Development and synthesis of 5-ethynyl-2'-deoxyuridine 5'-triphosphate: a nucleoside analogue for application of Pd(0)-catalyzed coupling reactions in DNA sequencing methodology

Abstract

5-Ethynyl-2'-deoxyuridine 5'-triphosphate and the corresponding phosphoramidate analogue have been prepared for the purpose of studying DNA bases as possible donors in energy transfer dye systems. The triphosphate was very difficult to obtain in good isolated yields. The proposed eventual aim of the triphosphate synthesis was to examine the use of the DNA backbone as a donor for a long-range energy transfer system to an acceptor attached to the DNA. Synthesis of the 5-ethynyl-2'-deoxyuridine 5'-triphosphate will allow attachment of the acceptor dyes after the fragments are made from the chain-terminator method of DNA sequencing. The benefit associated with this strategy includes bypassing solubility and synthetic problems associated with the attachment of largely hydrophobic dyes to these hydrophilic nucleotides.