Site-Specific Hydrolysis of RNA by Europium(III) Texaphyrin Conjugated to a Synthetic Oligodeoxyribonucleotide

Using guanidinium groups for the recognition of RNA and as catalysts for the hydrolysis of RNA

The guanidinium functional group is commonly used in nature to recognize and bind anions through ion pairing and hydrogen bonding. Specific hydrogen-bonding patterns can be found in crystal structures of simple guanidinium salts. Analysis of these simple salts reveals a variety of features which are found in natural systems. These features have been applied to a series of artificial phosphodiesterases for RNA. These receptors incorporate guanidinium groups positioned to mimic the hydrogen-bonding patterns found in simple guanidinium salts and natural enzymes. This paper outlines general guanidinium hydrogen-bonding patterns. Next, the complexation of phosphodiesters with a series of artificial receptors are analyzed in terms of counterions, solvent mixtures, and cavity flexibility. In addition, strategies to enhance catalysis through a pKa analysis of phosphoranes are addressed. Next, we describe how our findings were incorporated into second generation receptors/catalysts. Finally, our future work is discussed.

Modulation of RNase H activity by modified DNA probes: major groove vs minor groove effects

We have previously prepared ribozyme mimics and chemical nucleases from modified DNA containing pendant bipyridine and terpyridine groups. The ability of these modified DNA probes to support RNase H cleavage of complementary RNA is described. DNA/RNA duplexes were formed using DNA probes designed to deliver metal complexes via either the major groove or the minor groove of the duplex. The duplexes were treated with Escherichia coli RNase H. Modifications in the major groove produced the same RNA cleavage pattern as unmodified DNA probes. However, minor groove substituents inhibited RNA cleavage over a four-base region. Comparison was made with a DNA probe containing a 2'-OMe modification. Our results support enzyme binding in the minor groove of a DNA/RNA duplex. We do not observe cleavage directly across from the modified nucleoside. The RNA cleavage efficiency effected by RNase H and a DNA probe decreases as follows: unmodified DNA > or = C-5 modified DNA >> c2'-modified DNA > C1'-modified DNA. Results with 28-mer RNA substrates roughly parallel those obtained with a 159-mer RNA target. The differences observed between low and high MW RNA substrates can be explained by a much higher enzyme-substrate binding constant for the high MW target.

Kinetics and Mechanism of Facile and Selective Dephosphorylation of 2'-Phosphorylated and 2'-Thiophosphorylated Dinucleotides: Neighboring 3'-5' Phosphodiester Promotes 2'-Dephosphorylation

2'-Phosphorylated and 2'-thiophosphorylated dinucleotides U(2'-p)pU (1) and U(2'-ps)pU (2) were found to undergo facile 2'-specific dephosphorylation at 90 degrees C in neutral aqueous solution to give UpU, and the first-order rate constants of these reactions were determined by HPLC. Particularly, U(2'-ps)pU (2, k = 1.38 +/- 0.4 x 10(-)(3) s(-)(1), t(comp) = 1 h) was cleanly dephosphorylated ca. 100 times more rapidly than U(2'-p)pU (1, k = 1.41 +/- 0.05 x 10(-)(5) s(-)(1), t(comp) = 72 h). Dephosphorylations of 1 and 2 were faster than those of thymidine 3'-phosphate (8) and thymidine 3'-thiophosphate (9), respectively. The kinetic data observed were independent of the 2'- or 3'-position of the phosphate group and the kind of base moiety. The neighboring 3'-5' phosphodiester function most probably promotes the 2'-dephosphorylation efficiently. A branched trimer, U(2'-pU)pU (3), and related compounds having a substituent on the 2'-phosphoryl group, such as U(2'-pp-biotin)pU (4) and U(2'-ps-bimane)pU (5), were rather resistant to hydrolysis. The addition of divalent metal ions (Mg(2+), Mn(2+), Zn(2+), Ca(2+), Co(2+), and Cd(2+)) remarkably decreased the rate of 2'-de(thio)phosphorylation of 1 or 2. Among these metal ions, Zn(2+) most significantly inhibited the dephosphorylation. On the contrary, trivalent metal ions considerably accelerated the 2'-de(thio)phosphorylation of 1 or 2. The mechanism of 2'-dephosphorylation in the presence and absence of various metal ions is also discussed.

