Satu Mikkola

Cleavage and isomerization of UpU promoted by dinuclear metal ion complexes.

The catalysis of phosphoryl transfer by metal ions has been intensively studied in both biological and artificial systems, but the status of the transient pentacoordinate phosphoryl species (as transition state or intermediate) is the subject of considerable debate. We report that dinuclear metal ion complexes that incorporate second sphere hydrogen bond donors not only promote the cleavage of RNA fragments just as efficiently as the activated analogue HPNPP but also provide the first examples of metal ion catalyzed phosphate diester isomerization close to neutral pH. This observation implies that the reaction catalyzed by these complexes involves the formation of a phosphorane intermediate that is sufficiently long-lived to pseudorotate.

The effect of secondary structure on cleavage of the phosphodiester bonds of RNA.

This review discusses the effects the secondary structure of an RNA molecule has on the inherent reactivity of its phosphodiester bonds, and on the catalytic activity of metal ion-based cleaving agents. The basic principles of the intramolecular transesterification of RNA phosphodiester bonds, particularly cleavage, are first briefly described. Studies of the structural effects on the cleavage, in the absence and in the presence of metal ion catalysts, are then reviewed, and the sources of the reactivity differences observed in different structures are discussed.

The mechanism of the metal ion promoted cleavage of RNA phosphodiester bonds involves a general acid catalysis by the metal aquo ion on the departure of the leaving group

A series of uridine 3′-alkyl phosphates and 3′-aryl phosphates were synthesised and their cleavage was studied in the presence of Zn2+ aquo ions. A βlg value was determined for the Zn2+ promoted cleavage of both types of compounds. Comparison of the results obtained to those reported previously for the cleavage of the same substrates in the absence of metal ion catalysts suggests that the alkyl leaving group departs as an alcohol in the presence of metal ion catalysts. Furthermore, metal ion catalysts seem to enhance the departure. The aryl leaving group, in contrast, departs as an oxyanion.

Crystal structure, solution properties and hydrolytic activity of an alkoxo-bridged dinuclear copper(II) complex, as a ribonuclease model

Crystal structures, solution properties and ribonuclease activity of copper(II) complexes of a binucleating, bis-pyridyl ligand (N,N′-bis(2-pyridylmethyl)-1,3-diaminopropan-2-ol, L) have been investigated. The single-crystal X-ray structure of the mononuclear complex [CuL(ClO4)2] (1) shows distorted octahedral geometry around the metal ion, with the four nitrogens of the ligand in the equatorial plane of copper(II). A μ-alkoxo-bridged dinuclear complex is formed in the presence of a two-fold metal excess. Despite the symmetrical ligand, the two metal ions in [Cu2(LH−1)(DPP)(ClO4)(CH3OH)]ClO4 (2, DPP = diphenyl phosphate) have distinct, distorted octahedral (Cu1) and square pyramidal (Cu2) geometry. Beside the alkoxo-oxygen, the phosphate group of DPP also bridges the two metal centers in 2 in a μ-1,3-bridging mode. The complexes formed in aqueous solution are likely to have analogous structures to 1 and 2. The dinuclear [Cu2(LH−1)(OH)] complex efficiently promotes the hydrolysis/transesterification of both activated (2-hydroxypropyl p-nitrophenyl phosphate, hpnp) and non-activated, biological phosphodiesters (uridine-2′,3′-cyclic-monophosphate, cUMP and uridylyl-(3′,5′)-uridine, UpU). For example, a 2 mM solution of the dinuclear complex provides 5 orders of magnitude acceleration in the hydrolysis of cUMP. The proposed mechanisms include double Lewis-acid activation with intramolecular general base catalysis.

Hydrolysis of Phosphodiester Bonds within RNA Hairpin Loops in Buffer Solutions: the Effect of Secondary Structure on the Inherent Reactivity of RNA Phosphodiester Bonds

The hydrolysis of phosphodiester bonds of chimeric 2′-O-methyloligoribonucleotides was studied in buffer solutions. Pseudo-first-order rate constants for cleavage of phosphodiester bonds within hairpin loops were calculated and compared with those for cleavage of phosphodiester bonds within double-stranded stems and linear single-stranded oligonucleotides. No large differences in reactivity were observed: some of the hairpin structures studied were slightly less and others slightly more reactive than the linear reference. These results suggest that phosphodiester bonds within small hairpin loops are conformationally free to cleave by an in-line mechanism, but also that the secondary structure may influence the reactivity of phosphodiester bonds.

