Nuclease-free target recycling signal amplification for ultrasensitive multiplexing DNA biosensing

Robust nontarget DNA-triggered catalytic hairpin assembly amplification strategy for the improved sensing of microRNA in complex biological matrices

A simple but robust fluorescence strategy based on a nontarget DNA-triggered catalytic hairpin assembly (CHA) was constructed to probe microRNA-21 (miR-21). A short ssDNA rather than degradable target miRNA was employed as an initiator. Two molecular beacons needed to assist the CHA process were simplified to avoid unfavorable nonspecific interactions. In the presence of the target, the initiator was released from a partially duplex and triggered the cyclic CHA reaction, resulting in a significantly amplified optical readout. A wide linear range from 0.1 pM to 1000 pM for the sensing of miR-21 in buffer was achieved with a low detection limit of 0.76 pM. Fortunately, this strategy demonstrated an obviously improved performance for miR-21 detection in diluted serum. The fluorescence signals were enhanced remarkably and the sensitivity was further improved to 0.12 pM in 10% serum. The stability for miR-21 quantification and the capability for the analysis of single nucleotide polymorphisms (SNPs) were also improved greatly. More importantly, the biosensor could be applied to image miR-21 in different living tumor cells with high resolution, illustrating its promising potential for the assay of miRNAs in various complex situations for early-stage disease diagnosis and biological studies in cells.

Target-Catalyzed Assembly of Pyrene-Labeled Hairpins for Exponentially Amplified Biosensing

Rapid and sensitive detection of nucleic acids is vital for disease diagnosis. This work designed an enzyme-free isothermal strategy for rapid exponential signal amplification through target-triggered catalytic hairpin assembly (CHA) to induce the spatially sensitive fluorescent signal of the pyrene excimer. Functionally, this system consisted of three pyrene labelled hairpins (H1, H2, and H3) and one catalyst DNA C. In the presence of C, the CHA was activated to generate intermediate I, which contained a single-stranded region identical to the C sequence for initiating the second cycle of CHA to obtain 2I and thus achieved the exponential formation of I along with the switching of pyrene excimer. The fluorescent signal of the pyrene excimer could be further enhanced via the inclusion of γ-cyclodextrin and showed a linear increase upon increasing logarithm of C concentration. Through the introduction of a helping hairpin H4-containing C sequence and a region specific to the target, this strategy could be extended to realize the quick and sensitive detection of different analytes. Using dengue virus RNA as an analyte model, the proposed fluorescent method showed a linear range from 0.1 to 50 nM with a limit of detection of 0.048 nM at 3σ and good selectivity. The excellent performance and convenient operation demonstrated its promising application in clinical disease diagnosis.

Isothermal Nucleic Acid Amplification Techniques and Their Use in Bioanalysis

Recently, there has been a rapid progress in the development of techniques for isothermal amplification of nucleic acids as an alternative to polymerase chain reaction (PCR). The advantage of these methods is that the nucleic acids amplification can be carried out at constant temperature, unlike PCR, which requires cyclic temperature changes. Moreover, isothermal amplification can be conducted directly in living cells. This review describes the principles of isothermal amplification techniques and demonstrates their high efficiency in designing new highly sensitive detection methods of nucleic acids and enzymes involved in their modifications. The data on successful application of isothermal amplification methods for the analysis of cells and biomolecules with the use of DNA/RNA aptamers are presented.

Gold nano-flowers (Au NFs) modified screen-printed carbon electrode electrochemical biosensor for label-free and quantitative detection of glycated hemoglobin

Glycated hemoglobin (HbA1c) represents the average glucose level over the past three months and has been considered as the most important biomarker for the diagnosis of Type Ⅱ diabetes (T2D). Herein, a label-free and quantitative electrochemical biosensor based on 4-mercaptophenylboronic acid (4-MPBA) modified gold nano-flowers (Au NFs) substrate was developed for the determination of HbA1c. Under optimal conditions, the linear dynamic ranges of HbA1c (5 μg/mL - 1000 μg/mL) and HbA1c% (2%-20%) by cyclic voltammetry were achieved. The electrochemical biosensor showed great detection specificity towards HbA1c and relatively stability after storage at 4 °C. This method could also be applied in human serum system which holds great potential to be applied to monitor real blood samples of diabetes patients. In human serum system, the recovery rate could reach 103.8% and 99.0%. It could achieve fast detection, the total analysis time was less than 65 min, and the detection time was less than 10 s. Moreover, in terms of fabrication process, operation procedure, detection time and cost, this technique was superior to the current HbA1c detection methods suggesting great promise for the practical clinical use in the future.

