Fluorescent Probes for G‐Quadruplex Structures

Abstract

Mounting evidence supports the presence of biologically relevant G-quadruplexes in single-cell organisms, but the existence of endogenous G-quadruplex structures in mammalian cells remains highly controversial. This is due, in part, to the common misconception that DNA and RNA molecules are passive information carriers with relatively little structural or functional complexity. For those working in the field, however, the lack of available tools for characterizing DNA structures in vivo remains a major limitation to addressing fundamental questions about structure-function relationships of nucleic acids. In this review, we present progress towards the direct detection of G-quadruplex structures by using small molecules and modified oligonucleotides as fluorescent probes. While most development has focused on cell-permeable probes that selectively bind to G-quadruplex structures with high affinity, these same probes can induce G-quadruplex folding, thereby making the native conformation of the DNA or RNA molecule (i.e., in the absence of probe) uncertain. For this reason, modified oligonucleotides and fluorescent base analogues that serve as "internal" fluorescent probes are presented as an orthogonal means for detecting conformational changes, without necessarily perturbing the equilibria between G-quadruplex, single-stranded, and duplex DNA. The major challenges and motivation for the development of fluorescent probes for G-quadruplex structures are presented, along with a summary of the key photophysical, biophysical, and biological properties of reported examples.

Nanophotonics and supramolecular chemistry

“…Detection of particular chemical species accompanied by specific variations of fluorescence emission is a powerful method in analytical chemistry. Fluorescent probes that bind to specific ions through supramolecular recognition are widely used in analyses of living cells [40][41][42]. In particular, development of a fluorescent probe for Ca 2+ ion detection fura-2 6 by Tsien and coworkers [43] promoted significant activity in the corresponding research field.…”

A Thioflavin T-induced G-Quadruplex Fluorescent Biosensor for Target DNA Detection

“…9,20,21 Meanwhile, the G-quadruplex has also been widely applied in fluorescent biosensors [22][23][24] because it can specifically combine with some fluorescent dyes, causing significantly higher fluorescence intensities than those of dyes alone. 25,26 Among these dyes for G-quadruplex, thioflavin T (ThT) has increasingly attracted the attention of researchers to become a new focus in the construction of G-quadruplex fluorescent biosensors, mainly due to its satisfactory water solubility and low cost. 27 Compared to conventional dyes, such as N-methylmesoporphyrin IX (NMM) 28 and protoporphyrin IX (PPIX), 29 the system adopting ThT as a fluorescent probe for G-quadruplex avoids using an organic solvent to dissolve the dye.…”

Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes

“…Several methods based on circular dichroism (CD), fluorescence, NMR spectroscopy, and X‐ray crystallography techniques have provided valuable information on the structure and ligand‐binding affinities of GQs in cell‐free systems 10. Notably, FRET pair containing oligonucleotides (ONs),11 ligands,12 metal complexes,10c and fluorescent nucleobase analogues,13 which exhibit changes in their fluorescence properties upon folding, have been widely used to probe the formation and recognition properties of GQs. More recently, fluorescent GQ‐specific ligands and antibodies have been used to visualize DNA and RNA GQs in mammalian cells 14.…”