Contribution of potassium ion and split modes of G-quadruplex to the sensitivity and selectivity of label-free sensor toward DNA detection using fluorescence

Label-free ratiometric fluorescence detection of Pb2+via structure-specific fluorescent dyes and dual signal amplification

Lead ions (Pb2+) are a widely distributed and highly toxic heavy metal pollutant, which seriously threatens the environment, economy and human safety. Here, a label-free ratiometric fluorescent biosensor was constructed for Pb2+ detection using DNAzyme-driven target cycling and exonuclease III (Exo III)-mediated DNA cycling as a dual signal amplification strategy. The SYBR Green I (SGI) and N-methyl mesoporphyrin IX (NMM) used in this study are characterized by low cost, storage resistance, and short preparation time compared with conventional signaling probes labeled with fluorescent groups. Unlike the single-emission fluorescence strategy, monitoring the fluorescence intensity ratio of SGI and NMM can effectively reduce external interference to achieve accurate detection of Pb2+. DNAzyme structures on the surface of magnetic beads (MBs) can recognize Pb2+ and activate the target circulatory system to cleave single-stranded DNA (ssDNA). The ssDNA further initiated the Exo III-assisted DNA circulatory system to digest double-stranded DNA (dsDNA) and release guanine-rich G1. Finally, the fluorescence signals of SGI and NMM were weakened and enhanced, respectively. The sensing strategy achieved a wide linear range from 0.5 to 500 nM and a low limit of detection (LOD) of 26.4 pM. Furthermore, its anti-interference ability and potential applicability for Pb2+ detection in actual samples were verified. This work ingeniously combines the dual signal amplification strategy with the ratiometric sensing strategy constructed by structure-specific fluorescent dyes, which provides a promising method for constructing sensitive and accurate fluorescent biosensors.

Label-Free, Reusable, Equipment-Free, and Visual Detection of Hydrogen Sulfide Using a Colorimetric and Fluorescent Dual-Mode Sensing Platform

In this work, we have found for the first time that the fluorescence of rhodamine B (RhB) would be dramatically reduced after it bound to hemin/G-quadruplex and reacted with •OH. Based on this finding, we have designed a colorimetric and fluorescent dual-mode sensing platform for visual detection of hydrogen sulfide (H₂S). The constructed sensor is based on the formation of dsDNA and the G-quadruplex structure by the cytosine-Ag⁺-cytosine mismatch, causing H₂O₂-mediated catalysis to oxidize ABTS or RhB to induce a colorimetric or fluorescent change. In the presence of H₂S, the solution color for colorimetric and fluorescent assays would change from dark green to pink and from green (fluorescence off) to bright yellow (fluorescence on), respectively. This dual-mode assay showed high selectivity toward H₂S over other interference materials with a low measurable detection limit value (below than 2.5 μM), and it has been successfully applied to H₂S visual detection in real samples. Moreover, the dual-mode sensing strategy presented an excellent reutilization character both in colorimetric and fluorescent assays. This method was employed as a label-free, simple, fast, and equipment-free platform for H₂S detection with high selectivity and reusability. This work realized naked-eye detection both in colorimetric and fluorescent analysis at a lower concentration of H₂S, demonstrating a promising strategy for on-site visual detection of H₂S.

An entropy-driven signal-off DNA circuit for label-free, visual detection of small molecules with enhanced accuracy

An entropy-driven DNA circuit offers an efficient means of sensitive analyte detection with signal amplification. In this article, we rationally engineered an aptamer-based entropy-driven signal-off DNA circuit for colorimetric detection of small molecules. The proposed signal-off DNA circuit is activated by target small molecule binding to drive the collapse of G-quadruplex DNAzyme, accompanied by the colour change of the detection solution from dark blue to light blue. Entropy-driven recycling hybridization significantly magnified the input signal of the target small molecule. Such an assay enables naked-eye detection of adenosine triphosphate and oxytetracycline at concentrations as low as 0.5 μM and 1 μM respectively. Moreover, when compared with the signal-on DNA circuit, the entropy-driven signal-off DNA circuit for colorimetric detection has two advantages. Firstly, unlike in the signal-on DNA circuit, the unavoidable formation of waste complexes in the absence of a target in the signal-off DNA circuit has no influence on target detection performance as its background signal is only determined by the substrate complex. Secondly, the signal-on DNA circuit cannot distinguish false-positive signals generated by invasive catalysts (e.g., HRP, serum, Fe₃O₄), while the signal-off DNA circuit can distinguish those signals as undesired signals. Overall, the signal-off DNA circuit affords a novel strategy for sensitive and accurate detection of small molecules.