Biomolecular interfaces based on self-assembly and self-recognition form biosensors capable of recording molecular binding and release

This research proposed to create the next generation of versatile electrochemical-based biosensors capable of monitoring target capture and release as dictated by molecular binding or unbinding. The biosensor integrates cellular machines (i.e., microtubules, structural elements of cells and kinesin molecular motors involved in cellular transport) as functional units; its assembly is based on molecular self-assembly and self-recognition. Our results demonstrate that the designed biosensor was capable of allowing detection of binding and unbinding events based on redox reactions at user-controlled electrode interfaces. The analysis also showed that the sensitivity of the designed biosensor or its ability to record such events could be user-controlled at any given time by adjusting the energy source that "fuels" the system.

Smart Combination of Cyclodextrin Polymer Host-Guest Recognition and Mg2+-Assistant Cyclic Cleavage Reaction for Sensitive Electrochemical Assay of Nucleic Acids

A novel enzyme-free electrochemical sensing strategy was proposed for sensitive monitoring of DNA and miRNA by smart combination of the cyclic cleavage reaction of Mg²⁺-dependent DNAzyme and the host-guest inclusion between ferrocene-labeled hairpin probe (H-1) and nitrogen-doped reduced graphene oxide/β-cyclodextrin polymer (NRGO/β-CDP) nanocomposites. The synthesized NRGO/β-CDP nanocomposites with high electrocatalytic activity and recognition capability were modified on the glassy carbon electrode to construct the sensing platform. Upon the hybridization reaction of subunit DNA in the loop region with target sequence, the active DNAzyme was liberated from the caged structure, which bound with H-1 to catalyze its cleavage in the presence of Mg²⁺ and triggered the target recycling amplification for the cleavage of a large number of H-1. Each cleaved H-1 was divided into two single-stranded oligonucleotides, leading to an obvious enhancement of peak current by the molecular recognition of β-CDP on the electrode. Thus, the constructed biosensor showed high sensitivity and selectivity for DNA and miRNA assays, with wide concentration ranges of 0.01-1000 and 0.05-500 pM and low detection limits of 3.2 and 18 fM, respectively. This developed sensing strategy may become a promising nucleic acid detection method in bioassays and clinical diagnosis.

Direct Detection of Nucleic Acid with Minimizing Background and Improving Sensitivity Based on a Conformation-Discriminating Indicator

As is well-known, the nucleic acid indicator-based strategy is one of the major approaches to monitor the nucleic acid hybridization-mediated recognition events in biochemical analysis, displaying obvious advantages including simplicity, low cost, convenience, and generality. However, conventional indicators either hold strong self-fluorescence or can be lighted by both ssDNA and dsDNA, lacking absolute selectivity for a certain conformation, always with high background interference and low sensitivity in sensing; and additional processing (e.g., nanomaterial-mediated background suppression, and enzyme-catalyzed signal amplification) is generally required to improve the detection performance. In this work, a carbazole derivative, EBCB, has been synthesized and screened as a dsDNA-specific fluorescent indicator. Compared with conventional indicators under the same conditions, EBCB displayed a much higher selective coefficient for dsDNA, with little self-fluorescence and negligible effect from ssDNA. Based on its superior capability in DNA conformation-discrimination, high sensitivity with minimizing background interference was demonstrated for direct detection of nucleic acid, and monitoring nucleic acid-based circuitry with good reversibity, resulting in low detection limit and high capability for discriminating base-mismatching. Thus, we expect that this highly specific DNA conformation-discriminating indicator will hold good potential for application in biochemical sensing and molecular logic switching.