A new method for the synthesis of 5-foU-containing oligonuleotides by phosphoramidite chemistry and subsequent post-oxidation with sodium periodate was developed. 5-(1,2-Dihydroxyethyl)uracil-containing oligomers, which are readily converted to 5-foU-containing oligomers by sodium periodate oxidation, were synthesized according to the standard beta-cyanoethyl phosphoramidite chemistry. The phosphoramidite of a protected 5-(1,2-dihydroxyethyl)-2'-deoxyuridine derivative was prepared from 5-iodo-2'-deoxyuridine in 7 steps. UV melting behavior of these three oligomers demonstrated that the 5-foU-A base pair are less stable than the T-A base pair. Copyright (C) 1996 Published by Elsevier Science Ltd