RAPID RNA CLEAVAGE USING AN ANTISENSE SYSTEM WITH TWO TERPYRIDINE · Cu(II) COMPLEXES

An effective approach to promote sequence-specific RNA cleavage by an antisense 2′-O-methyloligonucleotide with a terpyridine · Cu(II) complex attached at the 5′-end was developed. We have synthesized a Cu(II) complex 3′-conjugate, which when used in a tandem fashion, greatly enhanced the RNA cleavage efficiency.     

Enhancing sequence-specific cleavage of RNA within a duplex region: incorporation of 1,3-propanediol linkers into oligonucleotide conjugates of serinol-terpyridine.

The syntheses and RNA cleavage efficiencies of a new series of oligonucleotide conjugates of Cu(II)-serinol-terpyridine and 1,3-propanediol are reported. These reagents, termed ribozyme mimics, were designed such that they would yield multiple unpaired RNA residues directly opposite the site of the RNA cleavage catalyst upon ribozyme mimic-RNA duplex formation. This design effect was implemented using the 1,3-propanediol linker 3, which mimics the three-carbon spacing between the 5'- and 3'-hydroxyls of a natural nucleotide. Incorporation of one or more of these 1,3-propanediol linkers at positions directly adjacent to the serinol-terpyridine modification in the ribozyme mimic DNA strand resulted in cleavage at multiple phosphates in a complementary 31-mer RNA target sequence. The linkers effectively created artificial mismatches in the RNA-DNA duplexes, rendering the opposing RNA residues much more susceptible to cleavage via the transesterification/hydrolysis pathway. The RNA cleavage products produced by the various mimics correlated directly with the number and locations of the linkers in their DNA strands, and the most active ribozyme mimic in the series exhibited multiple turnover in the presence of excess 31-mer RNA target.     

Comparison of the catalytic oxidation of cysteine and o-dianisidine by cupric ion and ceruloplasmin

Several features of the catalytic oxidation of cysteine by ceruloplasmin and nonenzymic Cu(II) at pH 7 have been compared. The oxidation of cysteine by ceruloplasmin has several properties in common with the Cu(II) catalyzed oxidation of cysteine: pH maxima, thiol specificity, lack of inhibition by anions, and high sensitivity to inhibition by copper complexing reagents. These two catalysts differed in their molecular activity, in their ability to oxidize penicillamine and thioglycolate, and in that H₂O₂ was produced as a primary product only during Cu(II) oxidation. The oxidation of cysteine by ceruloplasmin was compared also with the ceruloplasmin catalyzed oxidation of o-dianisidine, a classical pH 5.5 substrate. The mechanism of the oxidation of cysteine by ceruloplasmin at pH 7 differed from that of o-dianisidine oxidation because the latter substrate was inhibited by anions but not by copper complexing agents. Spectral and other data suggest that during the ceruloplasmin reaction with cysteine there is a one electron transfer from cysteine to ceruloplasmin resulting in the specific reduction of type lb Cu(II).     

Effect of CuSO4 and Cu(II)(Gly)2 on some indirect assays for superoxide dismutase activity

The effect of CuSO₄ and Cu(II)(Gly)₂ has been compared with that of superoxide dismutase on the ferricytochrome c reduction and on the nitroblue tetrazolium reduction by an enzymic or chemical flux of superoxide anion radicals as well as on o-dianisidine photooxidation. Both CuSO₄ and Cu(II)(Gly)₂ have been found to inhibit ferricytochrome c reduction as well as the aerobic and anaerobic nitroblue tetrazolium reduction with approximately equal efficiency. Unlike superoxide dismutase they proved capable of inhibiting o-dianisdine photooxidation. The effect of copper either as CuSO₄ or as Cu(II)(Cly)₂ has been established as being due to its interference with the indirect assays for superoxide dismutase activity used. The reasons for this interference have been examined and it is concluded that copper can react with a component of the indirect assay system and depending on the method used it either mimics SOD or acts contrary to the enzyme.     

