Synthesis and properties of oligonucleotides containing a 2,6-diamino-3-deazapurine:furanopyrimidine base pair

Furanopyrimidine (FPy) and 2,6-diamino-3-deazapurine ((DCPu)-Pu-3) nucleosides with the ability to interact in DDD and AAA H-bonding patterns, respectively, were prepared. The N-1 pK (a) value of the (DCPu)-Pu-3 nucleoside was estimated to be 6.4, which is due to the lack of a nitrogen atom at the 3-position, suggesting that (DCPu)-Pu-3 acts as a base interacting in a DDD H-bonding pattern under near physiological conditions. As (DCPu)-Pu-3 and FPy are expected to form a thermally stable DDD:AAA type of base pair in an oligodeoxynucleotide (ODN) duplex, they were incorporated into ODNs, and the T (m) value of the ODN duplex was determined. However, the ODN duplex containing a (DCPu)-Pu-3:FPy pair has a lower thermal stability than that containing a G:C pair does, although its thermal stability is equal to that of an ODN duplex with an A:T pair even under acidic conditions.