Exponential amplification of DNA with very low background using graphene oxide and single-stranded binding protein to suppress non-specific amplification

The fabrication of 1,2-dicarbonyl compound-caging isothermal exponential amplification strategy and its application in the highly sensitive detection of tumor exosomal miRNA

Exponential amplification reaction (EXPAR) possesses the advantage of high amplification efficiency, producing large amount of short nucleic acids in a short time. However, primer-independent DNA autosynthesis and nonspecific amplification caused by ab initio DNA self-synthesis increase the risk of high background signals, limiting its application in the fabrication of ultrasensitive sensors. In this study, we developed a new strategy called 1,2-dicarbonyl compound-caging EXPAR (caging-EXPAR) by innovatively modifying EXPAR templates with 1,2-dicarbonyl compounds. Five 1,2-dicarbonyl compounds including glyoxal and ninhydrin were chosen, all of which were proved to specifically bind to guanosine on the EXPAR template, efficiently reducing the background amplification of EXPAR and exhibiting an improved discrimination between the target and background. Possible mechanisms for the role of 1,2-dicarbonyl compounds in EXPAR were proposed, and three potential factors that could induce serious nonspecific amplification were investigated and verified. Caging-EXPAR provided a general, simple, convenient and beneficial strategy to slow down the generation of EXPAR background signals. Based on this method, choosing miRNA let-7a as a model, the minimum detectable amount was 10 zmol, which is 3 orders of magnitude less compared to traditional EXPAR. Most importantly, the strategy was successfully applied to monitor the expression level of the low-abundant miRNA in MCF-7 cell-derived exosomes. This highly portable and cost-effective method enhanced the real-time quantitative detection of specific nucleic acids in many fields such as clinical diagnosis and prognostic treatment and provided a complementary theoretical support for EXPAR background amplification, potentially improving and expanding the application of other amplification reactions.

A rolling circle mediated exponential amplification reaction with suppressed nonspecific amplification to detect pathogen RNA with high sensitivity

Respiratory infections caused by pathogens such as influenza virus and SARS-CoV-2 seriously threaten human life and health. RNA has been widely recognized as an important biomarker for diagnosing these pathogens, creating a growing need for rapid and accurate RNA detection methods. Isothermal nucleic acid amplification has emerged as a promising molecular diagnostics approach. Exponential amplification reactions (EXPAR) is a commonly used RNA detection method, known for its simplicity and rapid signal amplification in a short time. However, traditional EXPAR is only suitable for detecting short-sequence RNA, and 3'-end template interactions in the amplification reaction can lead to nonspecific amplification, which greatly limits its practical application. Here, we established an isothermal amplification method comprising a three-way junction (3-WJ) structure and dumbbell probe (DP) for the rapid and sensitive detection of pathogen RNA in a single closed tube, termed the rolling circle mediated exponential amplification reaction (RC-EXPAR). The introduction of the DP eliminated the 3'-end of the template, suppressing nonspecific amplification caused by the 3'-end extension in the reaction. Although the trigger generation by the 3-WJ structure is a linear amplification process, the RC-EXPAR amplifies the triggers exponentially to enhance signal output further and increase sensitivity. The proposed method showed a high sensitivity with a limit of detection (LOD) of 103 copies/mL. Moreover, RC-EXPAR demonstrated strong anti-interference capability in complex biological matrices. This work opens up new ideas for suppressing nonspecific amplification and provides a promising signal amplification strategy for rapid, sensitive, and specific pathogen detection in clinical.

Suitability evaluation of toehold switch and EXPAR for cell-free MicroRNA biosensor development

The development of a robust and cost-effective sensing platform for microRNA (miRNA) is of paramount importance in detecting and monitoring various diseases. Current miRNA detection methods are marred by low accuracy, high cost, and instability. The toehold switch riboregulator has shown promising results in detecting viral RNAs integrated with the freeze-dried cell-free system (CFS). This study aimed to leverage the toehold switch technology and portability to detect miRNA in the CFS and to incorporate the exponential amplification reaction (EXPAR) to bring the detection to clinically relevant levels. We assessed various EXPAR DNA templates under different conditions to enhance the accuracy of the sensing platform. Furthermore, different structures of toehold switches were tested with either high-concentration synthetic miRNA or EXPAR product to assess sensitivity. Herein, we elucidated the mechanisms of the toehold switch and EXPAR, presented the findings of these optimizations, and discussed the potential benefits and drawbacks of their combined use.