Rapid RNA cleavage using an antisense system with two terpyridine.Cu(II) complexes

An effective approach to promote sequence-specific RNA cleavage by an antisense 2'-O-methyloligonucleotide with a terpyridine.Cu(II) complex attached at the 5'-end was developed. We have synthesized a Cu(II) complex 3'-conjugate, which when used in a tandem fashion, greatly enhanced the RNA cleavage efficiency.     

Site-specific cleavage of DNA–RNA hybrids by zinc finger/FokI cleavage domain fusions

Zinc-finger proteins of the Cys₂His₂ type bind DNA–RNA hybrids with affinities comparable to those for DNA duplexes. Such zinc-finger proteins were converted into site-specific cleaving enzymes by fusing them to the FokI cleavage domain. The fusion proteins are active and under optimal conditions cleave DNA duplexes in a sequence-specific manner. These fusions also exhibit site-specific cleavage of the DNA strand within DNA–RNA hybrids albeit at a lower efficiency (≃50-fold) compared to the cleavage of the DNA duplexes. These engineered endonucleases represent the first of their kind in terms of their DNA–RNA cleavage properties, and they may have important biological applications.     

Sheet and chain polymeric transition metal complexes formed by N,N-o-phenylenedimethylenebis(pyridin-4-one)

The preparations are reported of the ‘extended reach’ ligand N,N^′-o-phenylene-dimethylenebis(pyridin-4-one) (o-XBP4) and of a range of its metal complexes with Mn(II), Co(II), Ni(II), Cu(II) and Zn(II), two of which have been shown by X-ray studies to have polymeric structures. In the compound [Mn(o-XBP4)(H₂O)₂(NO₃)](NO₃) the o-XBP4 ligands link ‘Mn(H₂O)₂(NO₃)’ units into chains which are then cross-linked into sheets by the bridging action of the coordinated nitrate. In [Cu(o-XBP4)(NO₃)₂] chains are also formed by the bridging action of the o-XBP4 ligands but here they simply pack trough-in-trough with no nitrate cross-linking. X-band EPR spectra are reported for these and the other Mn and Cu compounds as are relevant spectroscopic results for the other complexes.     

Sequence-specific cleavage of RNA in the absence of divalent metal ions by a DNAzyme incorporating imidazolyl and amino functionalities

Two modified 2′-deoxynucleoside 5′-triphosphates have been used for the in vitro selection of a modified deoxyribozyme (DNAzyme) capable of the sequence-specific cleavage of a 12 nt RNA target in the absence of divalent metal ions. The modified nucleotides, a C5-imidazolyl-modified dUTP and 3-(aminopropynyl)-7-deaza-dATP were used in place of TTP and dATP during the selection and incorporate two extra protein-like functionalities, namely, imidazolyl (histidine analogue) and primary amino (lysine analogue) into the DNAzyme. The functional groups are analogous to the catalytic Lys and His residues employed during the metal-independent cleavage of RNA by the protein enzyme RNaseA. The DNAzyme requires no divalent metal ions or other cofactors for catalysis, remains active at physiological pH and ionic strength and can recognize and cleave a 12 nt RNA substrate with sequence specificity. This is the first example of a functionalized, metal-independent DNAzyme that recognizes and cleaves an all-RNA target in a sequence-specific manner. The selected DNAzyme is two orders of magnitude more efficient in its cleavage of RNA than an unmodified DNAzyme in the absence of metal ions and represents a rate enhancement of 10⁵ compared with the uncatalysed hydrolysis of RNA.     

