phosphoramidite and 5-formyl-2--deoxyuridine

We report the synthesis of a 5-formyl-2'-deoxyuridine (5fU) phosphoramidite and the preparation of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications. Biophysical characterization of the synthetic oligonucleotides indicates that 5fU, but not the other T-derivatives, can alter DNA structures.

Topics: Deoxyuridine; DNA; Oligonucleotides; Organophosphorus Compounds; Thymine

A straightforward, efficient method for the synthesis of 5-formyl-2'-deoxyuridine (dfU) and solid-phase synthesis of oligodeoxynucleotides containing dfU using a phosphoramidite method are described. The synthesis of dfU is achieved by oxidation of the 5-methyl group in thymidine derivatives. However, incorporation of the dfU 3'-O-phosphoramidite into oligodeoxynucleotides proceeds in low yield, due to instability of the 5-formyl group under conditions used for automated DNA synthesis. Therefore, oligodeoxynucleotides containing a 5-(1,2-dihydroxyethyl)uracil derivative are first prepared and finally oxidized by periodate to give the desired oligodeoxynucleotides containing 5-formyluracil.

Topics: Biotechnology; Clinical Laboratory Techniques; Deoxyuridine; Oligodeoxyribonucleotides; Organophosphorus Compounds; Oxidation-Reduction; Thymidine