Preparation of hexaaza and heptaaza macrocycles functionalized with a single aminoalkyl pendant arm

A practical and reproducible route for the preparation of 1,4,7,10,13,16,19-heptaazacyclohenicosane (1), 1,4,7,10,13,16-hexaazacyclooctadecane (2), and 1,4,7,10,13,17-hexaazacycloicosane (3) bearing a single N-(2-aminoethyl) pendant arm has been developed. Richman-Atkins cyclization in the presence of caesium carbonate was applied to construct the macrocycle from 3-benzoyl-N1,N5-ditosyl-3-azapentane-1.5-diamine and the appropriate fully N-tosylated N alpha, N omega-bis(2-mesyloxyethyl) tri- or tetra-amine. The benzoyl group was selectively removed with potassium tert-butoxide, and the exposed nitrogen atom was reacted with N-tosylaziridine. The tosyl protections were removed with hydrogen bromide in acetic acid, and the product was converted to a free base with the aid of a strong anion exchange resin (OH- form).

Synthesis of 2,6,10,14,18,22-hexaazaspiro[11.11]tricosane, the first example of a spiro aza crown derived from 2,2-bis(aminomethyl)propane-1,3-diamine

Abstract 2,6,10,14,18,22-Hexaazaspiro[11.11]tricosane 1 has been prepared in seven steps from pentaerythritol. The key steps include two successive cyclizations by displacement of two tosyloxy groups from the appropriate pentaerythritol derivatives ( 4 ; 6 ) with 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD), each reaction being followed by sodium borohydride reduction. Hydrolysis of the spiro bis(hexahydro-1 H ,4 H ,7 H -3a,6a,9a-triazaphenalene) formed 1 .

Reactions of Adenosine with Bromo- and Chloromalonaldehydes in Aqueous Solution: Kinetics and Mechanism

Reactions of adenosine nucleosides with halogen substituted acetaldehydes and malonaldehydes have been studied and pseudo first-order rate constants have been determined. All the reactions yield 1,N6-etheno adducts, and with malonaldehydes, in addition to this, 11-formyl-1,N6-etheno adducts are also formed. Particular attention has been paid to the formation of the formyletheno products. The results obtained suggest that the reactions of adenine base with halogenated acetaldehydes and malonaldehydes are basically similar. It also seems that in reactions of halomalonaldehydes with adenosine, the etheno and formyletheno products are formed through the same initial reaction pathway i. e. the attack of the 6-amino group of the adenine base at the carbonyl carbon atom of the aldehyde.

Metal ion-promoted cleavage of mRNA 5′-cap models: hydrolysis of the triphosphate bridge and reactions of the N7-methylguanine base

Reactions of mRNA 5′-cap model compounds were studied to evaluate the potential of these reactions in the development of artificial RNases. Diadenosine triphosphate was used as a model for the triphosphate bridge, and its hydrolysis was studied in the presence of several Cu2+ complexes. The results of the kinetic experiments show that bifunctional catalysis by phosphate bound Cu2+ complexes is involved. The most efficient catalysis is achieved with complexes with acidic aqua ligands, and a metal ion-bound hydroxo ligand most probably acts as a nucleophile in the reaction. A detailed mechanism cannot, however, be suggested on the basis of the data. N7-methylguanosine and its 5′-monophosphate and diphosphate were used to study the reactions of the N7-methylguanine base of the mRNA 5′-cap moiety. While Cu2+ complexes efficiently enhance the hydrolysis of the triphosphate bridge, little effect on the reactions of the N7-methylguanine base was observed: neither the cleavage of the imidazole ring or the depurination of the nucleoside were enhanced to any significant extent.

A kinetic study on the chemical cleavage of nucleoside diphosphate sugars.

Nucleoside diphosphate sugars serve in essential roles in metabolic processes. They have, therefore, been used in mechanistic studies on glycosylation reactions, and their analogues have been synthesised as enzyme and receptor inhibitors. Despite extensive biochemical research, little is known about their chemical reactions. In the present work the chemical cleavage of two different types of nucleoside diphosphate sugars has been studied. UDP-Glc is phosphorylated at the anomeric carbon, whereas in ADP-Rib C-1 is unsubstituted, allowing hence the equilibrium between cyclic hemiacetal and acyclic carbonyl forms. Due to the structural difference, these substrates react via different pathways under slightly alkaline conditions: while UDP-Glc reacts exclusively by a nucleophilic attack of a glucose hydroxyl group on the diphosphate moiety, ADP-Rib undergoes a complex reaction sequence that involves isomerisation processes of the acyclic ribose sugar and results in a release of ADP.