Copper- and Arene-Catalyzed Cleavage of DNA

DNA was found to be cleaved by arenes and copper(II) salts in neutral solutions. The efficiency of this reaction is comparable with the DNA cleavage by such systems as Cu(II)–phenanthroline and Cu(II)–ascorbic acid in efficiency, but, unlike them, it does not require the presence of an exogenous reducing agent or hydrogen peroxide. The Cu²⁺–arene system does not cleave DNA under anaerobic conditions. Catalase, sodium azide as well as bathocuproine, a specific chelator of Cu(I), completely inhibit the reaction. Our results suggest that Cu(I) ions, superoxide radical and singlet oxygen participate in this reaction. It was shown by EPR and spin traps that the reaction proceeds with the formation of alkoxyl radicals capable of inducing breaks in DNA molecules. An efficient cleavage of DNA in the Cu(II)–o-bromobenzoic acid system requires the generation of radicals under the conditions of formation of a specific copper–DNA–o-bromobenzoic acid complex, in which copper ions are likely to be coordinated with oxygen atoms of the DNA phosphate groups.     

RNA double cleavage by a hairpin-derived twin ribozyme

The hairpin ribozyme is a small catalytic RNA that catalyses reversible sequence-specific RNA hydrolysis in trans. It consists of two domains, which interact with each other by docking in an antiparallel fashion. There is a region between the two domains acting as a flexible hinge for interdomain interactions to occur. Hairpin ribozymes with reverse-joined domains have been constructed by dissecting the domains at the hinge and rejoining them in reverse order. We have used both the conventional and reverse-joined hairpin ribozymes for the design of a hairpin-derived twin ribozyme. We show that this twin ribozyme cleaves a suitable RNA substrate at two specific sites while maintaining the target specificity of the individual monoribozymes. For characterisation of the studied ribozymes we have evaluated a quantitative assay of sequence-specific ribozyme activity using fluorescently labelled RNA substrates in conjunction with an automated DNA sequencer. This assay was found to be applicable with hairpin and hairpin-derived ribozymes. The results demonstrate the potential of hairpin ribozymes for multi-target strategies of RNA cleavage and suggest the possibility for employing hairpin-derived twin ribozymes as powerful tools for RNA manipulation in vitro and in vivo.     

Cu2+-DEPENDENT DNA-CLEAVING ACTIVITY OF ARENES

In the presence of Cu(II) ions, plasmid DNA is cleaved under physiological condition by different arenes at low concentrations. The cleavage was dependent on the presence of O₂. The DNA cleavage efficiency of the designed system arene-Cu is comparable to that of the well-known DNA cleaving reagents such as phenanthroline-Cu and ascorbic acid-Cu. However in contrast to the mentioned reagents, the system arene-Cu does not require external reducing agents or H₂O₂.     

Bilirubin-Cu(II) complex degrades DNA.

It has recently been reported that bilirubin forms a complex with Cu(II). In this paper we show that the formation of the complex results in the reduction of Cu(II) to Cu(I) and the redox cycling of the metal gives rise to the formation of reactive oxygen species, particularly hydroxyl radical. The bilirubin-Cu(II) complex causes strand breakage in calf thymus DNA and supercoiled plasmid DNA. Cu(I) was shown to be an essential intermediate in the DNA cleavage reaction by using the Cu(I) specific sequestering reagent neocuproine. Bilirubin-Cu(II) produced hydroxyl radical and the involvement of active oxygen species was established by the inhibition of DNA breakage by various oxygen radical quenchers.     

Highly efficient catalytic RNA cleavage by the cooperative action of two Cu(II) complexes embodied within an antisense oligonucleotide

Based on our recent studies of RNA cleavage by oligonucleotide–terpyridine·Cu(II) complex 5′- and/or 3′-conjugates, we designed 2′-O-methyloligonucleotides with two terpyridine-attached nucleosides at contiguous internal sites. To connect the 2′-terpyridine-modified uridine residue at the 5′-side to the 5′-O-terpyridyl nucleoside residue at the 3′-side, a dimethoxytrityl derivative of 5-hydroxypropyl-5′-O-terpyridyl-2′-deoxyuridine-3′-phosphoramidite was newly synthesized. Using this unit, we constructed two terpyridine conjugates, with either an unusual phophodiester bond or the bond extended by a propanediol(s)-containing linker. Cleavage reactions of the target RNA oligomer, under the conditions of conjugate excess in the presence of Cu(II), indicated that the conjugates precisely cleaved the RNA at the predetermined site and that one propanediol-containing linker was the most appropriate for inducing high cleavage activity. Furthermore, a comparison of the activity of the propanediol agent with those of the control conjugates with one complex confirmed that the two complexes are required for efficient RNA cleavage. The reaction of the novel cleaver revealed a bell-shaped pH–rate profile with a maximum at pH ~7.5, which is a result of the cooperative action of the complexes. In addition, we demonstrated that the agent catalytically cleaves an excess of the RNA, with the kinetic parameter k_cat/K_m = 0.118 nM^–1 h^–1.     

