Sensitive detection of microRNAs with hairpin probe-based circular exponential amplification assay

Autocatalytic DNA circuitries

Autocatalysis, a self-sustained replication process where at least one of the products functions as a catalyst, plays a pivotal role in life's evolution, from genome duplication to the emergence of autocatalytic subnetworks in cell division and metabolism. Leveraging their programmability, controllability, and rich functionalities, DNA molecules have become a cornerstone for engineering autocatalytic circuits, driving diverse technological applications. In this tutorial review, we offer a comprehensive survey of recent advances in engineering autocatalytic DNA circuits and their practical implementations. We delve into the fundamental principles underlying the construction of these circuits, highlighting their reliance on DNAzyme biocatalysis, enzymatic catalysis, and dynamic hybridization assembly. The discussed autocatalytic DNA circuitry techniques have revolutionized ultrasensitive sensing of biologically significant molecules, encompassing genomic DNAs, RNAs, viruses, and proteins. Furthermore, the amplicons produced by these circuits serve as building blocks for higher-order DNA nanostructures, facilitating biomimetic behaviors such as high-performance intracellular bioimaging and precise algorithmic assembly. We summarize these applications and extensively address the current challenges, potential solutions, and future trajectories of autocatalytic DNA circuits. This review promises novel insights into the advancement and practical utilization of autocatalytic DNA circuits across bioanalysis, biomedicine, and biomimetics.

Programmable DNA tweezers-SDA for ultra-sensitive signal amplification fluorescence sensing strategy

BACKGROUND

DNA tweezers, classified as DNA nanomachines, have gained prominence as multifunctional biosensors due to their advantages, including a straightforward structure, response mechanism, and high programmability. While the DNA tweezers demonstrate simultaneous, rapid, and stable responses to different targets, their detection sensitivity requires enhancement. Some small molecules, such as mycotoxins, often require more sensitive detection due to their extremely high toxicity. Therefore, more effective signal amplification strategies are needed to further enhance the sensitivity of DNA tweezers in biosensing.

RESULTS

We designed programmable DNA tweezers that detect small-molecule mycotoxins and miRNAs through simple sequence substitution. While the DNA tweezers demonstrate simultaneous, rapid, and stable responses to different targets, their detection sensitivity requires enhancement. We introduced the Strand Displacement Amplification (SDA) technique to address this limitation, proposing a strategy of novel programmable DNA tweezers-SDA ultrasensitive signal amplification fluorescence sensing. We specifically investigate the effectiveness of this approach concerning signal amplification for two critical mycotoxins: aflatoxin B1 (AFB1) and zearalenone (ZEN). Results indicate that the detection ranges of AFB1 and ZEN via this strategy were 1-10,000 pg mL -1 and 10-100,000 pg mL -1, respectively, with corresponding detection limits of 0.933 pg mL -1 and 1.07 pg mL -1. Compared with the DNA tweezers direct detection method for mycotoxins, the newly constructed programmable DNA tweezers-SDA fluorescence sensing strategy achieved a remarkable 104-fold increase in the detection sensitivity for AFB1 and ZEN.

SIGNIFICANCE

The constructed programmable DNA tweezers-SDA ultrasensitive signal-amplified fluorescence sensing strategy exhibits excellent detection performance for mycotoxins. The superb versatility of this strategy allows the developed method to be easily used for detecting other analytes by simply replacing the aptamer and cDNA, which has incredible potential in various fields such as food safety screening, clinical diagnostics, and environmental analysis.

