changes in the enzymatic activity in the presence of these osmolytes at concentrations of ≤1 M were observed by monitoring the RNase A-catalysed degradation of polyuridylic acid using ³¹P NMR spectroscopy. The decrease in activity caused by urea was counteracted by both glycine betaine and TMAO at a molar ratio of 1:1.4 and 1:1, respectively.</p><p>To investigate if the observed activity changes were accompanied by any detectable alteration in the gross conformation of RNase A, diffusion coefficients for the enzyme in the various osmolyte solutions were measured using pulsed-field gradient NMR. A pulse sequence suitable for diffusion measurements in highly concentrated aqueous osmolyte solutions was developed and assessed. The diffusion of RNase A was measured relative to a new internal standard, 2,2,5,5,-tetramethyl-1,4-dioxane. No clear, detectable change in the relative diffusion of RNase A was observed in these media.</p>

This thesis contains two parts. In the first part, general and versatile palladium-mediated 11C-C bond forming reactions for use in the production of radiotracers for Positron Emission Tomography (PET) were explored. Two complimentarty approaches were investigated: the coupling of [11C]methyl iodide with a vinyl stannane and the reaction of a [11C]methylated stannane with various organohalides. The former approach resulted in an improved, fully automated method for the synthesis of the potential cell proliferation tracer 1-(2’-deoxy-2’-fluoro-β-D-arabinofuranosyl)-[methyl-11C]- thymine. The tracer was obtained in an isolated decay-corrected radiochemical yield of 28% at 25 min after end of radionuclide production. In the latter approach, a [11C]methylated tricyclic stannane (5-[11C]methyl-1-aza- 5-stannabicyclo[3.3.3]undecane) was synthesised in 47% decay-corrected radiochemical yield, starting from [11C]methyl iodide. This stannane was successfully employed in palladium-mediated coupling reactions with aryl, heteroaryl and vinyl halides. In the second part, effects of the osmolytes glycine betaine, trimethylamine N-oxide (TMAO) and urea on Ribonuclease A (RNase A) were investigated using Nuclear Magnetic Resonance (NMR) spectroscopy. Changes in the enzymatic activity in the presence of these osmolytes at concentrations of ≤1 M were observed by monitoring the RNase A-catalysed degradation of polyuridylic acid using 31P NMR spectroscopy. The decrease in activity caused by urea was counteracted by both glycine betaine and TMAO at a molar ratio of 1:1.4 and 1:1, respectively. To investigate if the observed activity changes were accompanied by any detectable alteration in the gross conformation of RNase A, diffusion coefficients for the enzyme in the various osmolyte solutions were measured using pulsed-field gradient NMR. A pulse sequence suitable for diffusion measurements in highly concentrated aqueous osmolyte solutions was developed and assessed. The diffusion of RNase A was measured relative to a new internal standard, 2,2,5,5,-tetramethyl-1,4-dioxane. No clear, detectable change in the relative diffusion of RNase A was observed in these media.