RNase T1 mimicking artificial ribonuclease

Recently, artificial ribonucleases (aRNases)—conjugates of oligodeoxyribonucleotides and peptide (LR)₄-G-amide—were designed and assessed in terms of the activity and specificity of RNA cleavage. The conjugates were shown to cleave RNA at Pyr-A and G–X sequences. Variations of oligonucleotide length and sequence, peptide and linker structure led to the development of conjugates exhibiting G–X cleavage specificity only. The most efficient catalyst is built of nonadeoxyribonucleotide of unique sequence and peptide (LR)₄-G-NH₂ connected by the linker of three abasic deoxyribonucleotides (conjugate pep-9). Investigation of the cleavage specificity of conjugate pep-9 showed that the compound is the first single-stranded guanine-specific aRNase, which mimics RNase T1. Rate enhancement of RNA cleavage at G–X linkages catalysed by pep-9 is 10⁸ compared to non-catalysed reaction, pep-9 cleaves these linkages only 10⁵-fold less efficiently than RNase T1 (k_{cat_RNase T1}/k_cat__pep-9 = 10⁵).     

Photochemical Properties of Camptothecin in the Presence of Copper(II) Ions: The Role of Radicals as Prospective Species in Photodynamic Therapy

Camptothecin (CPT) is an anticancer drug that inhibits topoisomerase I (Topo I) by forming a ternary DNA-CPT-Topo I complex. However, it has also been shown that UVA-irradiated CPT in the absence of Topo I produces significant DNA damage to cancer cells. In this work, we explored and identified free radicals generated in these processes. From the low-temperature EPR spectrum of Cu(II)-CPT complex, a proximity between Cu(II) ion and 20-hydroxy group of lactone E ring of CPT is proposed. Upon irradiation (λ = 365 nm) of the Cu(II)-CPT complex in de-oxygenated dimethylsulfoxide (DMSO), the EPR signal of Cu(II) measured in situ at room temperature shows formal first-order exponential decay with a formal half-life of 11 min. By the use of a specific Cu(I) chelating agent, neocuproine, it was shown that, during this process, Cu(II) is reduced to Cu(I). The loss in EPR signal intensity of the Cu(II)-CPT complex upon irradiation is accompanied by the appearance of a new EPR signal at g ≈ 2.0022. Application of the spin trap nitrosodurene (ND) revealed that the main radical product formed upon continuous irradiation of CPT in DMSO solutions is the hydroxyl radical (trapped in DMSO as the ^•CH₃ adduct) and superoxide radical. Application of 2,2,6,6-tetramethyl-4-piperidinol has revealed that irradiation of CPT in aerated DMSO solution also leads to formation of singlet oxygen (¹O₂). Our spectroscopic experiments indicate that CPT is a promising photosensitizer and that radicals and singlet oxygen generated upon illumination play a central role in DNA cleavage and in the induction of apoptosis in cancer cells.     

