Mikko Oivanen

The effect of protecting groups of the nucleobase and the sugar moieties on the acidic hydrolysis of the glycosidic bond of 2-́deoxyadenosine: a kinet

Abstract The rate constants for the hydrolysis of several N 6 -substituted 2 - deoxyadenosines were measured at different concentrations of oxonium ion in order to assess the role of various N 6 and sugar protecting groups in depurination reaction encountered in nucleic acid synthesis. The site of protonation was established by recording the 15N NMR spectra in DMSO- d 6 both in the absence and presence of trifluoroacetic acid. The exceptional lability of the monocations of N 6-acyl-2 - deoxyadenosines has been accounted for by a preferred N 7 protonation.

Towards Nucleotide Prodrugs Derived from 2,2-Bis(hydroxymethyl)malonate and Its Congeners: Hydrolytic Cleavage of 2-Cyano-2-(hydroxymethyl)-3-methoxy-3-oxopropyl and 3-(Alkylamino)-2-cyano-2-(hydroxymethyl)-3-oxopropyl Protections from the Internucleosidic Phosphodiester and Phosphorothioate Linkages

Thymidylyl-(3′5′)-thymidine (TpT) and its stereoisomeric phosphoromonothioate analogs [P(R)]- and [P(S)]-Tp(s)T having the phosphate or thiophosphate linkage protected with a 2-cyano-2-{[(4,4′-dimethoxytrityl)oxy]methyl}-3-methoxy-3-oxopropyl group (see 5a,b), as well as [P(R)]-Tp(s)T bearing a S-(2-cyano-2-{[(4,4′-dimethoxytrityl)oxy]methyl}-3-oxo-3-[(2-phenylethyl)amino]propyl) protection (see 5c), were prepared. The kinetics of the cleavage of the protecting group from the corresponding detritylated compounds 6a–c was studied over a pH range from 2 to 7. All compounds undergo a hydroxide-ion-catalyzed reaction that releases the unprotected TpT (7a) or Tp(s)T (7b), in all likelihood by departure of the hydroxymethyl group as formaldehyde and concomitant elimination of the phosphodiester or phosphorothioate from the resulting carbanion. The half-life for the deprotection of 6a and 6b is ca. 6 s at pH 7 and 25°, and that of 6cca. 600 s. The reasonably fast release of Tp(s)T from 6c offers a novel method for temporary intrachain attachment of peptides to oligonucleotides to enhance the cellular uptake.

Mechanism for Acid-Catalyzed Hydrolysis of Nucleoside and Acyclonucleoside Analogues of Benzimidazole

Abstract A study has been made of a broad series of nucleosides and acyclonucleosides of a variety of benzimidazole analogues. Quantitative kinetic data are presented, and the mechanism of the reactions described, taking into account steric, electronic and conformational effects. The overall results are also compared with those of purine nucleosides.

Kinetics for the Acid-Catalyzed Hydrolysis of Purine and Cytosine 2′-Deoxy-4′-thionucleosides

Abstract Hydrolysis of adenine, guanine and cytosine 2′-deoxy-4′-thionucleosides in aqueous acid has been followed by HPLC. Stability of the compounds and mechanisms of hydrolysis are discussed in comparison with those of the corresponding native 2′-deoxynucleosides.

THE CHEMICAL STABILITY OF S-(2-ACYLTHIOETHYL) AND S-ACYLOXYMETHYL PROTECTED THYMIDYLYL-3′,5′-THYMIDINE PHOSPHOROMONOTHIOLATES AND THEIR DEACYLATION PRODUCTS IN AQUEOUS SOLUTION

The hydrolytic stability of the S-(2-acetylthioethyl) (1a,b), S-(2-pivaloyl- thioethyl) (2a,b), and S-acetyloxymethyl (3a,b) protected R P and S P phosphoromonothiolates of 3′,5′-TpT has been studied. Rather unexpectedly, an intramolecular hydroxide ion catalyzed acetyl migration from the protecting group to the nucleoside 3′- and 5′-hydroxy functions was found to compete with the intermolecular displacement of the AcSCH2CH2S- or AcOCH2S-ligand from the phosphorus atom of 1a,b and 3a,b, respectively. With the S-pivaloylthioethyl derivative 2a,b no such reaction took place. Additionally, the kinetics of the cleavage of the S-(2-mercaptoethyl) group from 4a,b, the products of enzymatic deacylation of 1a,b and 2a,b, were studied as a function of pH.