In recent years the application of single-molecule techniques to probe biomolecules and intermolecular interactions at single-molecule resolution has expanded rapidly. Here, I investigate a series of peptides and proteins in an attempt to gain a better understanding of nanopore sensing as a single-molecule technique. The analysis of retro, inversed, and retro-inversed isomers of glucagon and α-helical Fmoc-D2A10K2 peptide showed that nanopore sensing utilizing a wild-type α-hemolysin pore can distinguish between all four isomers while circular dichroism can only distinguish between chiral isomers, but not between directional isomers. The investigation of a series of proteins of different chemical and physical properties revealed important information about nanopore analysis of proteins. Contrary to some reports in the literature, all proteins analysed here induced large blockade events. The frequency of total events and the proportion of large blockade events were significantly reduced in tris(hydroxymethyl)aminomethane or 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid buffers and were only restored by the addition of ethylenediaminetetraacetic acid or the use of phosphate buffer, both of which can sequester metal ions. Furthermore, the results obtained with the proteins in the presence of ligands demonstrated that transient or partial unfolding of proteins can be detected by nanopore analysis confirming the usefulness of this technique for conformational studies or for protein/ligand interactions. Interestingly, while the blockade current histograms were different for each protein there was no obvious correlation between the properties of the proteins and the blockade current histograms. In an attempt to identify whether the large blockade events were translocation or intercalation, both an indirect and a direct approach were taken. The indirect approach which relies on the effect of voltage on the interaction of the molecule with the pore provided no conclusive answer to the question of protein translocation through the α-hemolysin pore. In contrast, the direct approach in which ribonuclease A is added to the cis side of the pore and then the trans side is tested for enzyme activity showed that ribonuclease A doesn't translocate through the α-hemolysin pore.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Este trabalho teve por finalidade avaliar algumas variÃveis fisiolÃgicas e bioquÃmicas de duas espÃcies de sorgo forrageiro submetidas a diferentes condiÃÃes de cultivo e de salinidade. Para isso, foram montados dois experimentos. No primeiro deles estudou-se tais variÃveis em Sorghum bicolor e Sorghum sudanense, em funÃÃo de diferentes nÃveis de estresse salino, enquanto no segundo, as variÃveis foram estudadas em duas fases distintas de desenvolvimento das duas espÃcies de sorgo, visando determinar em qual delas essas espÃcies sÃo mais resistentes aos efeitos deletÃrios da salinidade. No primeiro experimento, os tratamentos foram dispostos em esquema fatorial 2 à 5, composto por duas espÃcies (S. bicolor e S. sudanense) e cinco tratamentos (NaCl a 0, 25, 50, 75 e 100 mM). Nesse experimento, os parÃmetros de trocas gasosas foram pouco afetados pela salinidade, em ambas as espÃcies. O crescimento das plantas de ambas as espÃcies reduziu à medida que a salinidade aumentou. O potencial osmÃtico (&#61529;s) foliar foi fortemente reduzido pela salinidade nessas plantas, a qual aumentou significativamente a concentraÃÃo de solutos orgÃnicos nas duas espÃcies de sorgo. As concentraÃÃes de Na+ e Cl- aumentaram com a salinidade em ambas as espÃcies. S. bicolor e S. sudanense mantiveram o teor relativo de Ãgua sob condiÃÃes salinas igual ao do controle. Nas espÃcies de sorgo estudadas, os carboidratos solÃveis e os Ãons K+ e Cl- foram os que mais contribuÃram para o ajustamento osmÃtico das plantas. Nas folhas de S. bicolor, houve um aumento na atividade das peroxidases do ascorbato (APX) e do guaiacol (GPX) e uma reduÃÃo na atividade da catalase (CAT), enquanto a dismutase do superÃxido (SOD) nÃo foi afetada. Em S. sudanense, à medida que foram elevadas as doses de NaCl, observou-se um aumento na atividade da GPX e da SOD. Nas raÃzes, apenas a SOD apresentou aumento em atividade no S. bicolor. A atividade ribonucleÃsica nas folhas de ambas as espÃcies aumentou com as doses crescentes de NaCl, enquanto que nas raÃzes, ela foi reduzida à medida que o estresse salino intensificou-se. No segundo experimento, os tratamentos foram arranjados em esquema fatorial 2 à 3 à 2, composto por duas espÃcies (S. bicolor e S. sudanense), trÃs concentraÃÃes de sais na Ãgua de irrigaÃÃo (condutividades elÃtricas de 0,0; 4,0 e 8,0 dS m-1) e dois perÃodos de aplicaÃÃo do estresse salino Ãs plantas [desde a semeadura atà 25 dias depois (Fase I) e do 25 ao 50 dia apÃs a semeadura (Fase II)], com cinco repetiÃÃes. As principais alteraÃÃes nas trocas gasosas ocorreram na Fase II do desenvolvimento. O estresse salino reduziu o crescimento das plantas de sorgo em ambas as fases de desenvolvimento, porÃm essa reduÃÃo foi mais acentuada na Fase I. Os teores dos solutos orgÃnicos variaram em funÃÃo das fases de desenvolvimento, da espÃcie e da salinidade. Na Fase I, em ambas as espÃcies de sorgo, houve acrÃscimos nos teores de Na+ e K+ e reduÃÃo nos de Cl- pela salinidade, enquanto que, na Fase II do desenvolvimento, os teores de Na+ e K+ foram reduzidos e os de Cl-, aumentados, tanto em S. bicolor como em S. sudanense. Na Fase I do desenvolvimento, apenas a SOD, em S. bicolor, e a CAT, em S. sudanense, mostraram incrementos de atividade em resposta ao estresse salino. Jà na Fase II, nenhum aumento na atividade do sistema enzimÃtico antioxidativo foi observado em funÃÃo da salinidade, nas duas espÃcies estudadas. Na Fase I, a atividade da RNase, em ambas as espÃcies, foi reduzida com a salinidade, enquanto na Fase II do desenvolvimento, ela foi aumentada. O crescimento das plantas de S. sudanense foi ligeiramente mais afetado que o de S. bicolor. As espÃcies de sorgo forrageiro estudadas neste trabalho foram capazes de reduzir o &#61529;s foliar em concentraÃÃes elevadas de NaCl, o que pode ter contribuÃdo para um melhor ajustamento osmÃtico. AlÃm disso, nas condiÃÃes empregadas no primeiro experimento, S. bicolor pareceu ter um sistema antioxidante mais eficaz contra os efeitos da salinidade do que S. sudanense. Em relaÃÃo ao segundo experimento, o crescimento das plantas de sorgo forrageiro foi mais afetado quando o estresse salino foi aplicado em estÃdios iniciais do desenvolvimento. O estresse oxidativo causado pela salinidade parece nÃo ter sido suficiente para estimular o sistema de defesa enzimÃtico antioxidativo na Fase II do desenvolvimento, em ambas as espÃcies. AlÃm disso, o aumento na atividade RNÃsica pode indicar o papel desta enzima na proteÃÃo contra os efeitos deletÃrios da salinidade nessas espÃcies de sorgo. De modo geral, nÃo houve diferenÃas marcantes na tolerÃncia das plantas de S. bicolor e S. sudanense à salinidade. / This study aimed to evaluate some physiological and biochemical variables of two species of sorghum subjected to different growing conditions and salinity. For this, two experiments were set up. In the first study, the variables in Sorghum bicolor and Sorghum sudanense were evaluated according different levels of salinity stress. In the second, the variables were studied in two distinct phases of development of two species of sorghum, to determine which one of these species are more resistant to the deleterious effects of salinity. In the first experiment, treatments were arranged in a 5 à 2 factorial, consisting of two species (S. bicolor and S. sudanense) and five treatments (NaCl at 0, 25, 50, 75 and 100 mM). In this experiment, the gas exchange parameters were little affected by salinity in both species. Plant growth of both species decreased as salinity increased. The osmotic potential (&#968;s) leaves was strongly reduced by salinity in these plants, which significantly increased the concentration of organic solutes in the two species of sorghum. The concentrations of Na+ and Cl- increased with salinity in both species. S. bicolor and S. sudanense maintained relative water content under saline conditions the same as the control. In sorghum species studied, the soluble carbohydrates and the ions K+ and Cl- were the main contributors to the osmotic adjustment of plants. In leaves of S. bicolor, there was an increase in activity of ascorbate peroxidase (APX) and guaiacol (GPX) and a reduction in activity of catalase (CAT), while superoxide dismutase (SOD) was not affected. In S. sudanense, the activity of GPX and SOD increased with increasing salinity. In roots, just SOD activity in S. bicolor were increased with salt stress. Ribonuclease activity in the leaves of both species increased with increasing doses of NaCl, whereas in roots it was reduced as the salt stress intensified. In the second experiment, treatments were arranged in a factorial 2 à 3 à 2, composed of two species (S. bicolor and S. sudanense), three concentrations of salts in irrigation water (electrical conductivities of 0.0, 4.0 and 8.0 dS m-1) and two periods of application of salt stress to plants [from sowing until 25 days later (Phase I) and from 25th to 50th day after sowing (Phase II)], with five repetitions. The main changes in gas exchange occurred in Phase II development. The salt stress reduced plant growth of sorghum in both phases of development, but this reduction was more pronounced in Phase I. The levels of organic solutes varied according to the phases of development, species and salinity. In Phase I, in both species of