Synthesis and Kinetic Properties of Ribozyme Analogues Prepared Using Phosphoramidite Derivatives of Dysprosium(III) Texaphyrin

Ten-Coordinate Lanthanide [Ln(HL)(L)] Complexes (Ln = Dy, Ho, Er, Tb) with Pentadentate N3O2-Type Schiff-Base Ligands: Synthesis, Structure and Magnetism

A series of five neutral mononuclear lanthanide complexes [Ln(HL)(L)] (Ln = Dy3+, Ho3+ Er3+ and Tb3+) with rigid pentadentate N3O2-type Schiff base ligands, H2LH (1-Dy, 3-Ho, 4-Er and 6-Tb complexes) or H2LOCH3, (2-Dy complex) has been synthesized by reaction of two equivalents of 1,1′-(pyridine-2,6-diyl)bis(ethan-1-yl-1-ylidene))dibenzohydrazine (H2LH, [H2DAPBH]) or 1,1′-(pyridine-2,6-diyl)bis(ethan-1-yl-1-ylidene))di-4-methoxybenzohydrazine (H2LOCH3, [H2DAPMBH]) with common lanthanide salts. The terbium complex [Tb(LH)(NO3)(H2O)2](DME)2 (5-Tb) with one ligand H2LH was also obtained and characterized. Single crystal X-ray analysis shows that complexes 1–4 have the composition {[Ln3+(HL)−(L)2−] solv} and similar molecular structures. In all the compounds, the central Ln3+ ion is chelated by two interlocked pentadentate ligands resulting in the coordination number of ten. Each lanthanide ion is coordinated by six nitrogen atoms and four oxygen atoms of the two N3O2 chelating groups forming together a distorted bicapped square antiprismatic polyhedron N6O4 with two capping pyridyl N atoms in the apical positions. The ac magnetic measurements reveal field-induced single-molecule magnet (SMM) behavior of the two dysprosium complexes (with barriers of Ueff = 29 K at 800 Oe in 1-Dy and Ueff = 70 K at 300 Oe in 2-Dy) and erbium complex (Ueff = 87 K at 1500 Oe in 4-Er); complex 3-Ho with a non-Kramers Ho3+ ion is SMM-silent. Although 2-Dy differs from 1-Dy only by a distant methoxy-group in the phenyl ring of the ligand, their dynamic magnetic properties are markedly different. This feature can be due to the difference in long-range contributions (beyond the first coordination sphere) to the crystal-field (CF) potential of 4f electrons of Dy3+ ion that affects magnetic characteristics of the ground and excited CF states. Magnetic behavior and the electronic structure of Ln3+ ions of 1–4 complexes are analyzed in terms of CF calculations.

An efficient tRNA cleaver without additional co-reactants at physiological condition

A square-planar Cu(II) complex, [Cu(Me-Im)(gly-gly)]∙H₂O 1 (Me-Im = 1-methyl-imidazole, gly-gly = glycylglycinato), has been prepared and structurally characterized by single crystal X-ray. The complex 1 was tested for its ability to the transfer RNA by UV-vis spectroscopy, cyclic voltammetry (CV), capillary electrophoresis (CE). Comparative spectroscopic analysis shows a maximum fluorescence-quenching ratio of 0.41 of 1 upon binding to RNA, which gives a binding constant (K_b) of 1.24 × 10⁵ M^-1. Cyclic voltammograms of complex 1 attached on the mercaptoethanol (-SH) linked Au electrodes in phosphate buffer solution give a well-defined and quasi-reversible redox couple, indicate complex 1 can efficiently degrade the high-order structure of RNA in physiological conditions (pH 7.0 phosphate buffer solution at 37 °C) without additional co-reactants, yielding a digestion coefficient more than 90% within 113 h. This study targeting the genetic biomacromolecule degradation based on the strong binding of chemical nucleases paves an important way to the novel materials in the decontamination of microorganisms (e.g., bacteria and viruses) at mild condition.

Macrocyclic Metal Complex-DNA Conjugates for Electrochemical Sensing of Single Nucleobase Changes in DNA

The direct incorporation of macrocyclic cyclidene complexes into DNA via automated synthesis results in a new family of metal-functionalized DNA derivatives that readily demonstrate their utility through the ability of one redox-active copper(II)-containing strand to distinguish electrochemically between all four canonical DNA nucleobases at a single site within a target sequence of DNA.

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.