Entropy-driven DNA circuit with two-stage strand displacement for elegant and robust detection of miRNA let-7a

MicroRNAs (miRNAs) research in cancer diagnosis is expanding, on account of miRNAs were demonstrated to be key indicator of gene expression and hopeful candidates for biomarkers. In this study, a stable miRNA-let-7a fluorescent biosensor was successfully designed based on an exonuclease Ⅲ-assisted two-stage strand displacement reaction (SDR). First, an entropy-driven SDR containing a three-chain structure of the substrate is used in our designed biosensor, leading to reduce the reversibility of the target recycling process in each step. The target acts on the first stage to start the entropy-driven SDR, which generates the trigger used to stimulate the exonuclease Ⅲ-assisted SDR in the second stage. At the same time, we design a SDR one-step amplification strategy as a comparison. Expectly, this developed two-stage strand displacement system has a low detection limit of 25.0 pM as well as a broad detection range of 4 orders of magnitude, making it more sensitive than the SDR one-step sensor, whose detection limit is 0.8 nM. In addition, this sensor has high specificity across members of the miRNA family. Therefore, we can take advantage of this biosensor to promote miRNA research in cancer diagnosis sensing systems.

Isothermal exponential amplification reactions triggered by circular templates (cEXPAR) targeting miRNA

BACKGROUND

Isothermal exponential amplification reaction (EXPAR) is an emerging amplification technique that is most frequently used to amplify microRNA (miRNA). However, EXPAR also exhibits non-specific background amplification in the absence of the targeted sequence, which limits the attainable assay sensitivity of EXPAR.

METHODS AND RESULTS

A novel modified isothermal EXPAR based on circular amplification templates (cEXPAR) was developed in this study. The circular template consists of two same linear fragments that complement the target sequence, and these two linear fragments are separated by two nicking agent recognition sequences (NARS). Compared with the linear structure template, this circular template allows DNA or RNA fragments to be randomly paired with two repeated sequences and can be successfully amplified. This reaction system developed in this study could rapidly synthesize short oligonucleotide fragments (12-22 bp) through simultaneous nicking and displacement reactions. Highly sensitive chain reactions can be specifically triggered by as low as a single copy of target molecule, and non-specific amplification can be effectively eliminated in this optimized system. Moreover, the proposed approach applied to miRNA test can discriminate single-nucleotide variations between miRNAs.

CONCLUSION

The newly developed cEXPAR assay provides a useful alternative tool for rapid, sensitive, and highly specific detection of miRNAs.

Construction of an Autocatalytic Hybridization Assembly Circuit for Amplified In Vivo MicroRNA Imaging

Lowly expressed analyte in complex cytoplasmic milieu necessitates the development of non-enzymatic autocatalytic DNA circuits with high amplification and anti-interference performance. Herein, we engineered a versatile and robust stimuli-responsive autocatalytic hybridization assembly (AHA) circuit for high-performance in vivo bioanalysis. Under a moderately confined condition, the initiator motivated the autonomous and cooperative cross-activation of cascade hybridization reaction and catalytic DNA assembly for generating an exponentially amplified readout without the parasite steric hindrance and random diffusion side effects. The AHA circuit was systematically investigated by a series of experimental studies and theoretical simulations. The successively guaranteed target recognition and synergistically accelerated signal-amplification enabled the sensitive and selective detection of analyte, and realized the robust miRNA imaging in living cells and mice. This autocatalytic DNA circuit could substantially expand the toolbox for accurate diagnosis and programmable therapeutics.

Nonenzymatic Autonomous Assembly of Cross-Linked Network Structures from Only Two Palindromic DNA Components for Intracellular Fluorescence Imaging of miRNAs

