Highly Efficient Quadruped DNA Walker Guided by Ordered DNA Tracks for Rapid and Ultrasensitive Electrochemical Detection of miRNA-21

An electrochemical biosensor equipped with a logic circuit as a smart automaton for two-miRNA pattern detection

Detecting multiple targets in complex cellular and biological environments yields more reliable results than single-label assays. Here, we introduced an electrochemical biosensor equipped with computing functions, acting as a smart automaton to enable computing-based detection. By defining the logic combinations of miR-21 and miR-122 as detection patterns, we proposed the corresponding AND and OR detection automata. In both logic gate modes, miR-21 and miR-122 could be replaced with single-stranded FO or FA, modified with Fc, binding to the S chain on the electrode surface. This process led to a significant decrease in the square wave voltammetry (SWV) of Fc on the same sensing platform, as numerous ferrocene (Fc)-tagged DNA fragments escaped from the electrode surface. Experimental results indicated that both automata efficiently and sensitively detected the presence of the two targets. This strategy highlighted how a small amount of target could generate a large current signal decrease in the logic automata, significantly reducing the detection limit for monitoring low-abundance targets. Moreover, the short-stranded DNA components of the detection automata exhibited a simple composition and easy programmability of probe sequences, offering an innovative detection mode. This simplified the complex process of detection, data collection, computation, and evaluation. The direct detection result ("0" or "1") was exported according to the embedded computation code. This approach could be expanded into a detection system for identifying other sets of biomarkers, enhancing its potential for clinical applications.

Efficient DNA walker guided by ordered cruciform-shaped DNA track for ultrasensitive and rapid electrochemical detection of lead ion

The rational design of DNA tracks is an effective pathway to guide the autonomous movement and high-efficiency recognition in DNA walkers, showing outstanding advantages for the cascade signal amplification of electrochemical biosensors. However, the uncontrolled distance between two adjacent tracks on the electrode could increase the risk of derailment and interruption of the reaction. Hence, a novel four-way balanced cruciform-shaped DNA track (C-DNT) was designed as a structured pathway to improve the effectiveness and stability of the reaction in DNA walkers. In this work, two kinds of cruciform-shaped DNA were interconnected as a robust structure that could avoid the invalid movement of the designed DNA walker on the electrode. When hairpin H2 was introduced onto the electrode, the strand displacement reaction (SDR) effectively triggered movements of the DNA walker along the cruciform-shaped track while leaving ferrocene (Fc) on the electrode, leading to a significant enhancement of the electrochemical signal. This design enabled the walker to move in an excellent organized and controllable manner, thus enhancing the reaction speed and walking efficiency. Compared to other walkers moving on random tracks, the reaction time of the C-DNT-based DNA walker could be reduced to 20 min. Lead ion (Pb2+) was used as a model target to evaluate the analytical performance of this biosensor, which exhibited a low detection limit of 0.033 pM along with a wide detection ranging from 0.1 pM to 500 nM. This strategy presented a novel concept for designing a high-performance DNA walker-based sensing platform for the detection of contaminants.

Isothermal strand displacement polymerase reaction (ISDPR)-assisted microchip electrophoresis for highly sensitive detection of cancer associated microRNAs

More and more studies have found that microRNAs (miRNAs) are markers of cancer, and detection of miRNAs is beneficial for early diagnosis and prognosis of cancer. In this paper, the isothermal strand displacement polymerase reaction (ISDPR), which is an enzyme-assisted nucleic acid amplification method, was studied to combine with microchip electrophoresis (MCE) for a simultaneously detection of two cancer related miRNAs named microRNA-21 (miR-21) and microRNA-221 (miR-221). In the ISDPR amplification, two different DNA hairpins (HPs) were specifically designed, so that miR-21 and miR-221 could respectively bind to HPs and started ISDPR amplification to generate two different products which were ultimately detected by MCE. The optimal conditions of ISDPR were carefully investigated, and the limits of detection (LOD) of miR-21 and miR-221 were as low as 0.35 fM and 0.25 fM (S/N = 3) respectively under these conditions. The human lung tumor cells and serum samples were analyzed by this ISDPR-MCE method and satisfactory results were obtained, which means that this method is of high sensitivity, high efficiency, low reagent consumption and simple operation in miRNAs detection.

A novel nanoprobe for visually investigating the controversial role of miRNA-34a as an oncogene or tumor suppressor in cancer cells

MiRNA-targeted therapy has become a hot topic in current cancer research. The key to this treatment strategy is to clarify the specific role of miRNA in cancer. However, the roles of some miRNAs acting as oncogenic or tumor suppressors are still controversial, which are influenced by different tumor types, even in the same cancer type. Hence, we designed a novel fluorescent nanoprobe based on polydopamine nanoparticles (PDA NPs) for simultaneously detecting caspase-3 and miRNA-34a within living cells. The specific role of miRNA-34a in different cancer cells could be further identified by studying the expression alterations of caspase-3 and miRNA-34a. Confocal imaging indicated that miRNA-34a indeed acted as a tumor suppressor in anticancer drug-treated MCF-7 and HeLa cells, where the effect of miRNA-34a remains controversial. The designed nanoprobe can offer a promising approach to ascertain the oncogenic or tumor-suppressing role of miRNA in different cancer cells with a simple visualization method, which has valuable implications for exploring the practicability of precision therapy focused on miRNA and evaluating the efficacy of new miRNA-targeted anticancer medications.

