Universal Dynamic DNA Assembly-Programmed Surface Hybridization Effect for Single-Step, Reusable, and Amplified Electrochemical Nucleic Acid Biosensing

Recent advances in electrochemical proximity ligation assay

Proximity ligation assay (PLA) is a vigorously developed homogeneous immunoassay assisted by DNA combining dual recognition of target protein by pairs of proximity probes, in which the detection of protein is tactfully converted to the detection of DNA. The booming developments in PLA have enabled a variety of ultrasensitive assays for the detection of protein and this concept of PLA is also extended to the detection of nucleic acids and some small molecule. The association between PLA and electrochemical method, defined as electrochemical proximity ligation assay (ECPLA), has gained much interests in disease diagnosis, food safety and environmental assays with the advantages, such as broad range of targets, simplicity, low cost and rapid response. In this review, we took a different perspective to present the history of PLA, the classical ECPLA biosensing methodology as well as the developments of ECPLA based on several key parameters, such as sensitivity, selectivity, reusability and generalization. In addition, the developments of PLA with electrochemiluminescence as readout are also presented. Finally, perspective and some unresolved challenges in ECPLA that can potentially be addressed have also been discussed.

Ionic Strength and Hybridization Position near Gold Electrodes Can Significantly Improve Kinetics in DNA-Based Electrochemical Sensors

A variety of electrochemical (EC) biosensors play critical roles in disease diagnostics. More recently, DNA-based EC sensors have been established as promising for detecting a wide range of analyte classes. Since most of these sensors rely on the high specificity of DNA hybridization for analyte binding or structural control, it is crucial to understand the kinetics of hybridization at the electrode surface. In this work, we have used methylene blue-labeled DNA strands to monitor the kinetics of DNA hybridization at the electrode surface with square-wave voltammetry. By varying the position of the double-stranded DNA segment relative to the electrode surface as well as the bulk solution's ionic strength (0.125-1.00 M), we observed significant interferences with DNA hybridization closer to the surface, with more substantial interference at lower ionic strength. As a demonstration of the effect, toehold-mediated strand displacement reactions were slowed and diminished close to the surface, while strategic placement of the DNA binding site improved reaction rates and yields. This work manifests that both the salt concentration and DNA hybridization site relative to the electrode are important factors to consider when designing DNA-based EC sensors that measure hybridization directly at the electrode surface.

Programmable mismatch-fueled high-efficiency DNA signal amplifier

Herein, by introducing mismatches, a high-efficiency mismatch-fueled catalytic multiple-arm DNA junction assembly (M-CMDJA) with high-reactivity and a high-threshold is developed as a programmable DNA signal amplifier for rapid detection and ultrasensitive intracellular imaging of miRNA. Compared with traditional nucleic acid signal amplification (NASA) with a perfect complement, the M-CMDJA possesses larger kinetic and thermodynamic favorability owing to the more negative reaction standard free energy (ΔG) as driving force, resulting in much higher efficiency and rates. Once traces of the input initiator react with the mismatched substrate DNA, it could be converted into amounts of output multiple-arm DNA junctions via the M-CMDJA as the functional DNA conversion nanodevice. Impressively, the mismatch-fueled catalytic four-arm DNA junction assembly (M-CFDJA) exhibits high conversion efficiency up to 1.05 × 108 in 30 min, which is almost ten times more than those of conventional methods. Therefore, the M-CMDJA could easily address the challenges of traditional methods: slow rates and low efficiency. In application, the M-CFDJA as a DNA signal amplifier was successfully used to develop a biosensing platform for rapid miRNA detection with a LOD of 6.11 aM and the ultrasensitive intracellular imaging of miRNA, providing a basis for the next-generation of versatile DNA signal amplification methods for ultimate applications in DNA nanobiotechnology, biosensing assay, and clinical diagnoses.

