Factors influencing the performance of G-quadruplex DNAzyme-based sensors

Diverse methods of reducing and confirming false-positive results of loop-mediated isothermal amplification assays: A review

Loop-mediated isothermal amplification (LAMP), a rapid and sensitive isothermal nucleic acid amplification method, is a promising alternative to other molecular amplification techniques due to its superior specificity and sensitivity. However, due to primer dimerization, LAMP results in nonspecific and nontemplate amplification. And during the amplification confirmation process, there is carry-over contamination. These factors can result in false-positive results that overestimate the amount of DNA, preventing accurate detection. This review outlined several techniques for reducing false-positive LAMP results before amplification and confirming false-positive results after amplification. Before the amplification step, DNA polymerase activity can be decreased with organic additives such as dimethyl sulfoxide, betaine, and pullulan to prevent nonspecific amplification. The enzyme uracil-DNA-glycosylase (UDG) can eliminate false-positive results caused by carry-over contamination, and the hot-start effect with gold nanoparticles can reduce nonspecific amplification. When confirming false-positive results using clustered regularly interspaced short palindromic repeats, guide RNA accurately detects LAMP amplification, allowing differentiation from nonspecific amplification. By confirming amplification, the colorimetric change in the deoxyribozyme (DNAzyme) formed by the reaction of the G-quadruplex sequence of the LAMP amplicon and hemin can distinguish false-positive results. Lateral flow immunoassay can distinguish false-positive results by accurately recognizing hybridized probes to LAMP amplicons.

Engineered DNAzyme Enables Homogeneous Detection of Cereulide via Polychromic Fluorescence Modality

Cereulide, the exotoxin of emetic Bacillus cereus, has garnered considerable attention due to its capacity to produce foodborne poisonings and great chemical stability. Herein, a G-quadruplex-hemin DNAzyme-based biosensor was developed to detect cereulide in the homogeneous solution. Due to the special ring structure and high affinity to K+, cereulide can be attracted and intercalated into the G-quadruplex; thus, the properties of the G4 DNAzyme can be altered. The melting temperature (Tm) of the G4 DNAzyme in the presence or absence of cereulide was 58.75 and 50.10 °C, respectively, proving the intercalation of cereulide into the G4 DNAzyme. By using the polychromic fluorescence modality of CdTe quantum dots and o-phenylenediamine to assess the variation in the catalytic activity of the DNAzyme, the intercalation of cereulide had bidirectional effects in G4 DNAzyme-mediated reactions, showing that the fluorescence intensity of CdTe quantum dots displayed a linear relationship with the concentration of cereulide from 0.16 to 40 μg/mL with the limit of detection (LOD) of 0.10 μg/mL, while the fluorescence intensity of DAP exhibited a linear relationship with the concentration of cereulide from 0.02 to 40 μg/mL with the LOD of 0.01 μg/mL. It will be a perspective step of controlling cereulide as a hazardous material in food or the environment.

Visual Assay for Methicillin-Resistant Staphylococcus aureus Based on Rolling Circular Amplification Triggering G-Quadruplex/Hemin DNAzyme Proximity Assembly

Nowadays, infections caused by methicillin-resistant Staphylococcus aureus (MRSA) have constituted a new challenge for anti-infective treatment. Precise identification and rapid clinical diagnostics of MRSA from other methicillin-sensitive strains entail assays with robust diagnostic efficiency and simple operation steps. Sensitive detection of MecA gene is promising to indicate MRSA infection, but it is challenged by the lack of isothermal and simple strategies. A visual assay based on isothermal rolling circular amplification and G-quadruplex/hemin (G4/hemin) DNAzyme proximity assembly was proposed for the immediate, efficient, and cost-effective detection of MecA in simple operation steps and in a single tube. The presence of MecA specifically drove the formation of circular templates, which further triggered isothermal amplification. The amplified product offered abundant binding sites for DNA-grafted hemin probes to form a novel proximity-assembled G4/hemin DNAzyme structure for colorimetric changing diagnosis. This tandem-repeated novel DNAzyme possessed higher catalytic activity and a lower background signal than traditional G4/hemin DNAzyme, ensuring sensitive discrimination of MRSA (limit of detection: 9.6 pM). Assay stability and antimatrix interference capability enable clinical application, which shows compared diagnostic ability with classic methods (100% sensitivity and 100% specificity) but possesses more simplified procedures and shorter turnaround time (<6 h). This colorimetric strategy in a nonsite-specific and hypersensitive manner holds foreseeable prospects in clinical diagnostic and research applications.

