Synthesis of Novel Modified Uracil for Dual-Purposes: Quenching and Photoswitching

Hybridization of nucleic acids is considered the cornerstone for many biomedical applications as antigene and antisense. Recently, much effort has been devoted to regulation nucleic acid hybridization using external stimuli as light. Azobenzene, photochromic molecule, has been widely used for photoregulation of nucleic acid through geometrical structural change from trans to cis isomer and reverse with response of optical excitation with light at suitable wavelength. Despite the efficiency of azobenzenes in reversible photoswitching of nucleic acid-related activities, there are some drawbacks arising from the non-nucleosidic nature of the attached azobenzen. 4-(dimethylamino)azobenzene-4'-carboxylic acid (DABCYL), universal quencher, one of azobenzene derivatives that widely used as a quencher for nucleic acid detection using fluorescent probes technique. Here we report the synthesis of novel azo-based uracil derivatives that may have the potential dual-purposes as photo trigger and/or as a quencher that mimics the structure of the universal quencher DABCYL. The modified uracil is designed to have 4-(dimethylamino)phenylazo moiety at C5 position because of at this position there is no interference with the hydrogen bonding sites of uracil and therefore retain the base pairing ability with adenine.