A series of novel modifying reagents, including phosphoramidites and solid supports, have been synthesized, and used for the introduction of 1‐(phenylethynyl)pyrene (PEPy) and 9,10‐bis(phenylethynyl)anthracene (BPEA) fluorescent dyes into predetermined positions of synthetic oligonucleotides. These two fluorophores have been shown to constitute an energy donor−acceptor pair, and can be used as such in fluorescent oligonucleotide probes, designed for the detection and structural studies of nucleic acids. The sensitivity of the probe to duplex formation is demonstrated. The formation of the PEPy and BPEA excimers is reported for the first time on nucleic acids. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)

Four tetramethylindo(di)carbocyanine‐derived carboxylicacids have been prepared using a modified one‐pot procedure for the dye assembly. The acids were converted into oxysuccinimide esters and phosphoramidite reagents. The efficiency of the reagents in the labeling of oligonucleotides and proteins has been demonstrated. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)

Four fluorescent 5-alkynyl-2'-deoxyuridines were studied in DNA oligonucleotides and their duplexes. The fluorescence response to hybridization differs dramatically for nucleosides containing a perylene fluorochrome either conjugated or not conjugated to the nucleobase. The conjugated nucleoside, 5-(perylen-3-ylethynyl)-2'-deoxyuridine, shows enhanced long-wavelength emission in the DNA duplex, in contrast to the blue fluorescence of perylene on a flexible linker (in 5-[(perylen-3-yl)methoxyprop-1-ynyl]-2'-deoxyuridine), which is quenched upon duplex formation.

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