Kinetic Analysis of Diamine-Catalyzed RNA Hydrolysis

The catalysis of various amines for the hydrolysis of RNA has been kinetically investigated, and the catalytic rate constants for each of the ionic states of these amines are determined. Ethylenediamine and 1,3-propanediamine are highly active under the physiological conditions, mainly because they preferentially take the catalytically active monocationic forms. The catalysis of these diamines is further promoted by the intramolecular acid-base cooperation of the neutral amine and the ammonium ion. In contrast, monoamines overwhelmingly exist at pH 7 as the inactive cations. Potential application of the catalysis by the diamines and the related oligoamines is discussed.

Sequence-specific cleavage of yeast tRNA(Phe) with oligonucleotides conjugated to a diimidazole construct

Oligonucleotide derivatives conjugated to a chemical construction with two histamine residues imitating the catalytic center of ribonuclease A have been synthesized. In experiments with the conjugates complementary to the 3'-end and to the variable loop and the T loop of yeast tRNA(Phe), it was shown that the compounds can accomplish sequence-specific cleavage of the target RNA in physiologic conditions.

Site-specific photomodification of DNA by porphyrin-oligonucleotide conjugates synthesized via a solid phase H-phosphonate approach

meso-Tris(4-pyridyl)[[(omega-hydroxyhexamethylene)carbamoyl]phenyl ] porphyrin was converted to its H-phosphonate derivative and conjugated using solid phase synthesis with the 5'-hydroxyl group of deoxyribonucleotides d(TCTTCCCA) and d(T)12. These conjugates were transformed into their (N-methylpyridiniumyl)porphyrin analogs in the reaction with methyl iodide. A 532 nm laser beam was utilized to photoactivate both types of the conjugates in the presence of the target 22-mer and 16-mer oligonucleotides. Photoactivation of porphyrin-oligonucleotide conjugates resulted in site-specific DNA modification characterized by a main reaction site size of approximately 5 bases.

Creating RNA bulges: cleavage of RNA in RNA/DNA duplexes by metal ion catalysis

The manipulation of a single-stranded RNA target by forming different RNA/antisense hybrids demonstrates the possibility of cleaving the RNA strand within duplexes. This was achieved using the sequence composition of the antisense oligonucleotide, an approach that results in various bulges [unpaired base(s)] in the RNA target, which is then cleavable at these specific bulge sites under free metal ion or metal complex catalysis. RNA cleavages promoted by metal ions were performed under mild conditions and characterized by separating the RNA fragments carrying end label. The observed products result from intramolecular transesterification causing RNA strand scission. No detectable cleavage of the RNA was observed with either a fully complementary RNA/antisense hybrid or a bulged base in the antisense strand. A molecular modeling study of the RNA backbone suggests that the local conformation of the RNA backbone at a bulge in such hybrid duplexes greatly facilitates the metal-assisted catalytic cleavage. Endonucleolytic RNA cleavage within an RNA/antisense hybrid by metal complexes attached to the antisense oligonucleotide might lead to a new approach in antisense technology with artificial ribonucleases which operate with catalytic turnover.

Structure/nuclease activity relationships of DNA cleavers based on cationic metalloporphyrin-oligonucleotide conjugates

The covalent attachment of a managanese-tris(methylpyridiniumyl)porphyrin entity to an antisense oligonucleotide allowed sequence-selective oxidative cleavage of DNA when the metalloporphyrin was activated by potassium monopersulfate (KHSO5). We prepared several structurally modified metallo-porphyrin-oligonucleotide conjugates in order to find out the most efficient compound for in vitro DNA cleavage. The nature and the length of the tether were modulated, the metalloporphyrin entity was modified (metal, ligand), and different ways of activation of the metalloporphyrin were assayed. We noticed that the location of the peptidic bond within the linker could greatly affect the cleavage efficiency of the different conjugates. We showed that the most efficient conjugate for oxidative DNA cleavage was a manganese tetracationic porphyrin-oligonucleotide compound. When the metalloporphyrin moiety was activated by a reducing agent in the presence of molecular oxygen, DNA cleavage was efficient at suitable concentrations of the reducing agent, in order to avoid the reduction of the activated DNA cleaver, a putative high-valent metal-oxo species, by the excess of reducing agent.

