G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications

Abstract

Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.

Keywords: G-quadruplex; aptamers; fluorescence; microbes; nucleic acids; turn-on ligands.

Figure 1

Overview of G4 structure, detection, and application. (A) Chemical structure of a G-quartet, showing the interactions between H-bond donors and acceptors at the Watson–Crick and Hoogsteen edges. K⁺ is located at the core of G-quartet, which can provide further stabilization. (B) Parallel, anti-parallel and hybrid topologies of G4, demonstrating its polymorphism. (C) Anti- and syn- conformations of guanosine in a G-quartet that leads to wide, narrow, and medium grooves in (A). (D) Review overview. Red or purple boxes are topics that will be covered, while topics in the grey boxes were reviewed elsewhere. (see references for computational prediction [46,47], structural probing [48,49], and biophysical characterization [46,50]).

Figure 2

Schematic representation of ligand-enhanced fluorescence of G4. In the presence of ligand (top), it binds to G4 and results in enhancement in fluorescence. While in the absence of ligand (bottom), there is no such G4-ligand interaction, and hence no enhancement in fluorescence. This approach has been applied in different areas including but not limited to biosensing [72], cell imaging [51,52,73], enzymatic activity assay [74], and detecting G4 ligand inhibition of some enzymes [75,76] such as telomerase and ferrochelatase.

Figure 3

Representative applications of G-quadruplex-containing aptamers in biosensing, bioimaging and therapeutics. (A) Biosensors based on the conformational change of G-quadruplex-containing aptamers. Targets binding can destabilize/stabilize the G4 structure of aptamers and this conformational change is designed to cause signal change in the system. (B) Imaging metabolite (e.g., SAM) in living cells with fluorogenic RNA [159]. Reprinted with permission from [159]. Copyright 2012 American Association for the Advancement of Science. (C) Proposed mechanism of a photodynamic therapy strategy by using AS1411 as drug carrier to target cancer cells [160]. Reprinted with permission from [160].Copyright 2010 American Chemical Society.