Nucleosides and Nucleotides. 174. Synthesis of Oligodeoxynucleotides Containing 4‘-<i>C</i>-[2-[[<i>N</i>-(2-Aminoethyl)carbamoyl]oxy]ethyl]thymidine and Their Thermal Stability and Nuclease-Resistance Properties¹

Abstract

The synthesis and properties of oligodeoxynucleotides (ODNs) containing 4‘-C-[2-[[N-(2-aminoethyl)carbamoyl]oxy]ethyl]thymidine (3) are described. 4‘α-(2-Hydroxyethyl)thymidine (4), which is a precursor for phosphoramidite 5, was synthesized using a newly developed intramolecular radical cyclization reaction at the 4‘-position of thymidine derivative 7. The radical reaction of 4‘β-(phenylseleno)-3‘-O-(dimethylvinylsilyl)thymidine derivative 7, which was prepared from thymidine in several steps, with Bu3SnH and AIBN, followed by Tamao oxidation, gave either 4‘α-(2-hydroxyethyl) derivative 6 or 4‘α-(1-hydroxyethyl) derivative 13, respectively. With a low Bu3SnH concentration, the reaction gave 6, via 6-endo-radical-cyclized product 11, as a sole product in 87% yield. The reaction of 7 in the presence of excess Bu3SnH gave 13 in 75% yield, via 5-exo-cyclized product 12, as a diastereomeric mixture. The 4‘α-(2-hydroxyethyl) derivative 6 was then converted into a 4‘-C-[2-[[N-(2-aminoethyl)carbamoyl]oxy]ethyl]thymidine derivative 14, which was phosphitylated to give phosphoramidite 5 in 72% yield. In this study, 3 was incorporated into a nonadecamer, d[CTGGCTCAGCTCGTCTCAT]-3‘, and a heptadecamer, d[CTCGTACCATTCCGCTC]-3‘, instead of T at various positions. ODNs containing 3 were more resistant to nucleolytic hydrolysis by both snake venom phosphodiesterase (a 3‘-exonuclease) and DNase I (an endonuclease) than unmodified parent ODNs, although ODNs containing 3 only slightly destabilized duplex formation with both complementary DNA and RNA strands. Furthermore, the duplex formed by an ODN containing 3 and its complementary RNA was a good substrate for Escherichia coli RNase H.