BASE COMPOSITION ANALYSIS OF OLIGONUCLEOTIDES CONTAINING APURINIC SITES

Upon base composition analysis, oligonucleotides which are labeled at the 3'-terminus with fluorescein or biotin generate an additional, lat e eluting peak in the HPLC chromatogram. Investigation of this effect revealed the haptens acted as apurinic sites, and phosphodiesterase cl eavage of the phosphate bond between the upstream nucleotide and apuri nic site is inhibited. Extension of this work with a base-stable apuri nic site inserted into all possible junctures of 5'-TGAC-3' tetramers showed this to be a general eff ect. As a consequence of this work, ac id-catalyzed depurination resulting in apurinic sites can be monitored in oligonucleotide synthesis.