The sequence-specific cleavage of RNA by artificial chemical ribonucleases

Influence of conjugation and other structural changes on the activity of Cu²⁺ based PNAzymes

We have previously shown that PNA-neocuproine conjugates can act as artificial RNA restriction enzymes. In the present study we have additionally conjugated the PNA with different entities, such as oligoethers, peptides etc. and also constructed systems where the PNA is designed to clamp the target RNA forming a triplex. Some conjugations are detrimental for the activity while most are silent which means that conjugation can be done to alter physical properties without losing activity. Conjugation with a single oligoether close to the neocuproine does enhance the rate almost twofold compared to the system without the oligoether. The systems designed to clamp the RNA target by forming a triplex retain the activity if the added oligoT sequence is 5 PNA units or shorter and extends the arsenal of artificial RNA restriction enzymes. Changing the direction of a closing base pair, where the target RNA forms a bulge, from a GC to a CG pair enhances the rate of cleavage somewhat without compromising the selectivity, leading to the so far most efficient artificial nuclease reported.

Near-infrared luminescence and RNA cleavage ability of lanthanide Schiff base complexes derived from N,N'-bis(3-methoxysalicylidene)ethylene-1,2-diamine ligands

A complete series of lanthanide Schiff base salen-type complexes were prepared with trivalent lanthanide ions (Ln³⁺) and the N,N'-bis-(3-methoxysalicylidene)ethylene-1,2-diamine ligand (Ln³⁺=La³⁺, Ce³⁺, Pr³⁺, Nd³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Tb³⁺, Dy³⁺, Ho³⁺, Er³⁺, Tm³⁺, Yb³⁺, Lu³⁺). Three unique crystal structures of La³⁺ and Pr³⁺N,N'-bis-(3-methoxysalicylidene)ethylene-1,2-diamine complexes, with the La³⁺ complex prepared in two different synthetic approaches, are reported, namely a dimeric [La(H₂L)(NO₃)₃]₂ (H₂L=N,N'-bis-(3-methoxysalicylidene)ethylene-1,2-diamine) complex, an asymmetric two-centered [La₂(H₂L)₂(NO₃)₆] complex and a discrete mononuclear [Pr(H₂L)(NO₃)₂(H₂O)₂] complex. For Nd³⁺ and Sm³⁺, an isotypic mononuclear [Nd(H₂L)(NO₃)₃] and 1D polymeric [Sm(H₂L)(NO₃)₃(MeOH)]_n structure was obtained, respectively. The whole series of complexes was tested for their ability to cleave the 20-mer RNA oligonucleotide 5'-AGC-GAU-AAG-AUU-CAU-AUA-UC-3'. Additionally three complexes (Ln³⁺=Nd³⁺, Sm³⁺, Ho³⁺) were tested for the cleavage of the 12-mer RNA oligonucleotide 5'-GCA-CCC-UGU-CAG-3'. A detailed luminescence study was additionally carried out and revealed that the Eu³⁺ complex emitted bright red light upon excitation at both 285.8nm and 394.4nm. The Nd³⁺, Er³⁺, and Yb³⁺ complexes showed strong emission in the near-infrared region after excitation at 380nm.

Peptidyl-oligonucleotide conjugates demonstrate efficient cleavage of RNA in a sequence-specific manner

Described here is a new class of peptidyl-oligonucleotide conjugates (POCs) which show efficient cleavage of a target RNA in a sequence-specific manner. Through phosphoramidate attachment of a 17-mer TΨC-targeting oligonucleotide to amphiphilic peptide sequences containing leucine, arginine, and glycine, zero-linker conjugates are created which exhibit targeted phosphodiester cleavage under physiological conditions. tRNA(Phe) from brewer's yeast was used as a model target sequence in order to probe different structural variants of POCs in terms of selective TΨC-arm directed cleavage. Almost quantitative (97-100%) sequence-specific tRNA cleavage is observed for several POCs over a 24 h period with a reaction half-life of less than 1 h. Nontargeted cleavage of tRNA(Phe) or HIV-1 RNA is absent. Structure-activity relationships reveal that removal of the peptide's central glycine residue significantly decreases tRNA cleavage activity; however, this can be entirely restored through replacement of the peptide's C-terminal carboxylic acid group with the carboxamide functionality. Truncation of the catalytic peptide also has a detrimental effect on POC activity. Based on the encouraging results presented, POCs could be further developed with the aim of creating useful tools for molecular biology or novel therapeutics targeting specific messenger, miRNA, and genomic viral RNA sequences.