HYDROLYTIC REACTIONS OF 3'-DEOXY-3'-THIOINOSYLYL-(3'5')-URIDINE; AN RNA DINUCLEOTIDE CONTAINING A 3'-S-PHOSPHOROTHIOLATE LINKAGE

Abstract The course of hydrolysis of 3′-deoxy-3′-thioinosylyl-(3′ → 5′)-uridine (IspU) has been followed by HPLC over a wide pH-range. Two reactions of the internucleosidic thiophosphate linkage compete: (i) cleavage yielding thioinosine monophosphates and uridine, and (ii) isomerization to the 2′,5′-isomer of IspU. Under very acidic conditions, even acid-catalyzed depurination of the inosine moiety is observed. The stability of the thiophosphate linkage and the mechanisms of its rupture are discussed.

N23-ethenoguanosine and IA′-metamorphosine: 5N NMR Spectroscopy and elucidation of physico-chemical properties by kinetic and equilibrium measurements

Abstract Tautomerism, protonation and electronic properties of the base moieties of IA′-metamorphosine (1a), N2,3-ethenoguanosine (2a) and O6-benzyl-N2,3-ethenoguanosine (3a were investigated by 15N NMR spectroscopy. pKa values of the same compounds were determined spectrophotometrically, and hydrolytic stability of the N-glycosidic bond was studied at various hydronium ion concentrations. The base stacking ability and metal ion complexation of N2,3-ethenoguanosine and its 9-ethyl counterpart (7) were elucidated by phase distribution and potentiometric measurements.

DISACCHARIDE NUCLEOSIDES AND THEIR ENZYMATIC AND CHEMICAL INCORPORATION INTO OLIGONUCLEOTIDES

Abstract A high yield synthesis of different O-ribofuranosylnucleosides has been achieved. Kinetics of the acid-catalysed hydrolysis of disaccharide nucleosides has been studied. Chemical and enzymatic incorporation of 2′-O-ribofuranosyl-nucleoside residue into oligonucleotides was investigated.

Preparation, hydrolysis and intramolecular transesterification of 3'-deoxy-3'-thioinosine 3'-S-dimethylphosphorothiolate.

Abstract The hydrolytic reactions of the dimethyl ester of 3′-deoxy-3′-thioinosine 3′-S-phosphorothiolate have been followed over a wide aciditty range by HPLC. At pH > 3, only hydroxide ion catalyzed isomerization to the 2′-dimethylphosphate takes place, whereas under more acidic conditions hydrolysis to the 2′-monomethylphosphate and 3′-S-monomethylphosphorothiolate competes. The latter is the only product accumulating in very acidic solutions (1 M hydrochloric acid). Mechanisms of the reactions are discussed.

Cleavage of the Phosphodiester Bond of Uridylyl-(3′,5′)-8-Carboxymethylaminoadenosine by Hydronium, Hydroxide and Zinc(Ii) Ions: A Model Study Aimed at Elucidating the Potential of a Carboxylate Function as an Intramolecular Catalyst

Abstract Uridylyl-(3′,5′)-8-carboxymethylaminoadenosine has been synthesised, and its transesterification to uridine 2′,3′-cyclic phosphate in the presence and absence of Zn2+ ion has been studied. The results show that a carboxylate function in the vicinity of the phosphodiester bond accelerates the metal ion promoted cleavage but not the metal ion independent reaction. Under acidic conditions, the predominant reaction is the cleavage of the side chain, giving the 8-amino derivative.