Nucleic acid detection using G-quadruplex amplification methodologies

Abstract

In the last decade, there has been an explosion in the use of G-quadruplex labels to detect various analytes, including DNA/RNA, proteins, metals and other metabolites. In this review, we focus on strategies for the detection of nucleic acids, using G-quadruplexes as detection labels or as enzyme labels that amplify detection signals. Methods to detect other analytes are briefly mentioned. We highlight various strategies, including split G-quadruplex, hemin-G-quadruplex conjugates, molecular beacon G-quadruplex or inhibited G-quadruplex probes. The tandem use of G-quadruplex labels with various DNA-modifying enzymes, such as polymerases (used for rolling circle amplification), exonucleases and endonucleases, is also discussed. Some of the detection modalities that are discussed in this review include fluorescence, colorimetric, chemiluminescence, and electrochemical methods.

A split G-quadruplex-based DNA nano-tweezers structure as a signal-transducing molecule for the homogeneous detection of specific nucleic acids

“…A Gq is one of the well-characterized DNAzymes that has a guanine-rich sequence and exhibits peroxidase activity with the help of hemin as a co-factor (Travascio et al, 1998;Travascio et al, 2001). Because many detection methods for peroxidase activity are available, a Gq is often used in DNA-based sensor devices as a signal generator for specific nucleic acid detection (Lu et al, 2013;Roembke et al, 2013). One approach to add target-recognition ability to a Gq is the use of a split Gq sequence.…”

Porphyrins in complex with DNA: Modes of interaction and oxidation reactions

“…Consequently, as discussed in Section 2, the formation of activated compound I-type species is certainly not optimal and high concentration of H 2 O 2 is necessary. However, electron abstraction is relatively easy to achieve (with several possible oxidative species, compound I, compound II, free radicals) and the "peroxidase" mimicking capacity of hemin/quadruplex DNA complex, with H 2 O 2 in the presence of chromogenic and fluorogenic substrates, has led to a plethora of elegant applications [139,[182][183][184][185][186][187][188]. The peroxidase reactivity remains when hemin is covalently bound to a nucleic acid vector [185].…”

“…However, electron abstraction is relatively easy to achieve (with several possible oxidative species, compound I, compound II, free radicals) and the "peroxidase" mimicking capacity of hemin/quadruplex DNA complex, with H 2 O 2 in the presence of chromogenic and fluorogenic substrates, has led to a plethora of elegant applications [139,[182][183][184][185][186][187][188]. The peroxidase reactivity remains when hemin is covalently bound to a nucleic acid vector [185]. DNA aptamers capable of recognizing heme derivatives [180] and exhibiting peroxidase activity have been first obtained through in vitro selection techniques [189][190][191].…”

Enzyme-free colorimetric detection systems based on the DNA strand displacement competition reaction

“…When iron(lll)-protoporphyrin (hemin) is present as a cofactor, DNA containing four or higher tracts of guanines can form horseradish peroxidase mimicking DNAzymes, which effectively catalyze the H 2 O 2mediated oxidation of 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) into its radical form (ABTS − ) with an obvious color change due to its absorption at 420 nm [13,19]. The past decade witnessed an explosion of the use of G-quadruplexes peroxidase as an amplifying color reporter for the detection of nucleic acids [14] and other molecules [20], including proteins, small molecules, metal ions [21], etc. In addition to the general advantages of colorimetric sensor such as visibility to naked eyes, high sensitivity and low cost, DNAzymes received special attention because they can be stored as lyophilized powders at ambient temperature, and they can be reconstituted into active enzymes by simply dissolving in buffer.…”

“…For example, aptamers can rival antibodies in terms of binding affinity, and have thus been used for target recognition for developing homogeneous assays in a solution phase [10][11][12]. For the signal transduction DNA G-quadruplexes, which were found to have the ability to enhance hemin peroxidation [13], can serve as detection labels that amplify sensing signals [14]. In the present study, we exemplify the incorporation of the two above-mentioned elements into our SDC assay, to expand the design flexibility and potential target variety of this system.…”