Programmable High-Speed and Hyper-Efficiency DNA Signal Magnifier

Herein, a programmable dual-catalyst hairpin assembly (DCHA) for realizing the synchronous recycle of two catalysts is developed, displaying high reaction rate and outstanding conversion efficiency beyond traditional nucleic acid signal amplifications (NASA). Once catalyst I interacts with the catalyst II, the DCHA can be triggered to realize the simultaneous recycle of catalysts I and II to keep the highly concentrated intermediate product duplex I-II instead of the steadily decreased one in typical NASA, which can accomplish in about only 16 min and achieves the outstanding conversion efficiency up to 4.54 × 108 , easily conquering the main predicaments of NASA: time-consuming and low-efficiency. As a proof of the concept, the proposed DCHA as a high-speed and hyper-efficiency DNA signal magnifier is successfully applied in the rapid and ultrasensitive detection of miRNA-21 in cancer cell lysates, which exploits the new generation of universal strategy for the applications in biosensing assay, clinic diagnose, and DNA nanobiotechnology.

Target-directed enzyme-free dual-amplification DNA circuit for rapid signal amplification

Dynamic DNA circuits have shown promising potential for amplified biosensing and bioengineering applications at the molecular level. Here, an enzyme-free, single-step and rapid signal amplification DNA circuit was developed by integrating target-directed entropy-driven catalysis (EDC) and hybridization chain reaction (HCR) for analysis of nucleic acids and small molecules. The target catalyzes the self-assembly of the EDC premade substrate complex and fuel strands to release the hidden amplicon trigger (T), which was encoded with trigger sequences for the downstream HCR circuit. The released T could motivate the successive cross-opening of HCR hairpins yielding long DNA nanowires and generated tremendously amplified fluorescence signals. Notably, this EDC-HCR circuit was driven by entropy without the requirement of any enzymes, thus greatly reducing the cost. The design of the hidden amplicon trigger (T) avoided the production of waste by-products and improved the reaction rate. Furthermore, as a modular circuit, we also demonstrated that our EDC-HCR cascade sensing system could be used as a versatile sensing platform for the highly sensitive and selective detection of other analysts, e.g. ATP in serum samples, through simply programming the reorganization sequences of the initiator. Therefore, the flexible and versatile EDC-HCR platform holds great potential in the fields of clinical diagnosis and biochemical analysis.

An Integral Recognition and Signaling for Electrochemical Assay of Protein Kinase Activity and Inhibitor by Reduced Graphene Oxide-Polydopamine-Silver Nanoparticle-Ti4+ Nanocomposite

A novel electrochemical biosensing method for protein kinase (PKA) activity was demonstrated by using a reduced graphene oxide-polydopamine-silver nanoparticle-Ti4+ (rGO-PDA-AgNPs-Ti4+) nanocomposite. The obtained nanocomposite possessed an integral capability for phosphopeptide recognition and signal readout. The polydopamine modified reduced graphene oxide (rGO-PDA) was firstly prepared based on a self-polymerization method of dopamine. The silver ions were adsorbed onto polydopamine (PDA) layer and directly reduced into silver nanoparticles (AgNPs), which was used for electrochemical signal reporting. Then, the Ti4+ cations were attached onto the PDA layer for phosphopeptide recognition according to the strong coordination ability of PDA with Ti4+ and phosphate group. The prepared rGO-PDA-AgNPs-Ti4+ nanocomposites were characterized with different methods. The developed rGO-PDA-AgNPs-Ti4+ nanocomposites were then employed for electrochemical analysis of PKA-catalyzed kemptide phosphorylation. The sensitive detection toward PKA activity was realized with an experimental detection limit of about 0.01 U/mL. It may be also extended for the inhibitor evaluation. Thus, it provided a facile and sensitive means for electrochemical analysis of PKA activity and inhibitor screening.