CRISPR-Cas12a-assisted elimination of the non-specific signal from non-specific amplification in the Exponential Amplification Reaction

Non-specific amplification is a major problem in nucleic acid amplification resulting in false-positive results, especially for exponential amplification reactions (EXPAR). Although efforts were made to suppress the influence of non-specific amplification, such as chemical blocking of the template's 3'-ends and sequence-independent weakening of template-template interactions, it is still a common problem in many conventional EXPAR reactions. In this study, we propose a novel strategy to eliminate the non-specific signal from non-specific amplification by integrating the CRISPR-Cas12a system into two-templates EXPAR. An EXPAR-Cas12a strategy named EXPCas was developed, where the Cas12a system acted as a filter to filter out non-specific amplificons in EXPAR, suppressing and eliminating the influence of non-specific amplification. As a result, the signal-to-background ratio was improved from 1.3 to 15.4 using this method. With microRNA-21 (miRNA-21) as a target, the detection can be finished in 40 min with a LOD of 103 fM and no non-specific amplification was observed.

Programmable molecular circuit discriminates multidrug-resistant bacteria

Recognizing multidrug-resistant (MDR) bacteria with high accuracy and precision from clinical samples has long been a difficulty. For reliable detection of MDR bacteria, we investigated a programmable molecular circuit called the Background-free isothermal circuital kit (BRICK). The BRICK method provides a near-zero background signal by integrating four inherent modules equivalent to the conversion, amplification, separation, and reading modules. Interference elimination is largely owing to a molybdenum disulfide nanosheets-based fluorescence nanoswitch and non-specific suppression mediated by molecular inhibitors. In less than 70 ​min, an accurate distinction of various MDR bacteria was achieved without bacterial lysis. The BRICK technique detected 6.73 ​CFU/mL of methicillin-resistant Staphylococcus aureus in clinical samples in a proof-of-concept trial. By simply reprogramming the sequence panel, such a high signal-to-noise characteristic has been proven in the four other superbugs. The proposed BRICK method can provide a universal platform for infection surveillance and environmental management thanks to its superior programmability.

Magnetic ionic liquids as microRNA extraction solvents and additives for the exponential amplification reaction

The detection of microRNAs (miRNAs) from highly complex matrices has become an area of immense interest as their characterization in biological samples has been utilized for disease diagnosis and body fluid identification. However, conventional northern blotting miRNA detection lacks the sensitivity required to detect circulating miRNAs. Additionally, polymerase chain reaction-based methods for miRNA detection require modified oligonucleotides that are difficult to design. Exponential amplification reaction (EXPAR) is an isothermal amplification method used for miRNA detection that is simple to design but suffers from non-specific amplification that masks low concentration miRNAs. Previous studies have shown that magnetic ionic liquids (MILs) are a promising alternative to traditional nucleic acid extraction methods capable of preconcentrating DNA from complex matrices. In this study, three hydrophobic magnetic ionic liquids (MILs) were investigated as EXPAR additives and miRNA extraction solvents. The addition of MIL to the EXPAR buffer decreased the background signal from non-specific amplification and increased the reaction rate. Reactions containing MIL could detect miRNA at concentration levels down to 10 aM. In comparison, reactions that did not contain MIL could not discriminate 10 fM lethal-7a (let-7a) standards from the no trigger control (NTC). All three MILs extracted miRNA from 2-fold diluted plasma, artificial urine, and artificial saliva with only a 1 min dispersion step. By integrating the miRNA-enriched MIL into the EXPAR buffer, the extraction and detection of femtomolar concentrations of miRNA required only 10 min. In contrast, conventional spin column kits require at least 20 min to isolate miRNA, indicating that a dispersive MIL-based extraction is ideal for high throughput analysis of miRNA.

Activation of catalytic DNAzyme by binding-induced DNA displacement for homogeneous assay

The sensitive assays for protein, especially for the DNA-based assay, are often dependent on the amplification procedure with assistance of enzyme. Compared with a protein enzyme, deoxyribozyme (DNAzyme) exhibits similar catalytic activity and specificity and better flexibility. In this work, we streamlined the binding induced DNA displacement (BINDD) strategy for the activation of DNAzyme cleavage. Since the intrinsic element of DNAzyme is the nucleic acids, it is easy to join the BINDD by hybridization with an affinity probe. The activity of DNAzyme was initiated by the BINDD reaction mediated by the recognition affinity probe with target proteins. Upon DNAzyme release, it was able to catalyze and cleave the predesigned substrates, generating the enhanced fluorescence signal indicating the protein concentration. Such a constructed homogeneous assay is available and effective in human serum when it was used for detection of platelet derived growth factor-BB (PDGF-BB) and prostate specific antigen (PSA), with detection limits of 100 pM and 200 pM, respectively.