Characterization of MazF-Mediated Sequence-Specific RNA Cleavage in Pseudomonas putida Using Massive Parallel Sequencing

Under environmental stress, microbes are known to alter their translation patterns using sequence-specific endoribonucleases that we call RNA interferases. However, there has been limited insight regarding which RNAs are specifically cleaved by these RNA interferases, hence their physiological functions remain unknown. In the current study, we developed a novel method to effectively identify cleavage specificities with massive parallel sequencing. This approach uses artificially designed RNAs composed of diverse sequences, which do not form extensive secondary structures, and it correctly identified the cleavage sequence of a well-characterized Escherichia coli RNA interferase, MazF, as ACA. In addition, we also determined that an uncharacterized MazF homologue isolated from Pseudomonas putida specifically recognizes the unique triplet, UAC. Using a real-time fluorescence resonance energy transfer assay, the UAC triplet was further proved to be essential for cleavage in P. putida MazF. These results highlight an effective method to determine cleavage specificity of RNA interferases.     

Iron and Copper Act Synergistically To Delay Anaerobic Growth of Bacteria

Transition metals are known to cause toxic effects through their interaction with oxygen, but toxicity under anoxic conditions is poorly understood. Here we investigated the effects of iron (Fe) and copper (Cu) on the anaerobic growth and gene expression of the purple phototrophic bacterium Rhodopseudomonas palustris TIE-1. We found that Fe(II) and Cu(II) act synergistically to delay anaerobic growth at environmentally relevant metal concentrations. Cu(I) and Cu(II) had similar effects both alone and in the presence of ascorbate, a Cu(II) reductant, indicating that reduction of Cu(II) to Cu(I) by Fe(II) is not sufficient to explain the growth inhibition. Addition of Cu(II) increased the toxicity of Co(II) and Ni(II); in contrast, Ni(II) toxicity was diminished in the presence of Fe(II). The synergistic anaerobic toxicity of Fe(II) and Cu(II) was also observed for Escherichia coli MG1655, Shewanella oneidensis MR-1, and Rhodobacter capsulatus SB1003. Gene expression analyses for R. palustris identified three regulatory genes that respond to Cu(II) and not to Fe(II): homologs of cueR and cusR, two known proteobacterial copper homeostasis regulators, and csoR, a copper regulator recently identified in Mycobacterium tuberculosis. Two P-type ATPase efflux pumps, along with an F_oF₁ ATP synthase, were also upregulated by Cu(II) but not by Fe(II). An Escherichia coli mutant deficient in copA, cus, and cueO showed a smaller synergistic effect, indicating that iron might interfere with one or more of the copper homeostasis systems. Our results suggest that interactive effects of transition metals on microbial physiology may be widespread under anoxic conditions, although the molecular mechanisms remain to be more fully elucidated.     

The coordination chemistry of N-(2-aminophenyl)- and N-(3-aminophenyl)quinoline-2′-carboxamide; two potentially tridentate ligands containing secondary amide and N-donor groups

New complexes of the general formulae Co(o-LH)₂X₂ (XCl, NCS), Co(o-LH)₂Br₂·EtOH (EtOHethanol), M(o-LH)(NO₃)₂ (MCo, Ni), Ni(o-LH)₂X₂ (XCl, Br, NCS), Cu(o-L)X (XCl, Br), Zn(o-LH)X₂ (XCl, Br), Pd(o-L)Cl, Pt(o-LH)₂Cl₂·H₂O, M(m-LH)Cl₂·nH₂O (MCo, Ni, Pd; n=0, 0.5, 1), Cu(m-LH)Cl₂·EtOH, M(m-LH)₂Cl₂·nH₂O (MCo, Zn, Pt; n=0, 1), M(m-LH)Br₂ (MCu, Zn), M(m-LH)₂Br₂ (MCo, Ni), Co(m-LH)(NCS)₂ and Co(m-LH)₂(NCS)₂, where o-LH=N-(2-aminophenyl)quinoline-2′-carboxamide and m-LH=N-(3-aminophenyl)quinoline-2′-carboxamide, have been prepared. The complexes were characterised by elemental analyses, conductivity measurements, X-ray powder patterns, thermogravimetric analyses, magnetic moments and spectral (¹H NMR, IR, and electronic) studies. Copper(II) and palladium(II) promote amide deprotonation at nearly acidic pH on coordination with o-LH. A variety of stereochemistries is assigned for the complexes prepared. The deprotonated copper(II) and the nickel(II) and palladium(II) complexes of m-LH appear to be polymeric. The neutral amide group of the ligands is coordinated to the metal ions through oxygen, while N(amide)-coordination is observed for the deprotonated complexes. Coordination of the secondary amide group is not observed for Zn(m-LH)₂Cl₂, Pd(m-LH)Cl₂·0.5H₂O and platinum(II) complexes. The neutral ligand o-LH shows bidentate N(ring), O-behaviour, while the anion o-L⁻ exhibits tridentate N,N,N-coordination. m-LH acts as a monodentate, bidentate and tridentate ligand depending on the metal ion, the anion and the preparative conditions.     

