To aid in the evaluation of the structures of 2'-OMe-RNA complexes, we offer several CE phosphoramidites. 2'-OMe-T is useful in triplex studies while the 2-aminopurine derivative may be tested in ribozyme studies. By supporting an additional hydrogen bond, 2,6-diaminopurine (2-amino-adenosine) binds more strongly with uridine than does adenosine. Oligonucleotides containing 2'-OMe-5-Me-C and 2'-OMe-I would be of interest to researchers involved in triplex and antisense studies using 2'-OMe-RNA. The uses of 2'-OMe-5-bromo-U phosphoramidite range from crystallographic studies due to the heavy atom to cross-linking because of its photolability. 5-Fluoro-pyrimidine nucleosides have been useful as therapeutic agents and their effect on the structure and activity of oligonucleotides may be examined using the 2'-OMe-RNA derivatives. The 2,4,6-trimethylphenyl (TMP) protected 2'-OMe-U derivative is a convertible nucleoside and reaction with ammonia leads to the 5-fluoro-dC analogue. 2'-OMe-3-deaza-5-aza-C (Reverse C) derivative has the potential to mimic in oligonucleotides 5-azacytidine, a DNA methylase inhibitor. Its ability to bind as a C will likely be diminished.
Coupling: 6 minute coupling time
Deprotection: Complete deprotection takes 5 days at 55oC with ammonium hydroxide. Deprotection may be done with ammonium hydroxide:methylamine (1:1) at 55o C overnight if other bases are compatible.