sorghum, there were increases in levels of Na+ and K+ and reduced Cl- by salinity, whereas in Phase II development, the levels of Na+ and K+ were reduced and Cl- extended, both in S. bicolor as in S. sudanense. In Phase I of development, only SOD in S. bicolor, and CAT in S. sudanense showed activity increases in response to salt stress. In the Phase II, no increase in the activity of antioxidant enzyme system was observed as a function of salinity in both species. In Phase I, the activity of RNase in both species was reduced by salinity, while in Phase II development, it was expanded. Plant growth of S. sudanense was slightly more affected than the S. bicolor. Sorghum species studied in this work were able to reduce the leaf &#968;s high concentrations of NaCl, which may have contributed to a better osmotic adjustment. In addition, under the conditions employed in the first experiment, S. bicolor appeared to have a more effective antioxidant system against the effects of salinity than S. sudanense. For the second experiment, the growth of sorghum plants was more affected when the salt stress was applied in the early stage of development. The oxidative stress caused by salinity seems to have been sufficient to stimulate the enzymatic antioxidant defense system in Phase II development in both species. Furthermore, increased activity RNase may indicate the role of this enzyme in protecting against the deleterious effects of salinity in these species of sorghum. Overall, there were no marked differences in plant tolerance between S. bicolor and S. sudanense under salinity.

Antibiotics have been commonly used in medical practice for over 40 years. However, the misuse and overuse of current antibiotics is thought to be the primary cause for the increase in antibiotic resistance. Many current antibiotics target the bacterial ribosome. Antibiotics such as aminoglycosides and macrolides specifically target the 30S or 50S subunits to inhibit bacterial growth. During the assembly of the bacterial ribosome, ribosomal RNA of the 30S and 50S ribosomal subunits is processed by bacterial ribonucleases (RNases). RNases are also involved in the degradation and turnover of this RNA during times of stress, such as the presence of an antibiotic. This makes ribonucleases a potential target for novel antibiotics. It was shown that Escherichia coli mutants that were deficient for RNase III, RNase E, RNase R, RNase G, or RNase PH had an increase in ribosomal subunit assembly defects. These mutant bacterial cells also displayed an increased sensitivity to neomycin and paromomycin antibiotics. My research has also shown that an inhibitor of RNases, vanadyl ribonucleoside complex, potentiated the effects of an aminoglycoside and a macrolide antibiotic in wild type Escherichia coli, methicillin sensitive Staphylococcus aureus, and methicillin resistant Staphylococcus aureus. RNases are essential enzymes in both rRNA maturation and degradation. Based on this and previous work, the inhibition of specific RNases leads to an increased sensitivity to antibiotics. This work demonstrates that the inhibition of RNases might be a new target to combat antibiotic resistance.

<p>Degradation of the mRNA 3'-end located poly(A) tail is an important step for mRNA decay in mammalian cells. Thus, to understand mRNA decay in detail, it is important to identify the catalytic activities involved in degrading poly(A). We identified and purified a 54-kDa polypeptide responsible for poly(A)-specific 3' exonuclease activity in calf thymus extracts. The 54-kDa polypeptide is a proteolytic fragment of the poly(A)-specific ribonuclease (PARN) 74-kDa polypeptide. PARN is a divalent metal ion dependent, poly(A)-specific, oligomeric, processive and cap interacting 3' exonuclease. An active deadenylation complex, consisting of the poly(A)-tailed RNA substrate and PARN, has been identified. The interaction with the 5'-end cap structure stimulates PARN activity and also amplifies the processivity of the deadenylation reaction. Furthermore, the cap binding site and the active site of PARN are separate from each other. To characterise the active site of PARN, we per-formed side-directed mutagenesis, Fe²⁺-mediated hydroxyl radical cleavage and metal ion switch experiments. We have demonstrated that the conserved acidic amino acid residues D28, E30, D292 and D382 of human PARN are essential for PARN activity and that these amino acid residues are directly involved in the co-ordination of at least two metal ions in the active site of PARN. Phosphorothioate modification on RNA substrates revealed that the pro-R oxygen atom of the scissile phosphate group interacts directly with the metal ion(s). Based on our studies, we propose a model for the action of PARN. Similarly to what has been observed for ribozymes, aminoglycoside antibiotics inhibit PARN activity, most likely by the displacement of catalytically important divalent metal ions. Among the aminoglycoside antibiotics tested, neomycin B is the most potent inhibitor. We speculate that inhibition of enzymes using similar catalytic mechanisms as PARN could be a reason for the toxic side effects caused by aminoglycoside antibiotics in clinical practice. </p>

