Insights into how nucleotide supplements enhance the peroxidase-mimicking DNAzyme activity of the G-quadruplex/hemin system

ATP-enhanced peroxidase-like activity of gold nanoparticles

Gold nanoparticles (AuNPs) are known to possess intrinsic biological peroxidase-like activity that has applications in development of numerous biosensors. The reactivity of the Au atoms at the surface of AuNPs is critical to the performance of such biosensors, yet little is known about the effect of biomolecules and ions on the peroxidase-like activity. In this work, the effect of ATP and other biologically relevant molecules and ions over peroxidase-like activity of AuNPs are described. Contrary to the expectation that nanoparticles exposed to biomolecules may lose the catalytic property, ATP and ADP addition enhanced the peroxidase-like activity of AuNPs. The catalytic activity was unaltered by the addition of free phosphate, sulphate and carbonate anions however, addition of ascorbic acid to the reaction mixture diminished the intrinsic peroxidase-like activity of AuNPs, even in the presence of ATP and ADP. In contrast to AuNPs, ATP did not synergize and improve the peroxidase activity of the natural peroxidase enzyme, horseradish peroxidase.

Heme activation by DNA: isoguanine pentaplexes, but not quadruplexes, bind heme and enhance its oxidative activity

Guanine-rich, single-stranded, DNAs and RNAs are able to fold to form G-quadruplexes that are held together by guanine base quartets. G-quadruplexes are known to bind ferric heme [Fe(III)-protoporphyrin IX] and to strongly activate such bound hemes toward peroxidase (1-electron oxidation) as well as oxygenase/peroxygenase (2-electron oxidation) activities. However, much remains unknown about how such activation is effected. Herein, we investigated whether G-quadruplexes were strictly required for heme activation or whether related multi-stranded DNA/RNA structures such as isoguanine (iG) quadruplexes and pentaplexes could also bind and activate heme. We found that iG-pentaplexes did indeed bind and activate heme comparably to G-quadruplexes; however, iG-quadruplexes did neither. Earlier structural and computational studies had suggested that while the geometry of backbone-unconstrained iG-quintets templated by cations such as Na(+) or NH4 (+) was planar, that of iG-quartets deviated from planarity. We hypothesize that the binding as well as activation of heme by DNA or RNA is strongly supported by the planarity of the nucleobase quartet or quintet that interacts directly with the heme.

Synthetic multivalent DNAzymes for enhanced hydrogen peroxide catalysis and sensitive colorimetric glucose detection

A peroxidase-mimic DNAzyme is a G-quadruplex (G4) DNA-hemin complex, in which the G4-DNA resembles an apoenzyme, and hemin is the cofactor for hydrogen peroxide (H2O2) catalysis. Twenty-one-mer CatG4 is a well-proven G4-DNA as well as a hemin-binding aptamer for constituting a DNAzyme. This work studied if a multivalent DNAzyme with accelerated catalysis could be constructed using a multimeric CatG4 with hemin. We compared CatG4 monomer, dimer, trimer, and tetramer, which were prepared by custom oligo synthesis, for G4 structure formation. According to circular dichroism (CD) analysis, we found that a CatG4 multimer exhibited more active G4 conformation than the sum effect of equal-number CatG4 monomers. However, the DNAzyme kinetics was not improved monotonically along with the subunit number of a multimeric CatG4. It was the trivalent DNAzyme, trimeric CatG4:hemin, resulting in the rapidest H2O2 catalysis instead of a tetravalent one. We discovered that the trivalent DNAzyme's highest catalytic rate was correlated to its most stable hemin-binding G4 structure, evidenced by CD melting temperature analysis. Finally, a trivalent DNAzyme-based colorimetric glucose assay with a detection limit as low as 10 μM was demonstrated, and this assay did not need adenosine 5'-tri-phosphate disodium salt hydrate (ATP) as a DNAzyme boosting agent.

In situ generation of electron acceptor for photoelectrochemical biosensing via hemin-mediated catalytic reaction

A novel photoelectrochemical sensing strategy is designed for DNA detection on the basis of in situ generation of an electron acceptor via the catalytic reaction of hemin toward H2O2. The photoelectrochemical platform was established by sequential assembly of near-infrared CdTe quantum dots, capture DNA, and a hemin-labeled DNA probe to form a triple-helix molecular beacon (THMB) structure on an indium tin oxide electrode. According to the highly catalytic capacity of hemin toward H2O2, a photoelectrochemical mechanism was then proposed, in which the electron acceptor of O2 was in situ-generated on the electrode surface, leading to the enhancement of the photocurrent response. The utilization of CdTe QDs can extend the absorption edge to the near-infrared band, resulting in an increase in the light-to-electricity efficiency. After introducing target DNA, the THMB structure is disassembled and releases hemin and, thus, quenches the photocurrent. Under optimized conditions, this biosensor shows high sensitivity with a linear range from 1 to 1000 pM and detection limit of 0.8 pM. Moreover, it exhibits good performance of excellent selectivity, high stability, and acceptable fabrication reproducibility. This present strategy opens an alternative avenue for photoelectrochemical signal transduction and expands the applications of hemin-based materials in photoelectrochemical biosensing and clinical diagnosis.

