HYBRID OLIGONUCLEOTIDES CONTAINING STILBENE UNITS - EXCIMER FLUORESCENCE AND PHOTODIMERIZATION

Complementary pairs of oligonucleotides in which the stilbene chromophore is incorporated either in the middle or at the end of a 10 base pair sequence have been prepared and their spectroscopic and photochemical properties investigated. The individual oligonucleotides display fluorescence spectra and photoisomerization similar to that of a model 4,4'-stilbenedicarboxamide. Variations in fluorescence quantum yield and decay times are attributed to interactions with neighboring bases. One-to-one mixtures of complementary oligonucleotides form stable duplexes with melting temperatures of 40 and 46 degrees C, respectively, for the mid-strand and terminally labeled duplexes. Duplex formation results in hyperchromism of both the nucleotide and stilbene absorption bands and the appearance of broad, long-wavelength fluorescence attributed to an excited stilbene dimer. These duplexes provide a unique opportunity for the investigation of the here-to-for elusive stilbene excimer. The long wavelength absorption bands of both duplexes are efficiently bleached upon irradiation. Bleaching is a consequence-of stereospecific stilbene [2+2] photodimerization and results In the formation of cross-linked duplexes of high thermal stability. Excimer and monomer fluorescence are found to provide a highly sensitive probe of duplex formation and dissociation.