Ultrasensitive Field-Effect Biosensors Enabled by the Unique Electronic Properties of Graphene

This review provides a critical overview of current developments on nanoelectronic biochemical sensors based on graphene. Composed of a single layer of conjugated carbon atoms, graphene has outstanding high carrier mobility and low intrinsic electrical noise, but a chemically inert surface. Surface functionalization is therefore crucial to unravel graphene sensitivity and selectivity for the detection of targeted analytes. To achieve optimal performance of graphene transistors for biochemical sensing, the tuning of the graphene surface properties via surface functionalization and passivation is highlighted, as well as the tuning of its electrical operation by utilizing multifrequency ambipolar configuration and a high frequency measurement scheme to overcome the Debye screening to achieve low noise and highly sensitive detection. Potential applications and prospectives of ultrasensitive graphene electronic biochemical sensors ranging from environmental monitoring and food safety, healthcare and medical diagnosis, to life science research, are presented as well.

Physical and chemical template-blocking strategies in the exponential amplification reaction of circulating microRNAs

The detection of circulating miRNA through isothermal amplification wields many attractive advantages over traditional methods, such as reverse transcription RT-qPCR. However, it is challenging to control the background signal produced in the absence of target, which severely hampers applications of such methods for detecting low abundance targets in complex biological samples. In the present work, we employed both the cobalt oxyhydroxide (CoOOH) nanoflakes and the chemical modification of hexanediol to block non-specific template elongation in exponential amplification reaction (EXPAR). Adsorption by the CoOOH nanoflakes and the hexanediol modification at the 3' end effectively prevented no-target polymerization on the template itself and thus greatly improved the performance of EXPAR, detecting as low as 10 aM of several miRNA targets, including miR-16, miR-21, and miR-122, with the fluorescent DNA staining dye of SYBR Gold™. Little to no cross-reactivity was observed from the interfering strands present in 10-fold excess. Besides contributing to background reduction, the CoOOH nanoflakes strongly adsorbed nucleic acids and isolated them from a complex sample matrix, thus permitting successful detection of the target miRNA in the serum. We expect that simple but sensitive template-blocking EXPAR could be a valuable tool to help with the discovery and validation of miRNA markers in biospecimens. Graphical abstract.

Isothermal digital detection of microRNAs using background-free molecular circuit

MicroRNAs, a class of transcripts involved in the regulation of gene expression, are emerging as promising disease-specific biomarkers accessible from tissues or bodily fluids. However, their accurate quantification from biological samples remains challenging. We report a sensitive and quantitative microRNA detection method using an isothermal amplification chemistry adapted to a droplet digital readout. Building on molecular programming concepts, we design a DNA circuit that converts, thresholds, amplifies, and reports the presence of a specific microRNA, down to the femtomolar concentration. Using a leak absorption mechanism, we were able to suppress nonspecific amplification, classically encountered in other exponential amplification reactions. As a result, we demonstrate that this isothermal amplification scheme is adapted to digital counting of microRNAs: By partitioning the reaction mixture into water-in-oil droplets, resulting in single microRNA encapsulation and amplification, the method provides absolute target quantification. The modularity of our approach enables to repurpose the assay for various microRNA sequences.

Colorimetric detection of nucleic acid sequences in plant pathogens based on CRISPR/Cas9 triggered signal amplification

A colorimetric method is presented for the detection of specific nucleotide sequences in plant pathogens. It is based on the use of CRISPR/Cas9-triggered isothermal amplification and gold nanoparticles (AuNPs) as optical probes. The target DNA was recognized and broken up by a given Cas9/sgRNA complex. After isothermal amplification, the product was hybridized with oligonucleotide-functionalized AuNPs. This resulted in the aggregation of AuNPs and a color change from wine red to purple. The visual detection limit is 2 pM of DNA, while a linear relationship exists between the ratio of absorbance at 650 and 525 nm and the DNA concentration in the range from 0.2 pM to 20 nM. In contrast to the previous CRISPR-based amplification platforms, the method has significantly higher specificity with the single-base mismatch and can be visually read out. It was successfully applied to identify the Phytophthora infestans genomic DNA. Graphical abstract Schematic presentation of a colorimetric method for detection of Phytophthora infestans genomic DNA based on CRISPR/Cas9-triggered isothermal amplification. The Cas9 endonuclease cleaves DNA at the design site and the color changes from red to purple with increasing target DNA concentration.