General peroxidase activity of a parallel G-quadruplex-hemin DNAzyme formed by Pu39WT - a mixed G-quadruplex forming sequence in the Bcl-2 P1 promoter

Background

A 39-base-pair sequence (Pu39WT) located 58 to 19 base pairs upstream of the Bcl-2 P1 promoter has been implicated in the formation of an intramolecular mixed G-quadruplex structure and is believed to play a major role in the regulation of bcl-2 transcription. However, an extensive functional exploration requires further investigation. To further exploit the structure–function relationship of the Pu39WT-hemin DNAzyme, the secondary structure and peroxidase activity of the Pu39WT-hemin complex were investigated.

Results

Experimental results showed that when Pu39WT was incubated with hemin, it formed a uniparallel G-quadruplex-hemin complex in K⁺ or Na⁺ solution, rather than a mixed hybrid without bound hemin. Also, Pu39WT-hemin showed peroxidase activity (ABTS²⁻) in the presence of H₂O₂ to produce the colored radical anion (ABTS^•-), which could then be used to determine the parameters governing the catalytic efficiency and reveal the peroxidase activity of the Pu39WT-hemin DNAzyme.

Conclusions

These results demonstrate the general peroxidase activity of Pu39WT-hemin DNAzyme, which is an intramolecular parallel G-quadruplex structure. This peroxidase activity of hemin complexed with the G-quadruplex-forming sequence in the Bcl-2 gene promoter may imply a potential mechanism of hemin-mediated cellular injury.

Surface-immobilized DNAzyme-type biocatalysis

The structure of the double helix of deoxyribonucleic acid (DNA, also called duplex-DNA) was elucidated sixty years ago by Watson, Crick, Wilkins and Franklin. Since then, DNA has continued to hold a fascination for researchers in diverse fields including medicine and nanobiotechnology. Nature has indeed excelled in diversifying the use of DNA: beyond its canonical role of repository of genetic information, DNA could also act as a nanofactory able to perform some complex catalytic tasks in an enzyme-mimicking manner. The catalytic capability of DNA was termed DNAzyme; in this context, a peculiar DNA structure, a quadruple helix also named quadruplex-DNA, has recently garnered considerable interest since its autonomous catalytic proficiency relies on its higher-order folding that makes it suitable to interact efficiently with hemin, a natural cofactor of many enzymes. Quadruplexes have thus been widely studied for their hemoprotein-like properties, chiefly peroxidase-like activity, i.e., their ability to perform hemin-mediated catalytic oxidation reactions. Recent literature is replete with applications of quadruplex-based peroxidase-mimicking DNAzyme systems. Herein, we take a further leap along the road to biochemical applications, assessing the actual efficiency of catalytic quadruplexes for the detection of picomolar levels of surface-bound analytes in an enzyme-linked immunosorbent (ELISA)-type assay. To this end, we exploit an innovative strategy based on the functionalization of DNA by a multitasking platform named RAFT (for regioselectivity addressable functionalized template), whose versatility enables the grafting of DNA whatever its nature (duplex-DNA, quadruplex-DNA, etc.). We demonstrate that the resulting biotinylated RAFT/quadruplex systems indeed acquire catalytic properties that allow for efficient luminescent detection of picomoles of surface-bound streptavidin. We also highlight some of the pitfalls that have to be faced during optimization, notably demonstrating that highly optimized experimental conditions can make DNA pre-catalysts catalytically competent whatever their secondary structures.

A portable microchip for ultrasensitive and high-throughput assay of thrombin by rolling circle amplification and hemin/G-quadruplex system

In this work, a convenient and high-throughput colorimetric assay was developed on an aptamer-modified microchip for ultrasensitive detection of thrombin using rolling circle amplification and G-quadruplex DNAzyme. This system consisted of an aptamer-modified microchip and a secondary aptamer. The secondary aptamer contained a thrombin aptamer and a primer with a G-quadruplex circular template. RCA technology was used to improve the sensitivity by producing the multiple G-quadruplex units. To generate colorimetric signal, G-quadruplex DNAzyme was used to catalyze the H2O2-mediated oxidation of 2,2'-azinobis (3-ethylbenzothiozoline)-6-sulfonic acid. At the optimal conditions, the linear range for thrombin was 0.100-50.000 pg/mL, and the limit of detection was down to 0.083 pg/mL. Moreover, the developed method was successfully applied to detect thrombin from human plasma and serum, indicating that this approach has great potential in clinical diagnosis and medical investigation.

Nucleic acid detection using G-quadruplex amplification methodologies

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.

Aptamer degradation inhibition combined with DNAzyme cascade-based signal amplification for colorimetric detection of proteins

Combining the inhibition of aptamer degradation with DNA Enzyme (DNAzyme) cascade-based signal amplification, a label-free and sensitive colorimetric protein assay strategy was proposed.

Closer to nature: an ATP-driven bioinspired catalytic oxidation process

The capability of DNA to acquire enzyme-like properties has led to the emergence of the so-called DNAzyme field; herein, we take a further leap along this nature-inspired road, demonstrating that a template assembled synthetic G-quartet (TASQ) can act as a pre-catalyst for catalytic peroxidase-mimicking oxidation reactions, whatever its nature (guanine or guanosine-based G-quartets), in an ATP-dependent manner, thereby bringing this bioinspired TASQzyme process even closer to nature.

Ionic liquid as an efficient modulator on artificial enzyme system: toward the realization of high-temperature catalytic reactions

Herein, with the aid of ionic liquid, we demonstrate for the first time that highly stable Au/SiO2 hetero-nanocomposites can serve as a robust and recyclable peroxidase mimic for realizing high-temperature catalytic reactions. Our findings pave the way to use nanomaterials for the design and development of efficient biomimetic catalysts and, more significantly, to apply ionic liquid as a positive modulator in catalytic reactions.