Highly Sensitive Biosensing Applications of a Magnetically Immobilizable Covalent G-Quadruplex-Hemin DNAzyme Catalytic System

G-quadruplex/hemin (G4/hemin) DNAzymes are biosensing systems, but their application remains limited by an overall low activity and a rather high level of unwarranted background reactions. Here, these issues were addressed through the rational design of F3T-azaC-hemin, a G4-based construct in which the hemin is covalently linked to the G4 core and its binding site flanked with a nucleotide activator, here d(T-azaC). This design led to a G4-DNAzyme whose performances have been ca. 150-fold increased compared to the parent G4-based system. The utility of F3T-azaC-hemin was demonstrated here through the ultrasensitive chemiluminescent detection of miRNA-221. The limit of detection (LOD) has been decreased to the femtomolar range, making it a new and highly efficient molecular tool in the biosensing technology field.

Sequence Effect on the Activity of DNAzyme with Covalently Attached Hemin and Their Potential Bioanalytical Application

In this work we investigated the effect of a DNA oligonucleotide sequence on the activity of a DNAzyme with covalently attached hemin. For this purpose, we synthesized seven DNA-hemin conjugates. All DNA-hemin conjugates as well as DNA/hemin complexes were characterized using circular dichroism, determination of melting temperatures and pKa of hemin. We observed that hemin conjugation in most cases led to the formation of parallel G-quadruplexes in the presence of potassium and increased thermal stability of all studied systems. Although the activity of DNA-hemin conjugates depended on the sequence used, the highest activity was observed for the DNA-hemin conjugate based on a human telomeric sequence. We used this DNAzyme for development of "sandwich" assay for detection of DNA sequence. For this assay, we used electric chip which could conduct electricity after silver deposition catalyzed by DNAzyme. This method was proved to be selective towards DNA oligonucleotides with mismatches and could be used for the detection of the target. To prove the versatility of our DNAzyme probe we also performed experiments with streptavidin-coated microplates. Our research proved that DNAzyme with covalently attached hemin can be used successfully in the development of heterogeneous assays.

A cationic copolymer as a cocatalyst for a peroxidase-mimicking heme-DNAzyme

Heme binds to a parallel-stranded G-quadruplex DNA to form a peroxidase-mimicking heme-DNAzyme. An interpolyelectrolyte complex between the heme-DNAzyme and a cationic copolymer possessing protonated amino groups was characterized and the peroxidase activity of the complex was evaluated to elucidate the effect of the polymer on the catalytic activity of the heme-DNAzyme. We found that the catalytic activity of the heme-DNAzyme is enhanced through the formation of the interpolyelectrolyte complex due to the general acid catalysis of protonated amino groups of the polymer, enhancing the formation of the iron(iv)oxo porphyrin π-cation radical intermediate known as Compound I. This finding indicates that the polymer with protonated amino groups can act as a cocatalyst for the heme-DNAzyme in the oxidation catalysis. We also found that the enhancement of the activity of the heme-DNAzyme by the polymer depends on the local heme environment such as the negative charge density in the proximity of the heme and substrate accessibility to the heme. These findings provide novel insights as to molecular design of the heme-DNAzyme for enhancing its catalytic activity.

Investigation and improvement of catalytic activity of G-quadruplex/hemin DNAzymes using designed terminal G-tetrads with deoxyadenosine caps

It is generally acknowledged that G-quadruplexes (G4s) acquire peroxidase activity upon interaction with hemin. Hemin has been demonstrated to bind selectively to the 3′-terminal G-tetrad of parallel G4s via end-stacking; however, the relationships between different terminal G-tetrads and the catalytic functions of G4/hemin DNAzymes are not fully understood. Herein, the oligonucleotide d(AGGGGA) and its three analogues, d(AG^BrG^BrGGA), d(AG^BrGGG^BrA) and d(AG^BrGG^BrGA) (G^Br indicates 8-bromo-2′-deoxyguanosine), were designed. These oligonucleotides form three parallel G4s and one antiparallel G4 without loop regions. The scaffolds had terminal G-tetrads that were either anti-deoxyguanosines (anti-dGs) or syn-deoxyguanosines (syn-dGs) at different proportions. The results showed that the parallel G4 DNAzymes exhibited 2 to 5-fold higher peroxidase activities than the antiparallel G4 DNAzyme, which is due to the absence of the 3′-terminal G-tetrad in the antiparallel G4. Furthermore, the 3′-terminal G-tetrad consisting of four anti-dGs in parallel G4s was more energetically favorable and thus more preferable for hemin stacking compared with that consisting of four syn-dGs. We further investigated the influence of 3′ and 5′ deoxyadenosine (dA) caps on the enzymatic performance by adding 3′-3′ or 5′-5′ phosphodiester bonds to AG₄A. Our data demonstrated that 3′ dA caps are versatile residues in promoting the interaction of G4s with hemin. Thus, by increasing the number of 3′ dA caps, the DNAzyme of 3′A5′-5′GG3′-3′GG5′-5′A3′ with two 5′-terminal G-tetrads can exhibit significantly high catalytic activity, which is comparable to that of 5′A3′-3′GG5′-5′GG3′-3′A5′ with two 3′-terminal G-tetrads. This study may provide insights into the catalytic mechanism of G4-based DNAzymes and strategies for promoting their catalytic activities.