2-Acetyl-pyridinium 3-amino-2-chloro-pyridinium tetra-chloridocobaltate(II)

In the title complex, (C₅H₆ClN₂)(C₇H₈NO)[CoCl₄], the Co^II ions are tetra­hedrally coordinated. The crystal structure is built from hydrogen-bonded centrosymmetric tetra­mers of tetra­chloridocobaltate(II) dianions and 3-amino-2-chloro­pyridinium cations, additionally strengthened by significant π–π stacking of pyridinium rings [interplanar distance 3.389 (3) Å]. The tetra­mers are linked by N—H⋯Cl hydrogen bonds into chains; the second kind of cations, viz. 2-acetyl­pyridinium, are connected by N—H⋯Cl hydrogen bonds to both sides of the chain. The Co—Cl bond lengths in the dianion correlate with the number of hydrogen bonds accepted by the Cl atom. An intramolecular C—H⋯Cl interaction is also present.

Self-assembly in Schiff base lanthanide complexes — From supramolecular dimers to coordination polymers

A review is given of the latest contribution of the author’s research group to the coordination chemistry of Schiff base polyaza macrocycles and acyclic salicylaldimines. Focus is placed on the effectiveness of lanthanides in supramolecular self-assembly of the components leading to the formation of compounds with unusual properties and structures.Key words: Schiff base macrocycles, salicylaldimines, lanthanides, self-assembly, template synthesis.

Enhanced complexity and catalytic efficiency in the hydrolysis of phosphate diesters by rationally designed helix-loop-helix motifs

HJ1, a 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle, successfully catalyzes the cleavage of "early stage" DNA model substrates in an aqueous solution at pH 7.0, with a rate enhancement in the hydrolysis of heptyl 4-nitrophenyl phosphate of over three orders of magnitude over that of the imidazole-catalyzed reaction, k(2)(HJ1)/k(2)(Im) = 3135. The second-order rate constant, k(2)(HJ1) was determined to be 1.58x10(-4) M(-1) s(-1). The catalyst successfully assembles residues that in a single elementary reaction step are capable of general-acid and general-base catalysis as well as transition state stabilization and proximity effects. The reactivity achieved with the HJ1 polypeptide, rationally designed to catalyze the hydrolysis of phosphodiesters, is based on two histidine residues flanked by four arginines and two adjacent tyrosine residues, all located on the surface of a helix-loop-helix motif. The introduction of Tyr residues close to the catalytic site improves efficiency, in the cleavage of activated aryl alkyl phosphates as well as less activated dialkyl phosphates. HJ1 is also effective in the cleavage of an RNA-mimic substrate, uridine-3'-2,2,2-trichloroethyl phosphate (leaving group pK(a) = 12.3) with a second-order rate constant of 8.23x10(-4) M(-1) s(-1) in aqueous solution at pH 7.0, some 500 times faster than the reaction catalyzed by imidazole, k(2)(HJ1)/k(2)(Im) = 496.

Hairpin mimics with phenanthroline- and bipyridine-derived linkers

The synthesis and structural stabilities of modified oligonucleotide hairpins containing phenanthroline- and bipyridine-modified loops is reported. Phenanthroline (phen) and bipyridine (bipy) building blocks were synthesized, incorporated into DNA-oligonucleotides, and analyzed by thermal denaturation experiments. The so modified oligomers were found to form stable hairpin structures. Tm values were not affected by divalent transition metals.

Luminescense properties of new complexes of Eu(III) and Tb(III) with heterotopic ligands

As a result of coordination between ligands L and L' and europium(III) and terbium(III) ions, the new architectures were formed. The formulae of the complexes have been assigned on the basis of the spectroscopic data in solution and microanalyses. The europium complexes show excellent luminescence properties with high quantum yield (1b-Eu(3)L(2)) and effective intramolecular energy transfer from the ligand to the Eu(III) ions.