Integrated Micropillar Polydimethylsiloxane Accurate CRISPR Detection System for Viral DNA Sensing

A fully Integrated Micropillar Polydimethylsiloxane Accurate CRISPR deTection (IMPACT) system is developed for viral DNA detection. This powerful system is patterned with high-aspect-ratio micropillars to enhance reporter probe binding. After surface modification and probe immobilization, the CRISPR-Cas12a/crRNA complex is injected into the fully enclosed microchannel. With the presence of a double-stranded DNA target, the CRISPR enzyme is activated and denatures the single-stranded DNA reporters from the micropillars. This collateral cleavage releases fluorescence reporters into the assay, and the intensity is linearly proportional to the target DNA concentration ranging from 0.1 to 10 nM. Importantly, this system does not rely on the traditional dye-quencher-labeled probe, thus reducing the fluorescence background presented in the assay. Furthermore, our one-step detection protocol is performed on-chip at isothermal conditions (37 °C) without using complicated and time-consuming off-chip probe hybridization and denaturation. This miniaturized and fully packed IMPACT chip demonstrates sensitive and accurate DNA detection within 120 min and paves ways to the next-generation point-of-care diagnostics, responding to emerging and deadly pathogen outbreaks.

Ultrasensitive Electrochemical DNA Biosensor Fabrication by Coupling an Integral Multifunctional Zirconia-Reduced Graphene Oxide-Thionine Nanocomposite and Exonuclease I-Assisted Cleavage

In this work, a simple but sensitive electrochemical DNA biosensor for nucleic acid detection was developed by taking advantage of exonuclease (Exo) I-assisted cleavage for background reduction and zirconia-reduced graphene oxide-thionine (ZrO2-rGO-Thi) nanocomposite for integral DNA recognition, signal amplification, and reporting. The ZrO2-rGO nanocomposite was obtained by a one-step hydrothermal synthesis method. Then, thionine was adsorbed onto the rGO surface, via π-π stacking, as an excellent electrochemical probe. The biosensor fabrication is very simple, with probe DNA immobilization and hybridization recognition with the target nucleic acid. Then, the ZrO2-rGO-Thi nanocomposite was captured onto an electrode via the multicoordinative interaction of ZrO2 with the phosphate group on the DNA skeleton. The adsorbed abundant thionine molecules onto the ZrO2-rGO nanocomposite facilitated an amplified electrochemical response related with the target DNA. Since upon the interaction of the ZrO2-rGO-Thi nanocomposite with the probe DNA an immobilized electrode may also occur, an Exo I-assisted cleavage was combined to remove the unhybridized probe DNA for background reduction. With the current proposed strategy, the target DNA related with P53 gene could be sensitively assayed, with a wide linear detection range from 100 fM to 10 nM and an attractive low detection limit of 24 fM. Also, the developed DNA biosensor could differentiate the mismatched targets from complementary target DNA. Therefore, it offers a simple but effective biosensor fabrication strategy and is anticipated to show potential for applications in bioanalysis and medical diagnosis.

Construction of an ultrasensitive electrochemical sensing platform for microRNA-21 based on interface impedance spectroscopy

A hybridization chain reaction (HCR) amplification-based electrochemical impedimetric biosensor is fabricated for the quick, sensitive, and specific detection of miRNA-21 (miR-21) via monitoring of electrode interfacial property changes in real-time. Two sequences of H1 and H2 are adopted to trigger HCR amplification. A large amount of linear DNA concatemer are formed which could change the interfacial properties of the electrode. Interfacial charge transfer resistance difference (R_ct) is probed via electrochemical impedance spectroscopy (EIS) and Randles equivalent circuit. After amplifying via HCR, oligonucleotides with negatively charged repelling [Fe(CN)₆]^3-/4- ions can form a spatial blockage. HCR amplification strategy markedly enhanced the electrochemical signal with a limit of detection (LOD) down to 4.63 fM (S/N = 3). This strategy exhibited excellent selectivity for three different miRNAs: miR-199a, miR-141, and miR-155. Moreover, results show that the proposed method can be applied to miR-21 detection in the total RNA extracted from five cells. This work presents an enzyme-free and label-free EIS nucleic acid sensor for sensitively and selectively detecting miR-21, offering a promising approach in early diseases diagnosis.