PNAzymes that are artificial RNA restriction enzymes

DNA-cleaving restriction enzymes are well-known tools in biomedical and biotechnological research. There are, however, no corresponding enzymes known for RNA cleavage. There has been an ongoing development of artificial ribonucleases, including some attempts at sequence selectivity. However, so far these systems have displayed modest rates of cleavage, and in most cases, the cleaver has been used in excess or in stoichiometric amounts. In the current work, we present PNA-based systems (PNAzymes) that carry a Cu(II)-2,9-dimethylphenanthroline group and that act as site and sequence specific RNases. The general basis for the systems is that the target is cleaved at a nonbase paired region (RNA bulge) which is formed in the substrate upon binding of the PNAzyme. With this copper based system, cleavage takes place at virtually only one site and with a half-life of down to 30 min under stoichiometric conditions. Efficient turnover of RNA-substrate is shown with a 100-fold excess of substrate, thus, demonstrating true enzyme behavior. In addition, alteration of the sequence in the RNA bulge or a mismatch in the base-pairing region leads to substantial decreases in rate showing both kinetic resolution and binding discrimination in the substrate selectivity. The selectivity is further demonstrated by the substrates, with two potential cleavage sites differing in only one base, are cleaved only at the site that either does not have a mismatch or is kinetically preferred. We suggest that these systems can serve as a basis for construction of RNA restriction enzymes for in vitro manipulations.

DNA-Metal Base Pairs

Recent developments show encouraging results for the use of DNA as a construction material for nanometer-sized objects. Today, however, DNA-based molecular nanoarchitectures are constructed with mainly unmodified or at best end-modified oligonucleotides, thus shifting the development of functionalized DNA structures into the limelight. One of most recent developments in this direction is the substitution of the canonical Watson-Crick base pairs by metal complexes. In this way "metal-base pairs" are created, which could potentially impart magnetic or conductive properties to DNA-based nanostructures. This review summarizes research which started almost 45 years ago with the investigation of how metal ions interact with unmodified DNA and which recently culminated in the development of artificial ligand-like nucleobases so far able to coordinate up to ten metal ions inside a single DNA duplex in a programmable fashion.

Ferrocenyl-modified DNA: synthesis, characterization and integration with semiconductor electrodes

The ferrocenyl-nucleoside, 5-ethynylferrocenyl-2'-deoxycytidine (1) has been prepared by Pd-catalyzed cross-coupling between ethynylferrocene and 5-iodo-2'-deoxycytidine and incorporated into oligonucleotides by using automated solid-phase synthesis at both silica supports (CPG) and modified single-crystal silicon electrodes. Analysis of DNA oligonucleotides prepared and cleaved from conventional solid supports confirms that the ferrocenyl-nucleoside remains intact during synthesis and deprotection and that the resulting strands may be oxidised and reduced in a chemically reversible manner. Melting curve data show that the ferrocenyl-modified oligonucleotides form duplex structures with native complementary strands. The redox potential of fully solvated ferrocenyl 12-mers, 350 mV versus SCE, was shifted by +40 mV to a more positive potential upon treatment with the complement contrary to the anticipated negative shift based on a simple electrostatic basis. Automated solid-phase methods were also used to synthesise 12-mer ferrocenyl-containing oligonucleotides directly at chemically modified silicon <111> electrodes. Hybridisation to the surface-bound ferrocenyl-DNA caused a shift in the reduction potential of +34 mV to more positive values, indicating that, even when a ferrocenyl nucleoside is contained in a film, the increased density of anions from the phosphate backbone of the complement is still dominated by other factors, for example, the hydrophobic environment of the ferrocene moiety in the duplex or changes in the ferrocene-phosphate distances. The reduction potential is shifted >100 mV after hybridisation when the aqueous electrolyte is replaced by THF/LiClO(4), a solvent of much lower dielectric constant; this is consistent with an explanation based on conformation-induced changes in ferrocene-phosphate distances.

Developing the {M(CO)3}+ Core for Fluorescence Applications: Rhenium Tricarbonyl Core Complexes with Benzimidazole, Quinoline, and Tryptophan Derivatives

