HIGH-PERFORMANCE LIQUID-CHROMATOGRAPHY OF THE PHOTOPRODUCTS OF NUCLEIC-ACID COMPONENTS .3. DETECTION OF THE SECONDARY STRUCTURE DIFFERENCESIN SEQUENCE ISOMERIC SELF-COMPLEMENTARY OLIGONUCLEOTIDES

Reversed-phase high-performance liquid chromatography (RP-HPLC) was us ed to detect differences in the secondary structures of two self-compl ementary oligodeoxyribonucleotides. The [d(CCTTTAAAGG)]2 duplex assume s an ordinary B-conformation in aqueous solution, while [d(GGAAATTTCC) ]2 is known to contain in its central part a stretch of a more rigid B '-form conformation with significantly lowered fluctuational mobility of base pairs. The latter factor causes a marked difference in the amo unts of thymine cyclobutane photodimers formed under UV irradiation of corresponding duplexes as revealed by chromatography of two single-st randed oligonucleotides. Increasing the temperature below the duplex m elting temperature (stimulation of the B'-B structural transition) res ults in an increase in photodimer formation that was inhibited in the B'-form. Thus, we demonstrate the usefulness of RP-HPLC for duplex DNA structural studies.