Fusion of binary split allosteric aptasensor for the ultra-sensitive and super-rapid detection of malachite green

The complicated labeling procedure and high cost of split aptasensors have hitherto limited their application in the detection of hazardous substances. Herein we report the first examples of label-free aptasensors based on the fusion of a binary split G-quadruplex and malachite green (MG) aptamer, transducing recognition events into fluorescent signals through the allosteric regulation of the aptamer to achieve selective and sensitive detection. Specifically, RNA MGA was successfully converted into DNA MGA with comparable affinity and improved stability, thereby overcoming the limitations of poor stability and high expense. We subsequently split the DNA MGA and attached them to a G-rich DNA sequence at the 5' and 3' ends, to construct the binary split allosteric aptasensor. The performance of the binary split aptasensor for MG detection was significantly improved based on proposed allosteric regulation strategy, and the reconfiguration capability of the aptamers upon binding with targets was proven, providing the binary split aptasensor with superior sensitivity and selectivity. This sensing method has a wide dynamic detection range of 5 nmol·L^-1 to 500 μmol·L^-1, with a low limit of detection (LOD) of 4.17 nmol·L^-1, and achieves the ultra-sensitive and super-rapid detection of MG. This newly proposed aptasensor is equipped with the advantages of being label-free, time saving and economical. More importantly, this successful construction of a fused aptasensor expands the principles of split aptasensor design and provides a universal platform for the detection of environmental contaminants.

Exploration of intramolecular split G-quadruplex and its analytical applications

Distinct from intermolecular split G-quadruplex (Inter-SG), intramolecular split G-quadruplex (Intra-SG) which could be generated in a DNA spacer-inserted G-quadruplex strand has not been systematically explored. Not only is it essential for the purpose of simplicity of DNA-based bioanalytical applications, but also it will give us hints how to design split G-quadruplex-based system. Herein, comprehensive information is provided about influences of spacer length and split mode on the formation of Intra-SG, how to adjust its thermodynamic stability, and selection of optimal Intra-SG for bioanalysis. For instances, non-classical Intra-SG (e.g. 2:10, 4:8 and 5:7) displays lower stability than classical split strands (3:9, 6:6 and 9:3), which is closely related to integrity of consecutive guanine tract; as compared to regular Intra-SG structures, single-thymine capped ones have reduced melting temperature, providing an effective approach to adjustment of stability. It is believed that the disclosed rules in this study will contribute to the effective application of split G-quadruplex in the field of DNA technology in the future.

Programming a split G-quadruplex in a DNA nanocage and its microRNA imaging in live cells

A novel approach to program target-responsive devices by incorporating the split G4 motifs in a DNA nanocage has been developed. The rigid prism outcompetes the flexible one in reaction kinetics and signal/background ratios, which can be easily internalized by cells and successfully applied in microRNA imaging in live cells.

Label-Free, Visual Detection of Small Molecules Using Highly Target-Responsive Multimodule Split Aptamer Constructs

Colorimetric aptamer-based sensors offer a simple means of on-site or point-of-care analyte detection. However, these sensors are largely incapable of achieving naked-eye detection, because of the poor performance of the target-recognition and signal-reporting elements employed. To address this problem, we report a generalizable strategy for engineering novel multimodule split DNA constructs termed "CBSAzymes" that utilize a cooperative binding split aptamer (CBSA) as a highly target-responsive bioreceptor and a new, highly active split DNAzyme as an efficient signal reporter. CBSAzymes consist of two fragments that remain separate in the absence of target, but effectively assemble in the presence of the target to form a complex that catalyzes the oxidation of 2,2'-azino-bis(3-ethylbenzthiazoline)-6-sulfonic acid, developing a dark green color within 5 min. Such assay enables rapid, sensitive, and visual detection of small molecules, which has not been achieved with any previously reported split-aptamer-DNAzyme conjugates. In an initial demonstration, we generate a cocaine-binding CBSAzyme that enables naked-eye detection of cocaine at concentrations as low as 10 μM. Notably, CBSAzyme engineering is straightforward and generalizable. We demonstrate this by developing a methylenedioxypyrovalerone (MDPV)-binding CBSAzyme for visual detection of MDPV and 10 other synthetic cathinones at low micromolar concentrations, even in biological samples. Given that CBSAzyme-based assays are simple, label-free, rapid, robust, and instrument-free, we believe that such assays should be readily applicable for on-site visual detection of various important small molecules such as illicit drugs, medical biomarkers, and toxins in various sample matrices.

