DNA‐Templated Synthesis of Trimethine Cyanine Dyes: A Versatile Fluorogenic Reaction for Sensing G‐Quadruplex Formation

Abstract

A healthy glow: Fluorogenic peptide nucleic acids (PNAs) functionalized with indoline derivatives are used to specifically sense G‐quadruplex formation. Upon hybridization of both PNAs to the single‐stranded flanking arms of quadruplex DNA (see scheme), the synthesis of a trimethine cyanine dye is templated. Dye formation can be detected by the appearance of a characteristic fluorescence signal.

Dual Sensing of Hairpin and Quadruplex DNA Structures Using Multicolored Peptide Nucleic Acid Fluorescent Probes

“…The system was designed so that simultaneous and sequence-specific hybridization of both PNAs to a unique G-quadruplexcontaining oligonucleotide were the only conditions inducing the formation of a fluorescent trimethine cyanine dye (λ em = 563 nm). (27) Since the fluorescent properties of this trimethine cyanine dye were significantly different compared to those of Pna1 aldehyde (λ em = 476 nm) and to those of the pentamethine analogue formed when reacting Pna1 and Pna2 (λ em = 660 nm), we reasoned that it should be possible to simultaneously detect the formation of both hairpin and quadruplex DNAs using a non-overlapping, two-color "Cy3-Cy5" system. The system was designed so that a unique nucleophilic PNA, Pna2, could potentially react with two electrophilic PNA aldehydes, Pna1 and Pna3, to form a pentamethine (λ em = 660 nm) and a trimethine (λ em = 563 nm) cyanine dye, respectively.…”

“…Upon binding of both probes to the single-stranded flanking arms of a quadruplex, formation of a trimethine cyanine dye from two non-fluorescent precursors was templated. (27) Herein we describe the synthesis of a novel fluorescent Fisher's base aldehyde probe-head, its incorporation in a PNA strand, and the applications of the resulting fluorescently labeled probe for sensing hairpin DNA secondary structures. Reaction between this fluorescent Fisher's base aldehyde and a non-fluorescent indolenine molecule leads to the formation of a pentamethine cyanine dye (Cy5) absorbing and emitting at a significantly longer wavelength than its precursor.…”

A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes

“…Finally, the use of a different quadruplex structure as competitor is a tool in the quest for the molecular Holy Grail that a probe with specificity for a single type of quadruplex structure would represent (for recent examples, see Refs. [49,50]). …”

Cellular Detection of G‐Quadruplexes by Optical Imaging Methods

“…However, their passive quadruplex recognition might cast doubt on the reliability of the cellular imaging results. Alternative strategies such as hybridization Meguellati, Koripelly, & Ladame, 2010) and bimolecular fluorescence complementation (Liu, Zheng, Chen, Hao, & Tan, 2016) have been developed to allow for an active recognition of quadruplexes; however, their multipartner/multistep protocols might raise technical issues that, again, create uncertainties regarding the reliability of optical imaging results. In this context, we have developed a series of nature-inspired quadruplex ligands that actively fold into their fluorescent conformations in presence of their quadruplex targets.…”