Electrochemical nucleic acid sensors: Competent pathways for mobile molecular diagnostics

Electrochemical nucleic acid biosensor has demonstrated great promise in clinical diagnostic tests, mainly because of its flexibility, high efficiency, low cost, and easy integration for analytical applications. Numerous nucleic acid hybridization-based strategies have been developed for the design and construction of novel electrochemical biosensors for diagnosing genetic-related diseases. This review describes the advances, challenges, and prospects of electrochemical nucleic acid biosensors for mobile molecular diagnosis. Specifically, the basic principles, sensing elements, applications in diagnosis of cancer and infectious diseases, integration with microfluidic technology and commercialization are mainly included in this review, aiming to provide new insights and directions for the future development of electrochemical nucleic acid biosensors.

Highly sensitive detection of microRNA-21 by nitrogen-doped carbon dots-based ratio fluorescent probe via nuclease-assisted rolling circle amplification strategy

Highly sensitive and selective detection of microRNA-21 (miRNA-21) in biological samples is critical for the disease diagnosis and cancer treatment. In this study, a nitrogen-doped carbon dots (N-CDs)-based ratio fluorescence sensing strategy was constructed for miRNA-21 detection with high sensitivity and excellent specificity. Bright-blue N-CDs (λ_ex/λ_em = 378 nm/460 nm) were synthesized by facile one-step microwave-assisted pyrolysis method by using uric acid as the single precursor, and the absolute fluorescence quantum yield and fluorescence lifetime of N-CDs were 35.8% and 5.54 ns separately. The padlock probe hybridized with miRNA-21 firstly and then was cyclized by T4 RNA ligase 2 to form a circular template. At the present of dNTPs and phi29 DNA polymerase, the oligonucleotide sequence in miRNA-21 was prolonged to hybridize with the surplus oligonucleotide sequences in circular template, generating long and reduplicated oligonucleotide sequences containing abundant guanine nucleotides. Separate G-quadruplex sequences were generated after the addition of Nt.BbvCI nicking endonuclease, and then hemin bound with G-quadruplex sequence to construct the G-quadruplex DNAzyme. Such G-quadruplex DNAzyme catalyzed the redox reaction of o-phenylenediamine (OPD) with H₂O₂, finally producing the yellowish-brown 2,3-diaminophenazine (DAP) (λ_em = 562 nm). Due to the inner filter effect between N-CDs and DAP, the ratio fluorescence signal of DAP with N-CDs was utilized for sensitive detection of miRNA-21 with detection limit of 0.87 pM. Such approach has practical feasibility and excellent specificity for miRNA-21 analysis during highly homological miRNA family in HeLa cell lysates and human serum samples.

miRNA Detection for Prostate Cancer Diagnosis by miRoll-Cas: miRNA Rolling Circle Transcription for CRISPR-Cas Assay

Micro-RNA (miRNA) emerges as a promising type of biomarker for cancer diagnosis. There is an urgent need for developing rapid, convenient, and precise miRNA detection methods that may be conducted with limited laboratory facilities, especially in underdeveloped areas. Herein, we developed a miRNA detection method termed miRoll-Cas, where miRNA is first amplified by rolling circle transcription and then subject to CRISPR-Cas13a assay. Using miRoll-Cas, we realized the sensitive detection of multiple cancer-relevant miRNA markers (miR21, miR141, and Let7b) and specifically identified other variants of the Let7 family, which can accurately discriminate prostate cancer patients from healthy people. We envision that miRoll-Cas may be readily translated to clinical applications in the diagnosis of a variety of diseases beyond cancer.

Efficient Three-Dimensional DNA Nanomachine Guided by a Robust Tetrahedral DNA Nanoarray Structure for the Rapid and Ultrasensitive Electrochemical Detection of Matrix Metalloproteinase 2

