1, N6-Etheno-2′-deoxytubercidin and pyrrolo-C: synthesis, base pairing, and fluorescence properties of 7-deazapurine nucleosides and oligonucleotides

Abstract

The synthesis of 1, N 6-etheno-7-deaza-2′-deoxyadenosine ( 12b) which was prepared from 7-deaza-2′-deoxyadenosine ( 5a) with chloroacetaldehyde is described. Also the regioselective glycosylation of the 7-deazapurine-2-one at nitrogen-1 ( 19) furnishing the pyrrolo-C nucleoside 7a is reported and a side chain derivative with a terminal triple bond ( 7d) is prepared. The fluorescence properties of these nucleosides and related compounds were determined. The etheno nucleoside 12b is strongly fluorescent showing a Stokes shift of 134 nm and a quantum yield of Φ=0.53. It proved to be stable, both in acidic and in alkaline medium while the parent purine compound 10b is labile under both conditions. Compound 12b was converted into its phosphoramidite 14 and was incorporated into oligonucleotides. Compound 12b destabilizes oligonucleotide duplexes when it is located in the center of the molecule; it stabilizes when it is incorporated in the terminal base pair or acts as an overhanging nucleoside. Temperature-dependent fluorescent measurements yielded sigmoidal melting profiles when compound 12b is stacked to the terminal base pair while a linear decrease of the fluorescence is observed when the molecule is located opposite to the four canonical nucleosides in the center of the duplex.