Primer remodeling amplification-activated multisite-catalytic hairpin assembly enabling the concurrent formation of Y-shaped DNA nanotorches for the fluorescence assay of ochratoxin A

DNA can be configured into unique high-order structures due to its significantly high programmability, such as a three-way junction-based structure (denoted Y-shaped DNA), for further applications. Herein, we report a label-free fluorescent signal-on biosensor based on the target-driven primer remodeling rolling circle amplification (RCA)-activated multisite-catalytic hairpin assembly (CHA) enabling the concurrent formation of Y-shaped DNA nanotorches (Y-DNTs) for ultrasensitive detection of ochratoxin A (OTA). Two kinds of masterfully-designed probes, termed Complex I and II, were pre-prepared by the combination of a circular template (CT) with an OTA aptamer (S1), a substrate probe (S2) and hairpin probe 1 (HP1), respectively. Target OTA specifically binds to Complex I, resulting in the release of the remnant element in S2 and successive remodeling into a mature primer for RCA by phi29 DNA polymerase, thus a usable primer-CT complex is produced, which actuates primary RCA. Then, numerous Complex II probes can anneal with the first-generation RCA product (RP) with multiple sites to activate the CHA process. With the participation of endonuclease IV (Endo IV) and phi29, HP1 as a pre-primer containing a tetrahydrofuran abasic site mimic (AP site) in Complex II is converted into a mature primer to initiate additional rounds of RCA. So, countless Y-DNTs are formed concurrently containing a G-quadruplex structure that enables the N-methylmesoporphyrin IX (NMM) to be embedded, generating remarkably strong fluorescence signals. The biosensor was demonstrated to enable rapid and accurate highly efficient and selective detection of OTA with an improved detection limit of as low as 0.0002 ng mL^-1 and a widened dynamic range of over 4 orders of magnitude. Meanwhile, this method was proven to be capable of being used to analyze actual samples. Therefore, this proposed strategy may be established as a useful and practical platform for the ultrasensitive detection of mycotoxins in food safety testing.

A single-bead telomere sensor based on fluorescence resonance energy transfer

We present a 200 nm in-diameter single-bead sensor for the detection of single, unlabeled DNA molecules in solution using fluorescence resonance energy transfer technology. DNA-bound Alexa 488 and Crimson 625 loaded on commercial beads served as the donor and acceptor, respectively. Binding of the target DNA to the single bead sensor induces G-quadruplex stretching, resulting in a decrease in fluorescence energy transfer. G-rich telomere sequences formed a G-quadruplex structure in the presence of ZnTCPP, as demonstrated by the detection of two strong donor and acceptor signals. The sensitivity of the sensor was 1 fM. Under optimized conditions using a polydimethylsiloxane microfluidic device, we measured the number of sensor beads by direct counting. By controlling the flow rate via the probe volume, one sensing experiment can be completed in 5 minutes. Based on these results, we propose a new parameter-dependability (RS)-as a quantitative measure to judge the quality of a bio-sensor. This parameter is based on the ratio of the sensor and sensing sample fluorescence signals. This parameter can range from 0.1 to 100, where a value of 10 represents an optimized bio-sensor.

How to split a G-quadruplex for DNA detection: new insight into the formation of DNA split G-quadruplex

Here, we get a new insight into the formation of a split G-quadruplex from the viewpoints of the split mode and guanine base number. An unusual result is that the split mode 4 : 8 performed best in six split modes, including the frequently used mode 1 : 3 and 2 : 2 in the split G-quadruplex enhanced fluorescence assay. Circular dichroism spectra verified the conclusion. The application of the split G-quadruplex based assay in DNA detection was performed on the point mutations of the JAK2 V617F and HBB genes. A multi-target analysis method based on a pool of G-segments split from T30695 (GGGTGGGTGGGTGGGT) by the magic "law of 4 : 8" was established.

Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems

This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.

Quadruplex priming amplification for the detection of mRNA from surrogate patient samples

Simple and rapid methods for detecting mRNA biomarkers from patient samples are valuable in settings with limited access to laboratory resources. In this report, we describe the development and evaluation of a self-contained assay to extract and quantify mRNA biomarkers from complex samples using a novel nucleic acid-based molecular sensor called quadruplex priming amplification (QPA). QPA is a simple and robust isothermal nucleic acid amplification method that exploits the stability of the G-quadruplex nucleotide structure to drive spontaneous strand melting from a specific DNA template sequence. Quantification of mRNA was enabled by integrating QPA with a magnetic bead-based extraction method using an mRNA-QPA interface reagent. The assay was found to maintain >90% of the maximum signal over a 4 °C range of operational temperatures (64-68 °C). QPA had a dynamic range spanning four orders of magnitude, with a limit of detection of ~20 pM template molecules using a highly controlled heating and optical system and a limit of detection of ~250 pM using a less optimal water bath and plate reader. These results demonstrate that this integrated approach has potential as a simple and effective mRNA biomarker extraction and detection assay for use in limited resource settings.