Nanotechnology and nanomaterial-based no-wash electrochemical biosensors: from design to application

Nanotechnology and nanomaterial based electrochemical biosensors (ECBs) have achieved great development in many fields, such as clinical diagnosis, food analysis, and environmental monitoring. Nowadays, the single-handed pursuit of sensitivity and accuracy cannot meet the demands of detection in many in situ and point-of-care (POC) circumstances. More and more attention has been focused on simplifying the operation procedure and reducing detection time, and thus no-wash assay has become one of the most effective ways for the continuous development of ECBs. However, there are many challenges to realize no-wash detection in the real analysis, such as redox interferences, multiple impurities, non-conducting protein macromolecules, etc. Furthermore, the complex detection circumstance in different application fields makes the realization of no-wash ECBs more complicated and difficult. Thanks to the updated nanotechnology and nanomaterials, in-depth analysis of the obstacles in the detection process and various methods for fabricating no-wash ECBs, most issues have been largely resolved. In this review, we have systematically analyzed the nanomaterial based design strategy of the state-of-the-art no-wash ECBs in the past few years. Following that, we summarized the challenges in the detection process of no-wash ECBs and their applications in different fields. Finally, based on the summary and analysis in this review, we also evaluated and discussed future prospects from the design to the application of ECBs.

Programmable mismatch-fueled high-efficiency DNA signal converter

Herein, by directly introducing mismatched reactant DNA, high-reactivity and high-threshold enzyme-free target recycling amplification (EFTRA) is explored. The developed high-efficiency EFTRA (HEEFTRA) was applied as a programmable DNA signal converter, possessing higher conversion efficiency than the traditional one with perfect complement owing to the more negative reaction standard free energy (ΔG). Once traces of input target miRNA interact with the mismatched reactant DNA, amounts of ferrocene (Fc)-labeled output DNA could be converted via the EFTRA. Impressively, the Fc-labeled output DNA could be easily captured by the DNA tetrahedron nanoprobes (DTNPs) on the electrode surface to form triplex-forming oligonucleotide (TFO) at pH = 7.0 for sensitive electrochemical signal generation and the DTNPs could be regenerated at pH = 10.0, from which the conversion efficiency (N) will be accurately obtained, benefiting the selection of suitable mismatched bases to obtain high-efficiency EFTRA (HEEFTRA). As a proof of concept, the HEEFTRA as an evolved DNA signal converter is successfully applied for the ultrasensitive detection of miRNA-21, which gives impetus to the design of other signal converters with excellent efficiency for ultimate applications in sensing analysis, clinical diagnosis, and other areas.

Homogeneous Electrochemiluminescence Biosensor for the Detection of RNase A Activity and Its Inhibitor

Ribonuclease A (RNase A) is increasingly considered as a biomarker for tumor diagnosis, and it is of great significance to develop an ultrasensitive, cost-effective assay for RNase A detection. Electrochemiluminescence (ECL) technology has distinctive advantages in the development of biosensors for diverse targets. However, most of the ECL biosensors require the complex process of electrode modification, which is laborious and time consuming. In this work, an immobilization-free homogeneous ECL assay was developed for the highly sensitive detection of RNase A activity for the first time. On the basis of the fact that RNase A can specifically hydrolyze RNA at the site of ribonucleotide uracil (rU), a rU-containing chimeric DNA probe is designed and labeled with Ru(bpy)₃²⁺ (act as ECL indicator). The chimeric DNA probe hardly diffuses to the surface of negatively charged indium tin oxide (ITO) electrode due to the strong electrostatic repulsion between the negatively charged DNA and ITO electrode, resulting in a weak ECL signal detected. When the RNase A is present, the chimeric DNA probe is hydrolyzed into small fragments, which contains little negative charge and can diffuse easily to the ITO electrode surface due to the decreased electrostatic repulsion. In this case, an enhanced ECL signal can be detected. Under the optimal conditions, there is a linear relationship between the ECL signal and the concentration of RNase A in the range of 0.001-0.10 ng/mL, and the detection limit is 0.2 pg/mL. In addition, the proposed ECL sensing system is also applied to detect the RNase A inhibitor, taking As³⁺ as an example. The proposed homogeneous ECL sensing system provides a new approach for the highly sensitive and convenient detection of RNase A as well as other ribonucleases only by redesigning a responding chimeric DNA probe.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.

