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

Furanopyrimidine (FPy) and 2,6-diamino-3-deazapurine (DC3Pu) nucleosides with the ability to interact in DDD and AAA H-bonding patterns, respectively, were prepared. The N-1 pKa value of the DC3Pu nucleoside was estimated to be 6.4, which is due to the lack of a nitrogen atom at the 3-position, suggesting that DC3Pu acts as a base interacting in a DDD H-bonding pattern under near physiological conditions. As DC3Pu 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 Tm value of the ODN duplex was determined. However, the ODN duplex containing a DC3Pu: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.