Investigation of the peroxidase activities of G4/hemin DNAzymes using designed terminal G-tetrads by eliminating the steric effect of loop regions.

Improved performances of catalytic G-quadruplexes (G4-DNAzymes) via the chemical modifications of the DNA backbone to provide G-quadruplexes with double 3'-external G-quartets

Here we report on the design of a new catalytic G-quadruplex-DNA system (G4-DNAzyme) based on the modification of the DNA scaffold to provide the DNA pre-catalyst with two identical 3'-ends, known to be more catalytically proficient than the 5'-ends. To this end, we introduced a 5'-5' inversion of polarity site in the middle of the G4-forming sequences AG₄A and AG₆A to obtain d(^3'AGG^5'-^5'GGA^3') (or AG₂-G₂A) and d(^3'AGGG^5'-^5'GGGA^3') (or AG₃-G₃A) that fold into stable G4 whose tetramolecular nature was confirmed via nuclear magnetic resonance (NMR) and circular dichroism (CD) investigations. Both AG₂-G₂A and AG₃-G₃A display two identical external G-quartets (3'-ends) known to interact with the cofactor hemin with a high efficiency, making the resulting complex competent to perform hemoprotein-like catalysis (G4-DNAzyme). A systematic comparison of the performances of modified and unmodified G4s lends credence to the relevance of the modification exploited here (5'-5' inversion of polarity site), which represents a new chemical opportunity to improve the overall activity of catalytic G4s.

A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions

DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson-Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15-25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35-90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.

Catalytic Activities of Multimeric G-Quadruplex DNAzymes

G-quadruplex DNAzymes are short DNA aptamers with repeating G4 quartets bound in a non-covalent complex with hemin. These G4/Hemin structures exhibit versatile peroxidase-like catalytic activity with a wide range of potential applications in biosensing and biotechnology. Current efforts are aimed at gaining a better understanding of the molecular mechanism of DNAzyme catalysis as well as devising strategies for improving their catalytic efficiency. Multimerisation of discrete units of G-quadruplexes to form multivalent DNAzyes is an emerging design strategy aimed at enhancing the peroxidase activities of DNAzymes. While this approach holds promise of generating more active multivalent G-quadruplex DNAzymes, few examples have been studied and it is not clear what factors determine the enhancement of catalytic activities of multimeric DNAzymes. In this study, we report the design and characterisation of multimers of five G-quadruplex sequences (AS1411, Bcl-2, c-MYC, PS5.M and PS2.M). Our results show that multimerisation of G-quadruplexes that form parallel structure (AS1411, Bcl-2, c-MYC) leads to significant rate enhancements characteristic of cooperative and/or synergistic interactions between the monomeric units. In contrast, multimerisation of DNA sequences that form non-parallel structures (PS5.M and PS2.M) did not exhibit similar levels of synergistic increase in activities. These results show that design of multivalent G4/Hemin structures could lead to a new set of versatile and efficient DNAzymes with enhanced capacity to catalyse peroxidase-mimic reactions.

Precipitation SELEX: identification of DNA aptamers for calcium phosphate materials synthesis

DNA aptamers that enhance calcium phosphate mineral formation were identified using a novel precipitation SELEX method. The evolved DNA library was substantially enriched in G nucleotides and in predicted G-quadruplex structures, suggesting their importance in the mechanism of mineralization. This work could readily be extended to provide additional novel DNA aptamers for materials synthesis.

DNA G-Quadruplex-Based Assay of Enzyme Activity

DNA G-quadruplexes are special three-dimensional (3D) DNA nanostructures formed by specific G-rich DNA sequences. These 3D DNA nanostructures can bind with hemin and significantly improve the intrinsic peroxidase activity of hemin. Besides this function, they also enhance the fluorescence intensity of some G-quadruplex-specific dyes. Owing to these features, G-quadruplexes possess several superiorities in the detection of enzymes involved in nucleic acid metabolism, including facile probe fabrication without labeling, simple detection process without washing or separation steps, rapid observation by naked eyes, and easy integration with nucleic acid amplification strategies to amplify signals. Herein, we describe two strategies for label-free detection of enzyme activity based on DNA G-quadruplexes. To increase sensitivity, template-dependent and template-independent DNA amplifications were introduced for the amplification of G-rich DNA sequences. DNA methyltransferase and terminal deoxynucleotidyl transferase were detected as two model analytes, respectively.

Simple, PCR-free telomerase activity detection using G-quadruplex–hemin DNAzyme

A G-quadruplex DNAzyme-based telomerase activity detection method is developed by utilizing telomerase-triggered generation of short G-rich extension products.

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.