Tridentate ligands derived from benzimidazole, quinoline, and tryptophan have been synthesized, and their reactions with [NEt4]2[Re(CO)3Br3] have been investigated. The complexes 1-4 and 6 and 7 exhibit fac-{Re(CO)3N3} coordination geometry in the cationic molecular units, while 5 exhibits fac-{Re(CO)3N2O} coordination for the neutral molecular unit, where N3 and N2O refer to the ligand donor groups. The ligands bis(1-methyl-1H-benzoimidazol-2-ylmethyl)amine (L1), [bis(1-methyl-1H-benzoimidazol-2-ylmethyl)amino]acetic acid ethyl ester (L2), [bis(1-methyl-1H-benzoimidazol-2-ylmethy)amino]acetic acid methyl ester (L3), [bis(quinolin-2-ylmethyl)amino]acetic acid methyl ester (L4), 3-(1-methyl-1H-indol-3-yl)-2-[(pyridin-2-ylmethyl)amino]propionic acid (L5), 2-[bis(pyridin-2-ylmethyl)amino]-3-(1-methyl-1H-indol-3-yl)propionic acid (L6), and 2-[bis(quinolin-2-ylmethyl)amino]-3-(1-methyl-1H-indol-3-yl)propionic acid (L7) were obtained in good yields and characterized by elemental analysis, 1D and 2D NMR, and high-resolution mass spectrometry (HRMS). The rhenium complexes were obtained in 70-85% yields and characterized by elemental analysis, 1D and 2D NMR, HRMS, IR, UV, and luminescence spectroscopy, as well as X-ray crystallography for [Re(CO)3(L1)]Br (1), {[Re(CO)3(L2)]Br}2.NEt4Br . 8.5H2O (3(2).NEt4Br . 8.5H2O), [Re(CO)3(L4)]Br (4), and [Re(CO)3(L6)]Br (6). Crystal data for C21H19BrN5O3Re (1): monoclinic, P2(1)/c, a = 13.1851(5) A, b = 16.1292(7) A, c = 10.2689(4) A, beta = 99.353(1) degrees , V = 2154.8(2) A3, Z = 4. Crystal data for C56H73Br3N11O18.50 Re2 (3(2).NEt4Br . 8.5H2O): monoclinic, C2/c, a = 34.7760(19) A, b = 21.1711(12) A, c = 20.3376(11) A, beta = 115.944(1) degrees , V = 13464.5(1) A3, Z = 8. Crystal data for C26H21BrN3O5Re (4): monoclinic, P2(1)/c, a = 16.6504(6) A, b = 10.1564(4) A, c = 14.6954(5) A, beta = 96.739(1) degrees , V = 2467.9(2) A3, Z = 4. Crystal data for C27H24BrN4O5Re (6): monoclinic, P2(1), a = 8.7791(9) A, b = 16.312(2) A, c = 8.9231(9) A, beta = 90.030(1) degrees , V = 1277.8(2) A3, Z = 2.

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.

RNA hydrolysis and inhibition of translation by a Co(III)-cyclen complex

Metal ion-chelator catalysts based on main-group, lanthanide, or transition metal complexes have been developed as nonenzymatic alternatives for the hydrolysis of the phosphodiester bonds in DNA and RNA. Cobalt (III), with its high-charge density, is known for its ability to hydrolyze phosphodiesters with rate constants as high as 2 x 10(-4) s(-1). We have developed a kinetically inert Co(III)-cyclen-based complex, Co(III)-cycmmb that is very potent in inhibiting the translation of RNA into protein. Contact time as short as 10 min is sufficient to achieve the complete inhibition of the translation of a concentrated luciferase RNA solution into the enzyme in a cell-free translation system. The inhibition appears to proceed through two pathways. The first pathway involves the kinetic or substitutional inertness of Co(III) for the RNA template at short contact times. This interaction is mediated through the kinetic inertness of Co(III) for the phosphate groups of the nucleotides, as well as coordination of Co(III) to the nitrogenous bases. The second pathway occurs at longer contact times and is mediated by the hydrolysis of the phosphodiester backbone. This report represents the first demonstrated use of a metal-chelate complex to achieve the inhibition of the translation of RNA into protein. This Co(III) system can be useful in its present nonsequence-specific form as a novel viral decontamination agent. When functionalized to recognize specific nucleic acid sequences, such a system could potentially be used in gene-silencing applications as an alternative to standard antisense or RNAi technologies.

