HYBRID OLIGONUCLEOTIDES CONTAINING STILBENE UNITS - EXCIMER FLUORESCENCE AND PHOTODIMERIZATION

Complementary pairs of oligonucleotides in which the stilbene chromoph ore is incorporated either in the middle or at the end of a 10 base pa ir sequence have been prepared and their spectroscopic and photochemic al properties investigated. The individual oligonucleotides display fl uorescence spectra and photoisomerization similar to that of a model 4 ,4'-stilbenedicarboxamide. Variations in fluorescence quantum yield an d decay times are attributed to interactions with neighboring bases. O ne-to-one mixtures of complementary oligonucleotides form stable duple xes with melting temperatures of 40 and 46 degrees C, respectively, fo r the mid-strand and terminally labeled duplexes. Duplex formation res ults in hyperchromism of both the nucleotide and stilbene absorption b ands and the appearance of broad, long-wavelength fluorescence attribu ted to an excited stilbene dimer. These duplexes provide a unique oppo rtunity for the investigation of the here-to-for elusive stilbene exci mer. The long wavelength absorption bands of both duplexes are efficie ntly bleached upon irradiation. Bleaching is a consequence-of stereosp ecific stilbene [2+2] photodimerization and results In the formation o f cross-linked duplexes of high thermal stability. Excimer and monomer fluorescence are found to provide a highly sensitive probe of duplex formation and dissociation.