Synthesis of Dodecadeoxyribonucleotides Containing a Pyrrolo[2, 3-d]pyrimidine Nucleoside and Their Base-pairing Ability

Abstract

As a part of our studies to search for efficient hybridization probes, we synthesized partially self-complementary dodecanucleotides d(GGGAAF*NTTCCC)(N =T, C, A, G) containing a pyrrolo[2, 3-d]pyrimidine deoxynucleoside [7 a, dF*] by the solid-phase phosphotriester approach, and examined their properties. The hitherto-unknown nucleosides, 3-(β-D-2-deoxyribofuranosyl)pyrrolo[2, 3-d]pyrimidin-2(3 H)-one [7 a] and its 6-butyl derivative [7 b], which were fluorescent, were synthesized starting from a 5-iodo-2'-deoxycytidine derivative [3] via palladium-catalyzed coupling with trimethylsilylacetylene or 1-hexyne followed by copper-catalyzed intramolecular cycli'zation. From the measurement of thermal stabilitie s (Tm's) of dodecamer duplexes, it was found that F* base can pair only with G base and F*G base pair-containing duplex has a stability similar to that of the C⋅G base pair.