DEGRADATION OF OLIGONUCLEOTIDES BY VACUUM-UV RADIATION IN SOLID: ROLES OF THE PHOSPHATE GROUP AND BASES

Abstract— Vacuum-UV induced degradation of deoxyoligonucleotides in solid form was studied by thin-layer chromatography with special emphasis on the fragmentation products. First, the degradation scheme previously proposed for 2'-deoxyadenylyl-(3'-5')-2'-deoxyadenosine (dApdA), which states that deoxypentose of the adenylyl moiety is the initial site of destruction, was confirmed by employing 258, 275, and 285 nm, in combination, as scanning wavelengths of chromatograms. Consistent results were obtained with 2'-deoxyadenylyl-(3'-5')-2'-deoxycytidine (dApdC), for which adenine and 5'-monophosphate of deoxycytidine are the predicted products, although the efficiency for such degradation mode was found to be lower with dApdC than with dApdA. Cytosine residue, thus, appeared to exert a suppressive effect on the destruction of deoxypentose of the adenylyl moiety. Second, with 2'-deoxycytidylyl-(3'-5')-2'-deoxyadenosine (dCpdA) the same spectroscopic analysis revealed that both adenine and cytosine were released, as well as some unidentified products, which could not be precisely identified by their chromatographic positions as dAMP or dCMP, although they showed characteristic absorption properties of adenine or cytosine containing species. This suggests that the photodegradation mode of dideoxynucleoside monophosphates is not so unique as hypothesized above, but that it depends also on the sequence of base residues. Finally, a very poor sensitivity to photodegradation of thymidylyl-(3'-5')-2'-deoxycytidine(dTpdC) and thymidylyl-(3'-5')-thymidine (dTpdT) to vacuum-UV radiation suggests that any pyrimidine could decrease the damaging effect of high energy vacuum-UV photons.