Synthesis of oligonucleotides containing pyrazolo[3,4-d ]pyrimidines: The influence of 7-substituted 8-aza-7-deazaadenines on the duplex structure and stability

Abstract

The phosphoramidites 2a–d derived from 7-bromo- (1b), 7-iodo- (1c), 7-(hex-1-ynyl)- (1d) and 7-(2-phenylethynyl)- (1e) 8-aza-7-deaza-2′-deoxyadenosine were prepared. They were employed in the solid-phase synthesis of various oligonucleotides containing the 8-aza-7-deazaadenine system instead of that of adenine. Their Tm-values were measured and their thermodynamic data were determined. The replacement of adenine residues by 8-aza-7-deazaadenine 1a does not significantly influence the duplex stability, while the incorporation of 7-substituted derivatives 1b–e led to much more stable duplexes compared with their adenine-containing counterparts. From the CD spectra of the oligonucleotide duplexes it is evident that the overall structure of a parent DNA is retained when only very few modified bases are incorporated. Structural changes do occur when the number of modified residues is increased. This might be the result of the high-anti-conformation of the 7-substituted 8-aza-7-deaza-2′-deoxyadenosine residues.