A dynamic, ultra-sensitive and "turn-on" strategy for fluorescent detection of uranyl based on DNAzyme and entropy-driven amplification initiated circular cleavage amplification

A uranyl detection strategy with ultra-sensitivity was developed based on entropy-driven amplification and DNAzyme circular cleavage amplification. The cleavage of UO₂²⁺-specific DNAzyme produces a DNA fragment to initiate the entropy-driven amplification. Two DNA sequences released from the entropy-driven amplification are partly complementary. They can form an entire enzyme strand (E-DNA) of Mg²⁺-specific DNAzyme. The formed E-DNA can circularly cleave FAM-labeled probes on gold nanoparticles (AuNPs), causing the leaving of FAM from AuNPs and recovery of fluorescent signal. A linear relationship was obtained in the range from 30 pM to 5 nM between fluorescence intensity and concentration of UO₂²⁺. The limit of detection was low to 13 pM. This method showed a promising future for practical application in real water samples.

Application of hairpin DNA-based biosensors with various signal amplification strategies in clinical diagnosis

Biosensors have been commonly used in biomedical diagnostic tools in recent years, because of a wide range of application, such as point-of-care monitoring of treatment and disease progression, drug discovery, commonly use food control, environmental monitoring and biomedical research. Additionally, development of DNA biosensors has been increased enormously over the past few years as confirmed by the large number of scientific publications in this field. A wide range of techniques can be used for the development of DNA biosensors, such as DNA nano-machines and various signal amplification strategies. This article selectively reviews the recent advances in DNA base biosensors with various signal amplification strategies for detection of cancer DNA and microRNA, infectious microorganisms, and toxic metal ions.

Engineering high-performance hairpin stacking circuits for logic gate operation and highly sensitive biosensing assay of microRNA

Recently, hairpin stacking circuits (HSC) based on toehold-mediated strand displacement have been engineered to detect nucleic acids and proteins. However, the three metastable hairpins in a HSC system can potentially react non-specifically in the absence of a catalyst, limiting its practical application. Here, we developed a unique hairpin design guideline to eliminate circuit leakage of HSC, and the high-performance HSC was successfully implemented on logic gate building and biosensing. We began by analyzing the sources of circuit leakage and optimizing the toehold lengths of hairpins in the HSC system based on the surface plasmon resonance (SPR) technique. Next, a novel strategy of substituting two nucleotides in a specific domain, termed 'loop-domain substitution', was introduced to eliminate leakages. We also systematically altered the positions and numbers of the introduced substitutions to probe their potential contribution to circuit leakage suppression. Through these efforts, the circuit leakage of HSC was significantly reduced. Finally, by designing different DNA input strands, the logic gates could be activated to achieve the output signal. Using miRNA as a model analyte, this strategy could detect miRNA down to pM levels with minimized circuit leakage. We believe these work indicate significant progress in the DNA circuitry.