Herein, a giant-sized DNA nanoarray was subtly assembled by two kinds of independent tetrahedral DNA structures as the DNA track for a multi-armed three-dimensional (3D) DNA nanomachine to perform signal transduction and amplification efficiently, which was developed as an electrochemical biosensor for the rapid and ultrasensitive detection of matrix metalloproteinase 2 (MMP-2). Impressively, in contrast to conventional DNA walkers with inefficiency, which walked on random DNA tracks composed of a two-dimensional (2D) probe or a one-dimensional (1D) single-stranded (ss)DNA probe, the multi-armed 3D DNA nanomachine from exonuclease III (Exo III) enzyme-assisted target recycling amplification would be endowed with faster reaction speed and better walking efficiency because of the excellent rigidity and orderliness of the tetrahedral DNA nanoarray structure. Once the hairpin H3-label with the signal substance ferrocene (Fc) was added to the modified electrode surface, the multi-armed 3D DNA nanomachine would be driven to move along the well-designed nanoarray tracks by toehold-mediated DNA strand displacement, resulting in most of the ferrocene (Fc) binding to the electrode surface and a remarkable increase in electrochemical signals within 60 min. As a proof of concept, the prepared biosensor attained a low detection limit of 11.4 fg/mL for the sensitive detection of the target MMP-2 and was applied in Hela and MCF-7 cancer cell lysates. As a result, this strategy provided a high-performance sensing platform for protein detection in tumor diagnosis.

Self-Powered Biosensor for a Highly Efficient and Ultrasensitive Dual-Biomarker Assay

A dual-biomarker, self-powered biosensor was fabricated for the ultrasensitive detection of microRNA-21 (miRNA-21) and miRNA-155 based on enzymatic biofuel cells (EBFCs), catalytic hairpin assembly (CHA), and DNA hybridization chain reaction (HCR), with a capacitor and digital multimeter (DMM). In the presence of miRNA-21, the CHA and HCR are triggered and lead to the generation of a double-helix chain, which stimulates [Ru(NH₃)₆]³⁺ to move to the biocathode surface due to electrostatic interaction. Subsequently, the biocathode obtains electrons from the bioanode and reduces [Ru(NH₃)₆]³⁺ to [Ru(NH₃)₆]²⁺, which significantly increases the open-circuit voltage (E₁^OCV). When miRNA-155 is present, CHA and HCR cannot be completed, resulting in a low E₂^OCV. The self-powered biosensor allows for the simultaneous ultrasensitive detection of miRNA-21 and miRNA-155 with detection limits of 0.15 and 0.66 fM, respectively. Moreover, this self-powered biosensor exhibits the highly sensitive detection for miRNA-21 and miRNA-155 assay in human serum samples.

Well-Aligned Track-Accelerated Tripedal DNA Walker for Photoelectrochemical Recognition of Dual-miRNAs Based on Molecular Logic Gates

Post-transcriptional regulators, microRNAs (miRNAs), are involved in the occurrence and progression of various diseases. However, due to the complexity of disease-related miRNA regulatory networks, the typing and identification of miRNAs have remained challenging. Herein, a linear ladder-like DNA nanoarchitecture (LDN) was constructed to promote the movement efficiency of the tripedal DNA walker (T-walker), which was combined with the DNA-based logic gates and the PTCDA@PDA/CdS/WO₃ photoelectrode to develop a novel biosensor for the detection of dual-miRNAs. Two miRNAs, miR-122 and miR-21, were used as targets to operate the logic module, while its output, trigger strands (TSs), initiated a catalytic hairpin assembly (CHA) reaction to form a T-walker. By using LDN as the track, the T-walker efficiently unfolded hairpin 4, which further hybridized with the alkaline phosphatase-modified hairpin 5 (AP-H5). The remaining AP can catalyze the ascorbic acid 2-phosphate (AAP) into ascorbic acid (AA), an ideal electron donor, thus resulting in a photocurrent change. The photocurrent signals of both AND and OR gates displayed a linear relationship with the logarithm of dual-miRNA concentrations with detection limits of 10.1 and 13.6 fM, respectively. Moreover, the intelligent and rational design of DNA tracks gives impetus to create a well-organized sensing interface with wide application in clinical diagnosis and cancer monitoring.

NIR Photocontrolled Fluorescent Nanosensor under a Six-Branched DNA Nanowheel-Induced Nucleic Acid Confinement Effect for High-Performance Bioimaging

Although DNA nanotechnology is a promising option for fluorescent biosensors to perform bioimaging, the uncontrollable target identification during biological delivery and the spatially free molecular collision of nucleic acids may cause unsatisfactory imaging precision and sensitivity, respectively. Aiming at solving these challenges, we herein integrate some productive notions. On the one hand, the target recognition component is inserted with a photocleavage bond and a core-shell structured upconversion nanoparticle with a low thermal effect is further employed to act as the ultraviolet light generation source, under which a precise near-infrared photocontrolled sensing is achieved through a simple external 808 nm light irradiation. On the other hand, the collision of all of the hairpin nucleic acid reactants is confined by a DNA linker to form a six-branched DNA nanowheel, after which their local reaction concentrations are vastly enhanced (∼27.48 times) to induce a special nucleic acid confinement effect to guarantee highly sensitive detection. By selecting a lung cancer-associated short noncoding microRNA sequence (miRNA-155) as a model low-abundance analyte, it is demonstrated that the newly established fluorescent nanosensor not only presents good in vitro assay performance but also exhibits a high-performance bioimaging competence in live biosystems including cells and mouse body, propelling the progress of DNA nanotechnology in the biosensing field.