The abnormal expression of miRNA-21 is often found in tumor specimens and cell lines, and thus, its specific detection is an urgent need for the diagnosis and effective therapy of cancers. In this contribution, we demonstrate a palindrome-based hybridization chain reaction (PHCR) upon the stimuli of a short oligonucleotide trigger to perform the autonomous assembly of cross-linked network structures (CNSs) for the amplification detection of miRNA-21 and sensitive fluorescence imaging of cancerous cells. The building blocks are only two palindromic hairpin-type DNA strands that are separately modified with different fluorophores (Cy3 and Cy5), which is easily combined with the catalytic hairpin assembly (CHA) technique that can further amplify the signal output. Utilizing the CHA-PHCR assay system, a small amount of miRNA-21 can activate many triggers via CHA and in turn induce the PHCR-based CNS assembly from more DNA building blocks, bringing Cy3 and Cy5 into close proximity to each other and generating ultrasensitive fluorescence resonance energy transfer signals. As a result, target miRNA can be quantitatively detected down to as low as 10 pM with high assay specificity. The coexisting nontarget miRNAs and other biomacromolecules do not interfere with signal transduction. The developed assay system is suitable for screening different expression levels of miRNA-21 in living cells by fluorescence imaging. The palindrome-based cross-linking assembly can enhance the intracellular stability of assembled nanostructures by at least fivefold and exhibit the good universality for the detection of other miRNAs. Moreover, cancerous cells can be distinguished from healthy cells, and the CHA-PHCR assay is in good accordance with the gold standard PCR method, indicating a promising platform for the diagnosis of human cancers and other genetic diseases.

Non-enzymatic detection of miR-21 in cancer cells using a homogeneous mix-and-read smart probe assay

We report a new assay system for the detection of miR-21 in cancer cells. The new assay works at room temperature and it does not involve enzymatic amplification. It consists a hairpin smart probe, designed to specifically recognize miR-21 target sequence. We tested the performance and sequence recognition capability of the smart probe to confirm desired specifications. We used the smart probe for the sequence-specific recognition of synthetic miR-21 oligonucleotides as well as mismatch sequences and we found that the probe recognizes the target sequence-specifically, while discriminating against mismatched sequences. We determined the limit of detection and limit of quantitation for the miR-21 oligonucleotides to be 1.72 nM and 5.78 nM, respectively, while the sensitivity is 6.90 × 10¹¹ c.p.sM^-1. More importantly, we showed that the smart probe-based method is also sensitive and selective for miR-21 when applied to crude extractions from MCF-7 cancer cell line at room temperature, with the results showing high fluorescence signals for the MCF-7 samples while showing much less signals for samples that did not contain miR-21. Thus, this new smart probe system constitutes a homogeneous, mix-and-read detection technique that can provide reliable diagnostics of miR-21 cancer biomarker at room temperature.

Enzyme-free and copper-free strategy based on cyclic click chemical-triggered hairpin stacking circuit for accurate detection of circulating microRNAs

Accurate detection of circulating microRNAs (miRNAs) plays a vital role in the diagnosis of various diseases. However, enzyme-free amplification detection remains challenging. Here, we report an enzyme-free fluorescence resonance energy transfer assay termed "3C-TASK" (cyclic click chemical-triggered hairpin stacking kit) for the detection of circulating miRNA. In this strategy, the miRNA could initiate copper-free click chemical ligation reactions and the ligated products then trigger another hairpin stacking circuit. The first signal amplification was achieved through the recycling of the target miRNA in the click chemical ligation circuit, and the second signal amplification was realized through the recycling of ligated probes in a hairpin stacking circuit driven by thermodynamics. The two-step chain reaction event triggered by miRNAs was quantified by the fluorescence signal value so that accurate detection of target miRNA could be achieved. The 3C-TASK was easily controlled because no enzyme was involved in the entire procedure. Although simple, this strategy showed sensitivity with a detection limit of 8.63 pM and specificity for distinguishing miRNA sequences with single-base variations. In addition, the applicability of this method in complex biological samples was verified by detecting target miRNA in diluted plasma samples. Hence, our method achieved sensitive and specific detection of miRNA and may offer a new perspective for the broader application of enzyme-free chemical reaction and DNA circuits in biosensing.

