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Updated: May 20, 2026

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes
Published on: July 6, 2016
Synthetic routes to fluorescent dyes exhibiting large Stokes shifts
Sandra Rihn1, Pascal Retailleau, Antoinette De Nicola
1Laboratoire de Chimie Organique et Spectroscopies Avancées, UMR 7515 au CNRS, Université de Strasbourg, Ecole de Chimie, Polymères, Matériaux de Strasbourg, 25 rue Becquerel, 67087 Strasbourg, Cedex 02 France.
Abstract:
Derivatives of isomeric 2-(hydroxytolyl)-4,6-dimethylamino-1,3,5-triazines have been synthesized in high yields in a controlled manner using a multistep reaction sequence. Iodination of either 2-(1'-hydroxy-6'-methylphen-2'-yl)- or 2-(1'-hydroxy-4'-methylphen-2'-yl)-4,6-dimethylamino-1,3,5-triazine with ICl provides species differing in the positioning of the iodo group relative to the hydroxyl which readily undergo Suzuki, Sonogashira, and Heck reactions under Pd(0) catalysis. Thus, thienyl, bisthienyl, and 3,4-ethylenedioxythienyl groups have been directly grafted, while unsubstituted polycyclic aromatics such as pyrene and perylene have been linked via alkyne bridges, as have ethynyldifluoroborondipyrromethane (BODIPY) dyes prepared in situ. The presence of a hydrogen bond in the ground state involving the hydroxyl substituent has been established by proton NMR and several X-ray structure determinations. All of the new dyes with a simple substituent (phenyl, thienyl) exhibited a pronounced green fluorescence resulting from an intramolecular proton transfer in the excited state (ESIPT) which produces a large Stokes shift (>10,000 cm(-1)). With other dyes, the fluorescence of the keto form responsible for the ESIPT process could be used as the input energy in efficient intramolecular energy transfer processes. Replacing perylene with pyrene allowed reversal of the direction of energy transfer from the polyaromatic module to the keto form.
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