G-Quadruplex-Forming Aptamers-Characteristics, Applications, and Perspectives

Abstract

G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.

Keywords: G-quadruplexes; anticoagulants; antiviral agents; aptamers; aptasensors; cancer; conjugates; diagnostics; therapeutics.

Figure 1

G-quadruplex models for some anticoagulant agents.

Figure 2

G-quadruplex models of some antiproliferative agents. (A) shows one of possible structures formed by AS1411; (B) APTA-12 aptamer, Z corresponds to gemcitabine; (C) AT11 aptamer; (D) AT11-L0 aptamer; (E) T40214 aptamer; (F) T40231 aptamer.

Figure 3

G-quadruplex models for some antiviral agents.

Figure 4

Schematic preparation of fluorescent aptasensor system for Cu²⁺ detection (top) and its application using SERS-imaging and photothermal therapy (bottom) [117]. pMBA: 4- mercaptobenzoic acid, TEOS: tetraethylorthosilicate, APTMS: (3-aminopropyl)trimethoxysilane.

Figure 5

Fluorometric approach to quantify the based on thioflavin T dye [118].

Figure 6

The Forster resonance energy transfer (FRET)-based ATP aptasensors. (a) ATP-binding oligonucleotide labeled with red quantum dots (RQDs) and gold nanorods (AuNRs), which in the presence of ATP and berberine, folds into a G4 structure. FRET process results in the quenching of RQD fluorescence and an increase of berberine fluorescence is simultaneously observed. (b) Ag- and CD-labeled ATP-binding oligonucleotide system forming the G4 structure in the presence of ATP and berberine [119].

Figure 7

Representation of the electrochemical sensor based on IGA3 aptamer (E-AB) for the detection of insulin levels [21].

Figure 8

Mechanism of thrombin aptamer beacon action: (a) Aptamer beacon in quenched stem-loop conformation, (b) unfolded conformation, (c) aptamer in G-quartet conformation, and (d) aptamer beacon with bound thrombin [125].

Figure 9

Fluorescent detection of thrombin based on BSA-Cds QDs [126].

Figure 10

The model of action of aptasensor based on TBA conjugated with fluorophores: 6-carboxytetramethylrhodamine (TAMRA) (acceptor, A) and 6-carboxyfluorescein (FAM) (donor, D). FRET occurs when the distance between D and A is sufficient– (A) and (B). When the G4 is formed because of the presence of K⁺, the phenomenon is not observed (C) [136].

Figure 11

The chemical structure of potassium-sensing oligonucleotide (a) and the mechanism of K⁺ detection (b) [137].

Figure 12

G-quadruplex models of aptamers targeted toward myelin (A and B), codeine (C) and prion protein (D).