An intramolecular DNAzyme-based amplification for miRNA analysis with improving reaction kinetics and high sensitivity

Sensitive, specific and rapid methods for detecting microRNAs (miRNAs) play critical roles in disease diagnosis and therapy. Enzyme-free amplification techniques based on DNAzyme assembly have recently been developed for the highly specific miRNA analysis. However, traditional DNAzyme-based assembly (free DNAzyme) amplifiers is mainly dependent on the target-induced split DNAzyme fragments to assemble into activated DNAzyme structures, which have made a compromise between the sensitivity and specificity due to the random diffusion of dissociative probes in a bulk solution with poor kinetics. Herein, based on a rationally designed DNA probe, we developed an intramolecular DNAzyme assembly (intra-DNAzyme) method to overcome these challenges. The miR-373 is used as model analyte for our current proof-of-concept experiments. Compared with the free-DNAzyme method, our method showed significantly improved analytical performance in terms of dynamic range, assay sensitivity and speed. This method can detect miR-373 specifically with a detection limit as low as 4.3 fM, which is about 83.7 times lower than the previous free-DNAzyme method. This intra-DNAzyme strategy would be of great value in both basic research and clinical diagnosis.

Isothermal Self-Primer EXPonential Amplification Reaction (SPEXPAR) for Highly Sensitive Detection of Single-Stranded Nucleic Acids and Proteins

Development of versatile sensing methods for sensitive and specific detection of clinically relevant nucleic acids and proteins is of great value for disease monitoring and diagnosis. In this work, we propose a novel isothermal Self-primer EXPonential Amplification Reaction (SPEXPAR) strategy based on a rationally engineered structure-switchable Metastable Hairpin template (MH-template). The MH-template initially keeps inactive with its self-primer overhanging a part of target recognition region to inhibit polymerization. The present targets can specifically compel the MH-template to transform into an "activate" conformation that primes a target-recyclable EXPAR. The method is simple and sensitive, can accurately and facilely detect long-chain single-stranded nucleic acids or proteins without the need of exogenous primer probes, and has a high amplification efficiency theoretically more than 2ⁿ. For a proof-of-concept demonstration, the SPEXPAR method was used to sensitively detect the characteristic sequence of the typical swine fever virus (CSFV) RNA and thrombin, as nucleic acid and protein models, with limits of detection down to 43 aM and 39 fM, respectively, and even the CSFV RNA in attenuated vaccine samples and thrombin in diluted serum samples. The SPEXPAR method may serve as a powerful technique for the biological research of single-stranded nucleic acids and proteins.

MiR-191-5p is upregulated in culture media of implanted human embryo on day fifth of development

BACKGROUND

Morphological features are the most common criteria used to select human embryos for transfer to a receptive uterine cavity. However, such characteristics are not valid for embryos in cellular arrest. Even aneuploid embryos can have normal morphology, and some euploid embryos have aberrant morphology. The aim of this study was to quantify the expression profile of hsa-miR-21-3p, -24-1-5p, -191-5p, and -372-5p in culture media on day 5 of in vitro embryo development, and compare the profiles of two groups of media classified by outcome: successful (n = 25) or unsuccessful (n = 25) implantation pregnancy.

METHODS

Fifty patients were accepted in the Department of Reproductive Biology of a Hospital in México City, based on the Institutional inclusion criteria for in vitro fertilization. Embryos were transferred to the women on day 5 of cultivation, and the culture media were collected. RNA was isolated from each culture medium with TRIzol reagent, and microRNA (miRNA) expression was detected through RT-PCR with specific primers. Expression bands were quantified by reading optical density.

RESULTS

There was a 5.2-fold greater expression of hsa-miR-191-5p in the pregnancy-related culture media (p ≤ 0.001) and a 1.6-fold greater level of hsa-miR-24-1-5p (p = 0.043) in the media corresponding to non-pregnant women. No significant difference existed between the two groups hsa-miR-21-3p (p = 0.38) or hsa-miR-372-5p (p = 0.41).