Artificial ribonucleases

Mimicking the action of enzymes by simpler and more robust man-made catalysts has long inspired bioorganic chemists. During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, or, more precisely, mimics of ribozymes that cleave RNA in sequence-selective rather than base-selective manner, have received special attention. These artificial ribonucleases are typically oligonucleotides (or their structural analogs) that bear a catalytically active conjugate group and catalyze sequence-selective hydrolysis of RNA phosphodiester bonds.

Sequence selective hydrolysis of linear DNA using conjugates of Zr(IV) complexes and peptide nucleic acids

A series of conjugates of peptide nucleic acids (PNA) and Zr(IV) complexes was prepared. Their ability to hydrolyze DNA was tested using MALDI-TOF mass spectrometry and HPLC. The most efficient artificial restriction enzyme found, PNA conjugate with Zr(IV) complex of tris(hydroxymethyl)-aminomethane, cleaves DNA targets sequence selectively in close proximity to the Zr(IV) complex. It was demonstrated that cleavage products are substrates of terminal transferase.

Pentaaza macrocyclic ytterbium(iii) complex and solvent controlled supramolecular self-assembly of its dimeric μ-η2:η2peroxo-bridged derivatives

The unprecedented template action of ytterbium ion in the synthesis of pentaaza macrocyclic Schiff bases is exemplified by isolation and definitive identification of the seven-coordinate pentagonal bipyramidal complex with the formula of [YbLCl(2)]ClO(4) (1), where L is 2,14-dimethyl-3,6,10,13,19-pentaazabicyclo[13.3.1]nonadeca-1(19),2,13,15,17-pentaene, providing the first example of crystallographically characterized pentaaza macrocyclic ytterbium complex. For the first time the spectrum of the (2)F(7/2) --> (2)F(5/2) transition has been obtained for a molecular complex of ytterbium with organic ligands in which all ligand-field components of the ground and excited state are well displayed at room temperature. This complex is capable of forming a dimeric peroxo Yb(2)(mu-eta(2):eta(2)-O(2))L(2)(4+) (2) derivative containing the biologically significant planar side-on doubly bidentate coordination mode of the peroxide. Inclusion of the appropriate solvent molecule into the crystal structure generates supramolecular architectures (2a-d) in which the solvent controlled self-assembly is observed. Spectral properties of these complexes were found to be very important and promising in the area of ytterbium physicochemistry.

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 approximately 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 kcat/K(m) = 0.118 nM(-1) x h(-1).

Oligonucleotide conjugates as potential antisense drugs with improved uptake, biodistribution, targeted delivery, and mechanism of action

This review summarizes the effect of conjugating small molecules and large biomacromolecules to antisense oligonucleotides to improve their therapeutic potential. In many cases, favorable changes in pharmacokinetic and pharmacodynamic properties were observed. Opportunities exist to change the terminating mechanism of antisense action or to enhance the RNase H mode of action via conjugate formation.

Efficient new ribozyme mimics: direct mapping of molecular design principles from small molecules to macromolecular, biomimetic catalysts

Dramatic improvements in ribozyme mimics have been achieved by employing the principles of small molecule catalysis to the design of macromolecular, biomimetic reagents. Ribozyme mimics derived from the ligand 2,9-dimethylphenanthroline (neocuproine) show at least 30-fold improvements in efficiency at sequence-specific RNA cleavage when compared with analogous o-phenanthroline- and terpyridine-derived reagents. The suppression of hydroxide-bridged dimers and the greater activation of coordinated water by Cu(II) neocuproine (compared with the o-phenanthroline and terpyridine complexes) better allow Cu(II) to reach its catalytic potential as a biomimetic RNA cleavage agent. This work demonstrates the direct mapping of molecular design principles from small-molecule cleavage to macromolecular cleavage events, generating enhanced biomimetic, sequence-specific RNA cleavage agents.

Cleavage of yeast tRNAPhe with complementary oligonucleotide conjugated to a small ribonuclease mimic

An oligonucleotide conjugate bearing a chemical construct mimicking the catalytic center of ribonuclease A has been designed and studied. The conjugate efficiently cleaves yeast tRNAPhe at a single site adjacent to the target complementary sequence.