DNA-fueled target recycling-induced two-leg DNA walker for amplified electrochemical detection of nucleic acid

Taking advantage of the homogeneous and heterogeneous electrochemical biosensors, a simple, sensitive, and selective electrochemical biosensor is constructed by combining entropy-driven amplification (EDA) with DNA walker. This electrochemical biosensor realizes the biorecognition and EDA operation in homogeneous solution, which is beneficial to improve the recognition and amplification efficiency. A two-leg DNA walker generated by EDA can walk on the surface of gold electrode for cleaving the immobilized substrate DNA and releasing the electroactive labels, giving rise to a significant decrease of the electrochemical signal. The immobilization of the electroactive labels ensures the reproducibility and reliability of the biosensor. The present cascade amplification assay can be applied to detect target DNA with a detection limit of 0.29 fM, and base mutations can be easily distinguished. Moreover, the proposed electrochemical biosensor shows a satisfactory performance for the detection of target DNA in human serum. Thus, the novel electrochemical biosensor holds promising potential for a future application in disease diagnosis.

Ultrasensitive detection of prostate specific antigen by electrochemical aptasensor using enzyme-free recycling amplification via target-induced catalytic hairpin assembly

Based on the target-induced catalytic hairpin assembly and bimetallic catalyst, the enzyme-free recycling amplification strategy for sensitive detection of prostate specific antigen (PSA) has been designed. The aptamer and its complementary DNA (C-apt) are modified on the magnetic particles. The aptamer-PSA binding event can release the C-apt that triggers the catalytic assembly between hairpin capture DNA and hairpin help DNA. Then the catalytic hairpin assembly leads to cyclic reuse the C-apt and the generation of many opened hairpin capture DNA, which can associate with the prepared Au/Pt-polymethylene blue (PMB) probes to yield electrochemical signal. Meanwhile, the Au/Pt-PMB probes exhibit excellent electrocatalytic ability for H₂O₂ to magnify the response current. The designed sensor possesses a wide dynamic range of 10fgmL^-1 to 100ngmL^-1 and ultra-low detection limit of 2.3fgmL^-1. The present method has good performance in real serum sample analysis. This strategy is promising to be extended to provide a highly sensitive platform for various target analytes.

Label-Free Photoelectrochemical "Off-On" Platform Coupled with G-Wire-Enhanced Strategy for Highly Sensitive MicroRNA Sensing in Cancer Cells

MicroRNA (miRNAs) quantification, especially at low abundance, is vital for disease diagnosis, prognosis, and therapy. Herein we develop a distinctive label-free "off-on" configuration for photoelectrochemical (PEC) sensing platform fabrication, coupled with DNA four-way junction (4J) architecture as well as G-wire superstructure for signal amplification. In addition, ultrathin copper phosphate nanosheets (CuPi NSs) coating Au nanoparticles (Au-CuPi NSs) serve as a highly efficient photocathode substrate. To improve the sensitivity, and avoid the false positive signals, the quencher, gold nanoparticles (GNPs), is utilized to switch off the PEC signal because of the commendable surface plasmon resonance (SPR) absorption. Subsequently, ingenious DNA 4J architecture is applied to export proportional c-myc regions for target quantification. Assisted with the G-wire superstructure formation, the enhancer 5,10,15,20-tetra(4-sulfophenyl)-21H,23H-porphyrin (TSPP) is coupled on the substrate to switch on the PEC signal, thus realizing the miRNA assay with persuasive accuracy, high sensitivity, and low detection limit. In addition, we execute the miRNA detection in prostate carcinoma cell line 22Rv1, and acquire desirable quantitative capability. Remarkably, the prepared PEC sensing platform not only realizes the highly efficient miRNAs quantification, but also uncovers a marvelous horizon for sensing platform fabrication.

Ferrocene conjugated oligonucleotide for electrochemical detection of DNA base mismatch

We describe the synthesis, binding, and electrochemical properties of ferrocene-conjugated oligonucleotides (Fc-oligos). The key step for the preparation of Fc-oligos contains the coupling of vinylferrocene to 5-iododeoxyuridine via Heck reaction. The Fc-conjugated deoxyuridine phosphoramidite was used in the Fc-oligonucleotide synthesis. We show that thiol-modified Fc-oligos deposited onto gold electrodes possess potential ability in electrochemical detection of DNA base mismatch.