CONCLUSIONS

Regarding adequate in vitro embryo development, hsa-miR-191-5p could possibly represent a positive biomarker, while has-miR-24-1-5p may indicate poor prognosis. This former miRNA modulates IGF2BP-1 and IGF2R, associated with the implantation window. On the other hand, hsa-miR-24-1-5p may be related to a poor prognosis of human embryo development.

One-step enzyme-free detection of the miRNA let-7a via twin-stage signal amplification

MicroRNAs (miRNAs) play a significant role in diverse biological processes. The abnormal expression of miRNAs is related to the development of cancers and various diseases. It is of great importance to sensitively and accurately detect miRNAs for early disease diagnosis and treatment. Here, a new fluorescence strategy was initially proposed for the enzyme-free sensing of let-7a by combining the strand displacement reaction (SDR) with the hybridization chain reaction (HCR). The sensor was successfully applied to the detection of the let-7a gene with a wide linear range from 25 pM to 250 nM and a limit of detection (LOD) of 9.01 pM. The fluorescence intensity has a good linear relationship with the logarithm of the target concentration. In addition, the biosensor allowed for the highly sensitive detection of the target genes even in complex human serum samples. With simple operation yet improved detection capability for let-7a, the developed fluorescent biosensor thus shows great potential for early clinical diagnosis as well as biological research.

Versatile Electrochemiluminescence and Photoelectrochemical Detection of Glutathione Using Mn2+ Substitute Target by DNA-Walker-Induced Allosteric Switch and Signal Amplification

Glutathione (GSH) serves vital functions in biological systems and associates with various human diseases. In this work, a versatile electrochemiluminence (ECL) and a photoelectrochemical (PEC) "signal on" biosensing platform were developed for a sensitive assay of GSH by a Mn²⁺-powered DNAzyme amplification strategy combined with DNA-walker-triggered allosteric conversion. First, MnO₂ nanosheets were reduced to Mn²⁺ by GSH; then, Mn²⁺ as a substitute target triggered DNAzyme-assisted cleavage-cycling amplification to generate numerous DNA output (s3). Meanwhile, the DNA molecular machine was introduced to bridge signal probes for versatile biosensing, which included hairpin DNA as a track and an arm as a walker. The presence of DNA output (s3) activated the swing arm to hybridize with hairpin DNA and then cut it by Nt.BbvCI, which initiated autonomous walking of the arm for forming a large number of streptavidin (SA) aptamers. Thus, a large number of CdS:Mn-SA tags as versatile signal probes was linked to the electrode by specific SA-aptamer binding, generating highly enhanced ECL and PEC signals for sensitive detection of the target. The present biosensing system take advantage of metal ion-based DNAzyme amplification, a DNA walker machine, multi-signals of QDs, and specificity of aptamers, which can provide a universal and efficient biosensing method for detecting various targets. The designed strategy demonstrated good performance for a GSH assay in human serum samples, showing more promising applications than other reported methods.

Electrochemiluminescence biosensor for miRNA-21 based on toehold-mediated strand displacement amplification with Ru(phen)32+ loaded DNA nanoclews as signal tags

A novel electrochemiluminescence (ECL) biosensor was developed for high sensitive and selective detection of miRNA-21 based on the efficient and specific toehold-mediated strand displacement (TMSD) amplification with Ru(phen)₃²⁺ loaded DNA nanoclews (NCs-Ru(phen)₃²⁺) as signal tags. The stable DNA nanoclews, synthesized by a simple rolling circle amplification reaction, were employed to load with Ru(phen)₃²⁺ efficiently as ECL signal tags to amplify the signals. As for TMSD, the substrate strand (Sub) was initially hybridized with P1 and P2 to form DNA duplex structures with a toehold 1. miRNA-21 could hybridize with the toehold 1 and trigger the TMSD amplification with the help of assist strand, releasing lots of P1 stands from DNA duplex structures. The TMSD technique realized the converting and amplification of the single miRNA-21 input to lots of output DNA (namely P1) with good selectivity, simultaneously. Output P1 were designed to expand the stem-locked region of HP, which were immobilized on the Au electrodes firstly. Subsequently, the opened HP could hybridize with the Ru(phen)₃²⁺, capturing the ECL signal tags closed to the sensing surface. The ECL intensity of the system had a linear relationship with the logarithm of the miRNA-21 concentration in the range of 1.0 fM to 100 pM with a limit of detection of 0.65 fM. The strategy was further applied to detect miRNA-21 in complex samples, and the result was consistent with the qRT-PCR.