Studies on galactose oxidase active site model complexes: effects of ring substituents on Cu(II)-phenoxyl radical formation

Copper(II) complexes of new N₃O- and N₂O₂-donor tripodal ligands bearing one or two o-substituted phenol moieties have been synthesized as models for the galactose oxidase active site. The complexes of 2-[N-(1-methyl-2′-imidazolylmethyl)-N-(6″-methyl-2″-pyridylmethyl)-aminomethyl)]-4-methyl-6-methylthiophenol (MeSL), [Cu(MeSL)Cl], and N-(6-methyl-2-pyridylmethyl)-N,N-bis(2′-hydroxy-3′,5′-di-tert-butylbenzyl)amine (t-buL2mepy), [Cu(t-buL2mepy)(H₂O)], have been revealed by X-ray structural analysis to have a square-pyramidal structure with one and two phenolate oxygens in the basal plane, respectively. [Cu(MeSL)Cl] was converted into a Cu(II)-o-methylthiophenoxyl radical species by electrochemical or Ce(IV) oxidation. An o-methoxyphenoxyl radical in a similar complex was considerably more stable than the 2,4-di(tert-butyl)phenoxyl radical. While t-buL2mepy reacted with Cu(ClO₄)₂ to give [Cu(t-buL2mepy)(H₂O)] without disproportionation, an N2O2-donor ligand containing an o-methoxyphenol, a 2,4-di(tert-butyl)phenol, and an N-methylimidazole moiety gave a phenoxyl radical complex exhibiting the characteristic absorption peak at 478 nm as a reddish powder by the reaction with Cu(ClO₄)₂ as a result of spontaneous disproportionation. It exhibited a quasi-reversible redox wave at E_1/2=0.34 V (vs. Ag/AgCl) in CH₃CN, which is lower than the potentials of the copper complexes of various N₃O-donor ligands, and oxidized ethanol to acetaldehyde with a low turnover number.     

NAR Breakthrough Article: Sequence-specific cleavage of dsRNA by Mini-III RNase

Ribonucleases (RNases) play a critical role in RNA processing and degradation by hydrolyzing phosphodiester bonds (exo- or endonucleolytically). Many RNases that cut RNA internally exhibit substrate specificity, but their target sites are usually limited to one or a few specific nucleotides in single-stranded RNA and often in a context of a particular three-dimensional structure of the substrate. Thus far, no RNase counterparts of restriction enzymes have been identified which could cleave double-stranded RNA (dsRNA) in a sequence-specific manner. Here, we present evidence for a sequence-dependent cleavage of long dsRNA by RNase Mini-III from Bacillus subtilis (BsMiniIII). Analysis of the sites cleaved by this enzyme in limited digest of bacteriophage Φ6 dsRNA led to the identification of a consensus target sequence. We defined nucleotide residues within the preferred cleavage site that affected the efficiency of the cleavage and were essential for the discrimination of cleavable versus non-cleavable dsRNA sequences. We have also determined that the loop α5b-α6, a distinctive structural element in Mini-III RNases, is crucial for the specific cleavage, but not for dsRNA binding. Our results suggest that BsMiniIII may serve as a prototype of a sequence-specific dsRNase that could possibly be used for targeted cleavage of dsRNA.