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Issue 21, 2016
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2′-O-Methyl- and 2′-O-propargyl-5-methylisocytidine: synthesis, properties and impact on the isoCd–dG and the isoCd–isoGd base pairing in nucleic acids with parallel and antiparallel strand orientation

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Abstract

Oligonucleotides containing 2′-O-methylated 5-methylisocytidine (3) and 2′-O-propargyl-5-methylisocytidine (4) as well as the non-functionalized 5-methyl-2′-deoxyisocytidine (1b) were synthesized. MALDI-TOF mass spectra of oligonucleotides containing 1b are susceptible to a stepwise depyrimidination. In contrast, oligonucleotides incorporating 2′-O-alkylated nucleosides 3 and 4 are stable. This is supported by acid catalyzed hydrolysis experiments performed on nucleosides in solution. 2′-O-Alkylated nucleoside 3 was synthesized from 2′-O-5-dimethyluridine via tosylation, anhydro nucleoside formation and ring opening. The corresponding 4 was obtained by direct regioselective alkylation of 5-methylisocytidine (1d) with propargyl bromide under phase-transfer conditions. Both compounds were converted to phosphoramidites and employed in solid-phase oligonucleotide synthesis. Hybridization experiments resulted in duplexes with antiparallel or parallel chains. In parallel duplexes, methylation or propargylation of the 2′-hydroxyl group of isocytidine leads to destabilization while in antiparallel DNA this effect is less pronounced. 2′-O-Propargylated 4 was used to cross-link nucleosides and oligonucleotides to homodimers by a stepwise click ligation with a bifunctional azide.

Graphical abstract: 2′-O-Methyl- and 2′-O-propargyl-5-methylisocytidine: synthesis, properties and impact on the isoCd–dG and the isoCd–isoGd base pairing in nucleic acids with parallel and antiparallel strand orientation

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Publication details

The article was received on 22 Mar 2016, accepted on 25 Apr 2016 and first published on 26 Apr 2016


Article type: Paper
DOI: 10.1039/C6OB00622A
Org. Biomol. Chem., 2016,14, 4927-4942

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    2′-O-Methyl- and 2′-O-propargyl-5-methylisocytidine: synthesis, properties and impact on the isoCd–dG and the isoCd–isoGd base pairing in nucleic acids with parallel and antiparallel strand orientation

    S. K. Jana, P. Leonard, S. A. Ingale and F. Seela, Org. Biomol. Chem., 2016, 14, 4927
    DOI: 10.1039/C6OB00622A

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