Detection of Several Homologous MicroRNAs by a Single Smart Probe System Consisting of Linear Nucleic Acid Blockers

We report a universal smart probe (SP) that is capable of detecting several homologous let-7 microRNAs (miRNAs). While the SP is complementary to let-7a, and therefore, strongly binds to this target, due to sequence homology, the SP also has equal propensity to non-specifically hybridize with let-7b and let-7c, which are homologous to let-7a. The fluorescence signal of the SP was switched off in the absence of any homologous member target, but the signal was switched on when any of the three homologous members was present. With the assistance of nucleic acid blockers (NABs), this SP system can discriminate between homologous miRNAs. We show that the SP can discriminate between let-7a and the other two sequences by using linear NABs (LNABs) to block non-specific interactions between the SP and these sequences. We also found that LNABs used do not cross-react with the let-7a target due to the low LNABs:SP molar ratio of 6:1 used. Overall, this SP represents a universal probe for the recognition of a homologous miRNA family. The assay is sensitive, providing a detection limit of 6 fmol. The approach is simple, fast, usable at room temperature, and represents a general platform for the in vitro detection of homologous microRNAs by a single fluorescent hairpin probe.

A label-free aptamer-based biosensor for microRNA detection by the RNA-regulated fluorescence of malachite green

MicroRNAs (miRNAs) have been considered as promising molecular biomarkers for disease diagnosis, prognosis, as well as drug development. Herein, we wish to report a low background and label-free aptamer-based biosensor for miRNA assay by RNA-regulated fluorescence of malachite green (MG). In this biosensor-based strategy, target miRNA can specifically hybridize with the DNA extension template to form the T7 in vitro transcription system. Then the following transcription amplification produces a large number of MG RNA aptamers (MGAs) which light up the fluorescence of the MG, achieving significant fluorescence enhancement for miRNA quantitative analysis. The aptamer-based biosensor exhibits high sensitivity with a quite low detection limit of 10 amol target miRNA and high specificity to clearly discriminate very similar miRNA family members, even only one base difference. Furthermore, we have demonstrated that the biosensor is practical and reliable for the quantitative detection of miRNA in complex real samples.

A modified exponential amplification reaction (EXPAR) with an improved signal-to-noise ratio for ultrasensitive detection of polynucleotide kinase

We reported a modified exponential amplification reaction strategy and applied it to design an ultrasensitive biosensor for the detection of endogenous polynucleotide kinase activity at single-cell level.

An Enzyme-Free MicroRNA Assay Based On Fluorescence Counting of Click Chemical Ligation-Illuminated Magnetic Nanoparticles with Total Internal Reflection Fluorescence Microscopy