Noncovalent interactions are involved in many biological processes in which biomolecules bind specifically and reversibly to a partner. Often, proteins do not have a biological activity without the presence of a partner, a ligand. Biological signals are produced when proteins interact with other proteins, peptides, oligonucleotides, nucleic acids, lipids, metal ions, polysaccharides or small organic molecules. Some key steps in the drug discovery process are based on noncovalent interactions. We have focused our research on the steps involving ligand screening, competitive binding and ‘off-target’ binding. The first paper in this thesis investigated the complicated electrospray ionization process with regards to noncovalent complexes. We have proposed a model that may explain how the equilibrium between a protein and ligand changes during the droplet evaporation/ionization process. The second paper describes an evaluation of an automated chip-based nano-ESI platform for ligand screening. The technique was compared with a previously reported method based on nuclear magnetic resonance (NMR), and excellent correlation was obtained between the results obtained with the two methods. As a general conclusion we believe that the automated nano-ESI/MS should have a great potential to serve as a complementary screening method to conventional HTS. Alternatively, it could be used as a first screening method in an early phase of drug development programs when only small amounts of purified targets are available. In the third article, the advantage of using on-line microdialysis as a tool for enhanced resolution and sensitivity during detection of noncovalent interactions and competitive binding studies by ESI-MS was demonstrated. The microdialysis device was improved and a new approach for competitive binding studies was developed. The last article in the thesis reports studies of noncovalent interactions by means of nanoelectrospray ionization mass spectrometry (nanoESI-MS) for determination of the specific binding of selected drug candidates to HSA. Two drug candidates and two known binders to HSA were analyzed using a competitive approach. The drugs were incubated with the target protein followed by addition of site-specific probes, one at a time. The drug candidates showed predominant affinity to site I (warfarin site). Naproxen and glyburide showed affinity to both sites I and II. / QC 20100705

Degradation of the mRNA 3'-end located poly(A) tail is an important step for mRNA decay in mammalian cells. Thus, to understand mRNA decay in detail, it is important to identify the catalytic activities involved in degrading poly(A). We identified and purified a 54-kDa polypeptide responsible for poly(A)-specific 3' exonuclease activity in calf thymus extracts. The 54-kDa polypeptide is a proteolytic fragment of the poly(A)-specific ribonuclease (PARN) 74-kDa polypeptide. PARN is a divalent metal ion dependent, poly(A)-specific, oligomeric, processive and cap interacting 3' exonuclease. An active deadenylation complex, consisting of the poly(A)-tailed RNA substrate and PARN, has been identified. The interaction with the 5'-end cap structure stimulates PARN activity and also amplifies the processivity of the deadenylation reaction. Furthermore, the cap binding site and the active site of PARN are separate from each other. To characterise the active site of PARN, we per-formed side-directed mutagenesis, Fe2+-mediated hydroxyl radical cleavage and metal ion switch experiments. We have demonstrated that the conserved acidic amino acid residues D28, E30, D292 and D382 of human PARN are essential for PARN activity and that these amino acid residues are directly involved in the co-ordination of at least two metal ions in the active site of PARN. Phosphorothioate modification on RNA substrates revealed that the pro-R oxygen atom of the scissile phosphate group interacts directly with the metal ion(s). Based on our studies, we propose a model for the action of PARN. Similarly to what has been observed for ribozymes, aminoglycoside antibiotics inhibit PARN activity, most likely by the displacement of catalytically important divalent metal ions. Among the aminoglycoside antibiotics tested, neomycin B is the most potent inhibitor. We speculate that inhibition of enzymes using similar catalytic mechanisms as PARN could be a reason for the toxic side effects caused by aminoglycoside antibiotics in clinical practice.