New method for detection of T4 polynucleotide kinase phosphatase activity through isothermal EXPonential amplification reaction

A new method has been developed for the sensitive detection of T4 PNKP activity based on the isothermal EXPonential amplification reaction.

First characterization of a biphasic, switch-like DNA amplification

We report the first DNA amplification chemistry with switch-like characteristics: the chemistry is biphasic, with an expected initial phase followed by an unprecedented high gain burst of product oligonucleotide in a second phase. The first and second phases are separated by a temporary plateau, with the second phase producing 10 to 100 times more product than the first. The reaction is initiated when an oligonucleotide binds and opens a palindromic looped DNA template with two binding domains. Upon loop opening, the oligonucleotide trigger is rapidly amplified through cyclic extension and nicking of the bound trigger. Loop opening and DNA association drive the amplification reaction, such that reaction acceleration in the second phase is correlated with DNA association thermodynamics. Without a palindromic sequence, the chemistry resembles the exponential amplification reaction (EXPAR). EXPAR terminates at the initial plateau, revealing a previously unknown phenomenon that causes early reaction cessation in this popular oligonucleotide amplification reaction. Here we present two distinct types of this biphasic reaction chemistry and propose dominant reaction pathways for each type based on thermodynamic arguments. These reactions create an endogenous switch-like output that reacts to approximately 1 pM oligonucleotide trigger. The chemistry is isothermal and can be adapted to respond to a broad range of input target molecules such as proteins, genomic bacterial DNA, viral DNA, and microRNA. This rapid DNA amplification reaction could potentially impact a variety of disciplines such as synthetic biology, biosensors, DNA computing, and clinical diagnostics.

Sensing at the Surface of Graphene Field-Effect Transistors

Recent research trends now offer new opportunities for developing the next generations of label-free biochemical sensors using graphene and other two-dimensional materials. While the physics of graphene transistors operated in electrolyte is well grounded, important chemical challenges still remain to be addressed, namely the impact of the chemical functionalizations of graphene on the key electrical parameters and the sensing performances. In fact, graphene - at least ideal graphene - is highly chemically inert. The functionalizations and chemical alterations of the graphene surface - both covalently and non-covalently - are crucial steps that define the sensitivity of graphene. The presence, reactivity, adsorption of gas and ions, proteins, DNA, cells and tissues on graphene have been successfully monitored with graphene. This review aims to unify most of the work done so far on biochemical sensing at the surface of a (chemically functionalized) graphene field-effect transistor and the challenges that lie ahead. The authors are convinced that graphene biochemical sensors hold great promise to meet the ever-increasing demand for sensitivity, especially looking at the recent progresses suggesting that the obstacle of Debye screening can be overcome.

Comprehensive evaluation of molecular enhancers of the isothermal exponential amplification reaction

The exponential amplification reaction (EXPAR) is an emerging isothermal nucleic acid amplification method with high potential for molecular diagnostics due to its isothermal nature and high amplification efficiency. However, the use of EXPAR is limited by the high levels of non-specific amplification. Hence, methods that can improve the specificity of EXPAR are desired to facilitate its widespread adoption in practice. Herein, we proposed a strategy to improve EXPAR performance by using molecular enhancers. Eight small molecules were investigated, including ethylene glycol, propylene glycol, betaine, dimethyl sulfoxide (DMSO), trehalose, tetramethylammonium chloride (TMAC), bovine serum albumin (BSA) and single-stranded binding (SSB) proteins. A combination of kinetic and end-point analysis was adopted to investigate how these molecules affected EXPAR performance. Trehalose, TMAC, BSA and SSB proteins were found to have positive effects on EXPAR with trehalose being able to increase the efficiency of EXPAR. In contrast, TMAC, BSA and SSB proteins were shown to increase the specificity of EXPAR. We applied our findings to demonstrate the combination of trehalose and TMAC could simultaneously improve both the efficiency and specificity of an EXPAR-based miRNA detection method. The information provided in this study may serve as a reference to benefit the wider isothermal amplification community.