Hybrid Oligonucleotides Containing Stilbene Units. Excimer Fluorescence and Photodimerization

Abstract

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 °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.

Design and Synthesis of Efficient Fluorescent Dyes for Incorporation into DNA Backbone and Biomolecule Detection

“…After 12 h, the reaction solvent was removed in vacuum and the residue was directly subject to a silica gel column eluted with CH 2 …”

“…The reaction was diluted with CHCl 3 , and washed with aqueous NaHCO 3 , extracted with CHCl 3 . The organic layer was collected, dried over Na 2 SO 4 , concentrated, and the residue was subject to a silica gel column eluted with CH 2 …”

“…A mixture of 30 (18 mg, 0.038 mmol) and 33 (60 mg, 0.1 mmol, 2.6 equiv) in anhydrous CH 2 Cl 2 (10 mL) was heated to 60 °C for 24 h. After the system was cooled to room temperature, the reaction solvent was removed in vacuum and the residue was directly subject to a silica gel column eluted with CH 2 …”

“…The obtained solid was dissolved in DMF with a catalytic amount of I 2 and the mixture was refluxed for 4 days. After evaporation of the solvent, the residue was purified by chromatography on a silica gel column eluted with CH 2 To a solution of bis-ylide precursor, 1,4-Phenylenebis(methylene)bis(chlorotriphenyl) phosphorane (430 mg, 0.62 mmol), in THF (5 mL) was added n-BuLi (0.76 mL, 1.2 mmol, 1.6 M in Hexanes) dropwise at 0 °C under argon. The mixture was stirred at room temperature for 0.5 h and cooled to −78 °C.…”

“…If the recovered starting material was counted, the total yield of the monotritylation would be 67% based on the consumed starting material. 'H NMR ( 2 Cl 2 (20 mL) was added 2.7 equivalent of diisopropylethylamine (0.08 mL). Then chloro-N,N-diisopropylaminocyanoethoxyphosphane (0.05 mL, ~1.2 equal) was added dropwise at room temperature under argon.…”