Catalytic Hydrolysis of Phosphate Diesters by Lanthanide(III) Cryptate (2.2.1) Complexes

Lanthanide(III) Cryptate (2.2.1) chlorides (Ln(2.2.1)Cl(3); Ln = La (1a), Ce(1b), and Eu(1c); (2.2.1) = 4,7,13,16,21-pentaoxa-1,10-diazabicyclo[8.8.5]tricosane) are effective for the catalytic hydrolysis of bis(4-nitrophenyl) phosphate. Kinetic studies reveal that the europium(III) complex (1c) catalyzes the hydrolysis to produce 6 equiv of 4-nitrophenol with a significant rate (k(1) = 1.5 x 10(-)(4) s(-)(1) at 0.40 mM) at pH 8.5 and 50 degrees C. The catalytic activity of the complexes is increased with decreasing the ionic size, i.e, La < Ce < Eu. While the use of hydrogen peroxide further increase the activity of 1b (k(1) = 1.6 x 10(-)(3) s(-)(1) at 0.40 mM), the presence of molecular oxygen does not affect the activity at all. Crystal of 1a.CH(3)OH([La(2.2.1)(Cl)(2)](Cl)(CH(3)OH)) belongs to the space group Pnma with a = 17.072(3) Å, b = 19.037(3) Å, c = 14.725(2) Å, V = 4786(1) Å(3), Z = 8, D(x)() = 1.691 g cm(-)(3), &mgr; = 21.7 cm(-)(1). The encryptated metal ion is nine-coordinated, and all the heteroatoms of the cryptate (2.2.1) ligand coordinate the metal center to form a bowl-shaped structure. Two coordinating chloride anions are located on the open face with a cis geometry. The existence of coordinated water to the europium(III) complex 1c in the aqueous solution was confirmed by time-resolved Eu(III) luminescence spectroscopy. From the decay constants in H(2)O and D(2)O, the numbers of coordinated water molecules (q) are found to be 3.02 at pH of 5.0. The above kinetic and spectroscopic observation are supportive of mechanisms in which the metal complexes act as a center for binding and activation as well as a source of nucleophilic metal hydroxides.

A non-ionic water-soluble pentaphyrin derivative. Synthesis and cytotoxicity

The synthesis of the water soluble tetrahydroxypentaphyrin derivative, 1, is described. This species, which forms complexes with both small neutral molecules and uranyl cation, has been studied as a possible cytotoxic agent. Cytotoxic studies performed with the human T lymphoma cell line (JURKAT) revealed that pentaphyrin 1 exhibits toxicity at microM concentrations comparable with other water soluble, porphyrin-type systems such as the pyridinium metalloporphyrins.

Efficient sequence-specific cleavage of RNA using novel europium complexes conjugated to oligonucleotides

BACKGROUND

A general method allowing the selective destruction of targeted mRNA molecules in vivo would have broad application in biology and medicine. Metal complexes are among the best synthetic catalysts for the cleavage of RNA, and covalent attachment of suitable metal complexes to oligonucleotides allows the cleavage of complementary single-stranded RNAs in a sequence-specific manner.

RESULTS

Using novel europium complexes covalently linked to an oligodeoxyribonucleotide, we have achieved the sequence-specific cleavage of a complementary synthetic RNA. The complexes are completely resistant to chemical degradation under the experimental conditions. The cleavage efficiency of the conjugate strongly depends on the nature of the linker between the oligonucleotide and the complex. Almost complete cleavage of the RNA target has been achieved within 16 h at 37 degrees C.

CONCLUSIONS

The results will be important for improving the efficacy of antisense oligonucleotides and will provide a basis for the design of synthetic RNA restriction enzymes. Conjugates of the kind described here may also find application as chemical probes for structural and functional studies of RNA.