Four-way junction-driven DNA strand displacement and its application in building majority logic circuit

We introduced a four-way DNA junction-driven toehold-mediated strand displacement method. Separation of the different functional domains on different strands in the four-way junction structure and usage of glue strand to recombine them for different logic gates make the design more flexible. On the basis of this mechanism, a majority logic circuit fabricated by DNA strands was designed and constructed by assembling three AND gates and one OR gate together. The output strand drew the G-rich segments together to form a split G-quadruplex, which could specifically bind PPIX and enhance its fluorescence. Just like a poll with three voters, the high fluorescence signal would be given off only when two or three voters vote in favor. Upon slight modification, the majority circuit was utilized to select the composite number from 0 to 9 represented by excess-three code. It is a successful attempt to integrate the logic gates into a circuit and to achieve desired functions.

Inhibition of G-quadruplex assembling by DNA ligation: a versatile and non-covalent labeling strategy for bioanalysis

Through tuning relative thermodynamic stabilities (I, II and III), DNA ligation was coupled to split G-quadruplex probes and a versatile, non-covalent labelling and fluorescent strategy was constructed based on inhibition of template-directed G-quadruplex assembling by ligation reaction. The non-covalent complex between G-quadruplex and fluorescent probe was employed as signalling label and thus covalent modification of DNA probes with fluorescent probes was avoided. Selective detection of small biomolecules (ATP and NAD(+)) in the nanomolar range was realized due to the cofactor-dependent activity of DNA ligases (T4 and Escherichia coli DNA ligase). By virtue of the simple strategy, the effect of mismatch position of single-base mismatched template DNA on the ligation efficiency was validated. Meanwhile, highly mismatch-influenced ligation efficiency of ligase endows the cost-effective strategy great potential for single-nucleotide polymorphism (SNP) analysis. The non-covalent labeling strategy provides a versatile and cost-effective platform for monitor of DNA ligation, cofactor detection, SNP analysis and other ligase-based assays.

A visible multi-digit DNA keypad lock based on split G-quadruplex DNAzyme and silver microspheres

A novel visible multi-digit DNA keypad lock system was fabricated based on split G-quadruplex DNAzyme and silver microspheres. The final result of the keypad lock can be easily recognized by the naked eye and the number of inputs for the keypad lock can be flexibly adjusted. This molecular platform showed excellent scalability and flexibility.

Enzyme-free unlabeled DNA logic circuits based on toehold-mediated strand displacement and split G-quadruplex enhanced fluorescence

Adopting fluorescence of PPIX enhanced by a split G-quadruplex and toehold mediated strand displacement reaction, a series of unlabeled fluorescent logic gates is set up and some of them are cascaded into circuits. Controlled release of PPIX, which is also a photosensitizer in photodynamic diagnosis and therapy, is realized by this circuit, making it a wise choice for DNA computing.

Highly sensitive detection of microRNAs based on isothermal exponential amplification-assisted generation of catalytic G-quadruplex DNAzyme

It is well-known that microRNAs (miRNAs) have become an ideal class of biomarker candidates for clinical diagnosis of cancers, thus sensitive and selective detection of microRNAs is of great significance in understanding biological functions of miRNAs, early-phase diagnosis of cancers, as well as discovery of new targets for drugs. In this work, we have developed a sensitive method for microRNAs detection based on isothermal exponential amplification-assisted generation of catalytic G-quadruplex DNAzyme, and demonstrated its practical application in biological sample of cell lysate. The assay involves a combination of polymerase strand extension, single-strand nicking and catalytic reaction of G-quadruplex/hemin complex. It is designed such that, the target miRNA initiates the efficient synthesis of two kinds of short oligonucleotide fragments in the continuous cycle of the polymerization, nicking and displacement reactions, by means of thermostable polymerase and nicking endonuclease. One fragment has the same sequence as the target miRNA, except that the deoxyribonucleotides and thymine replace the ribonucleotides and uridine in the miRNA, to activate new cyclic chain reactions of polymerization, nicking and displacement reactions as the target miRNA. The other is the signal molecule of horseradish peroxidase (HRP)-mimicking G-quadruplex DNAzyme. With such designed signal amplification processes, the proposed assay showed a quantitative analysis of sequence-specific miRNAs in a wide range from 1 fM to 100 nM with a low detection limit of 1 fM. Moreover, this assay demonstrated excellent differentiation ability for the mismatch miRNAs targets and good performance in biological samples.