Rhenium Tricarbonyl Core Complexes of Thymidine and Uridine Derivatives

Thymidine and uridine were modified at the C2' and C5' ribose positions to form amine analogues of the nucleosides (1 and 4). Direct amination with NaBH(OAc)3 in DCE with the appropriate aldehydes yielded 1-{5-[(bis(pyridin-2-ylmethyl)amino)methyl]-4-hydroxytetrahydrofuran-2-yl}-5-methyl-1H-pyrimidine-2,4-dione (L1), 1-{5-[(bis(quinolin-2-ylmethyl)amino)methyl]-4-hydroxytetrahydrofuran-2-yl}-5-methyl-1H-pyrimidine-2,4-dione (L2), and 1-[3-(bis(pyridin-2-ylmethyl)amino)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-1H-pyrimidine-2,4-dione (L5), while standard coupling procedures of 1 and 4 with 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid (2) and 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid (3) in the presence of HOBT-EDCI in DMF provided a second novel series of bifunctional chelators: 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid [(3-hydroxy-5-(5-methyl-4-oxo-3,4-dihydro-2H-pyrimidin-1-yl)tetrahydrofuran-2-yl)methyl] amide (L3), 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid [(3-hydroxy-5-(5-methyl-4-oxo-3,4-dihydro-2H-pyrimidin-1-yl)tetrahydrofuran-2-yl)methyl] amide (L4), 5-(bis(pyridin-2-ylmethyl)amino)pentanoic acid [2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl] amide (L6), and 5-(bis(quinolin-2-ylmethyl)amino)pentanoic acid [2-(2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-3-yl] amide (L7). The rhenium tricarbonyl complexes of L1-L4, L6, and L7, [Re(CO)3(LX)]Br (X=1-4, 6, 7: compounds 5-10, respectively), have been prepared by reacting the appropriate ligand with [NEt4][Re(CO)3Br3] in methanol. The ligands and their rhenium complexes were obtained in good yields and characterized by common spectroscopic techniques including 1D and 2D NMR, HRMS, IR, cyclic voltammetry, UV, and luminescence spectroscopy and X-ray crystallography. The crystal structure of complex 6.0.5NaPF6 displays a facial geometry of the carbonyl ligands. The nitrogen donors of the tridentate ligand complete the distorted octahedral spheres of the complex. Crystal data: monoclinic, C2, a = 24.618(3) A, b = 11.4787(11) A, c = 15.5902(15) A, beta = 112.422(4) degrees , Z = 4, D(calc) = 1.562 g/cm3.

Binding of europium(III) ions to RNA stem loops: role of the primary hydration sphere in complex formation

Understanding the process by which RNA molecules fold into stable structures includes study of the role of site-bound metal ions. Because the alkaline earth metal ions typically associated with RNA structure [most often Mg(II)] do not provide convenient spectroscopic signals, replacement with metal ions having spectroscopically useful properties has been a valuable approach. The luminescence properties of the lanthanide(III) series, in particular europium(III), have made them useful in the study of complexation with biomolecules. We review the physical, chemical, and spectroscopic characteristics of Eu(III) that contribute to its value as a probe of RNA-metal ion interactions, and examples of information obtained from studies of Eu(III) bound to small RNA stem loops. Although Eu(III) has similar site preference to Mg(II), luminescence and isothermal titration calorimetry measurements indicate that Ln(III) loses water molecules from the inner hydration sphere more readily than does Mg(II), resulting in more direct coordination between RNA and the metal ion and very different energetics of binding. In some cases, e.g., a GAAA tetraloop, binding appears to occur by a lock and key process; in the same base sequence containing certain deoxynucleoside substitutions that alter loop structure, binding appears to occur by an induced fit process.

An approach to metal-assisted DNA base pairing: novel beta-C-nucleosides with a 2-aminophenol or a catechol as the nucleobase

The metal-chelating beta-C-nucleoside having a phenylenediamine moiety as the nucleobase was previously found to form a stable 2:1 complex with a Pd(2+) ion in aqueous media, where hydrogen bonding is replaced by metal coordination in the base pairing, thereby creating a novel hybridization motif in duplex DNA. In this regard, we have further designed two types of artificial beta-C-nucleosides possessing a metal-chelating site (a 2-aminophenol or a catechol) as the nucleobase moiety. These artificial nucleosides are directed toward controlling the net charges of the metal-assisted base pairs. This paper describes convenient syntheses of the artificial nucleosides bearing a 2-aminophenol or a catechol moiety. Each nucleoside was directly synthesized through 2'-deoxy derivative via a Friedel-Crafts coupling reaction as the key step between the aromatic ring and ribose moiety, whereas the nucleoside having a phenylenediamine moiety was prepared in rather longer steps through an RNA type intermediate followed by the removal of 2'-hydroxyl group.

A bridge between the RNA and protein worlds? Accelerating delivery of chemical reactivity to RNA and DNA by a specific short peptide (AAKK)(4)

BACKGROUND

RNA can catalyze diverse chemical reactions, leading to the hypothesis that an RNA world existed early in evolution. Today, however, catalysis by naturally occurring RNAs is rare and most chemical transformations within cells require proteins. This has led to interest in the design of small peptides capable of catalyzing chemical transformations.

RESULTS

We demonstrate that a short lysine-rich peptide (AAKK)(4) can deliver a nucleophile to DNA or RNA and amplify the rate of chemical modification by up to 3400-fold. We also tested similar peptides that contain ornithine or arginine in place of lysine, peptides with altered stereochemistry or orientation, and peptides containing eight lysines but with different spacing. Surprisingly, these similar peptides function much less well, suggesting that specific combinations of amino acids, charge distribution, and stereochemistry are necessary for the rate enhancement by (AAKK)(4).

CONCLUSIONS

By appending other reactive groups to (AAKK)(4) it should be possible to greatly expand the potential for small peptides to directly catalyze modification of DNA or RNA or to act as cofactors to promote ribozyme catalysis.