MicroRNAs (miRNAs) have been considered as promising cancer biomarkers. However, the simple but sensitive detection of low levels of miRNAs in biological samples still remains challenging. Herein, we wish to report an entirely enzyme-free, simple, and highly sensitive miRNA assay based on the counting of cycling click chemical ligation (3CL)-illuminated fluorescent magnetic nanoparticles (MNPs) with a total internal reflection fluorescence microscopy (TIRFM). In this strategy, each miRNA molecule can trigger many cycles of click chemical ligation reactions to produce plentiful ligated oligonucleotides (ODNs) with both 5'-biotin and 3'-fluorophore, resulting in efficient signal amplification. It is worth noting that only the ligated ODNs can bring fluorophores onto streptavidin-functionalized MNPs (STV-MNPs). Notably, merely 10 fluorescent molecules on each 50 nm MNP can make it bright enough to be clearly visualized by the TIRFM, which can significantly improve the detection sensitivity for miRNA. Through fluorescence counting of individual MNPs and integrating their fluorescence intensities, the amount of target miRNA can be quantitatively determined. This miRNA assay can be accomplished in a mix-and-read manner just by simply mixing the enzyme-free 3CL reaction system with the MNPs before TIRFM imaging, which avoids tedious immobilization, washing, and purification steps. Despite the extremely simple operation, this strategy exhibits high sensitivity with a quite low detection limit of 50 fM target miRNA as well as high specificity to well discriminate miRNA sequences with a single-base variation. Furthermore, the applicability of this method in real biological samples is also verified through the accurate detection of the miRNA target in cancer cells.

Portable fluorescence-based microRNA detection system based on isothermal signal amplification technology

MicroRNAs (miRNAs) diagnostics can be useful for diagnosing or confirming miRNA abundance and are used in screening tests and to assess changes in miRNAs in vivo. At present, the use of traditional nucleic acid amplification assays to detect miRNAs has been limited in laboratory environment because of the time, equipment, and technical expertise required to perform these assays. A specialized, rapid affordable miRNA detection system is necessary when there are limited resources or point-of-care testing needs. We designed a portable and affordable fluorescence-based miRNA detection system based on isothermal signal amplification technology, using SYBR Green II as a fluorescent dye. To reduce costs, we chose LED as a light source and designed the corresponding optical path for LED. The portable detection system shows results consistent with those by real-time PCR, and can be used to detect miR-183 with a limit of detection of approximately 2 fmol. We used the system to detect miR-183 in tissues and blood from patients with hepatocellular carcinoma (HCC). The results from the portable detection device were compared with those from clinical trials and indicated that the miR-183 fluorescence signal could successfully identify HCC and provide information related to cancer progression.

Single-step, high-specificity detection of single nucleotide mutation by primer-activatable loop-mediated isothermal amplification (PA-LAMP)

Loop-mediated isothermal amplification (LAMP) is a useful platform for nucleic acids detection in point-of-care (POC) situations, and development of single-step, close-tube LAMP reactions for specific detection of single nucleotide mutations (SNMs) remains a challenge. We develop a novel primer-activatable LAMP (PA-LAMP) strategy that enables highly specific and sensitive SNM detection using single-step, close-tube reactions. This strategy designs a terminal-blocked inner primer with a ribonucleotide insertion, which is cleaved and activated specifically to perfectly matched targets by ribonuclease (RNase) H2, to realize efficient amplification of mutant genes. It has shown dynamic responses of mutant target in a linear range from 220 aM to 22 pM with a lowest detectable concentration of 22 aM. It also demonstrates very high specificity in identifying the mutant in a large excess of the wild-type with a discrimination ratio as high as ∼10,000. It has been successfully applied to mutation detection of genomic DNA in tumor cells. The PA-LAMP strategy provides a useful, portable and affordable POC platform for highly sensitive and specific detection of genetic mutations in clinical applications.

Rational construction of a DNA nanomachine for HIV nucleic acid ultrasensitive sensing

HIV nucleic acids, one kind of significant biomarker, play an important role in fundamental studies and clinical diagnosis. Importantly, the early accurate diagnosis for HIV nucleic acids at ultralow concentrations can potentially extend the life of patients. In the current work, we developed a DNA nanomachine on gold nanoparticles (AuNPs) coupling rolling circle amplification and DNA walker cascade amplification for ultrasensitive detection of HIV nucleic acids. This DNA nanomachine sensing strategy exhibits a significantly low detection limit down to 1.46 fM. Furthermore, this DNA nanomachine biosensor is capable of detecting target DNA in real samples because of its high selectivity and sensitivity. Moreover, the DNA nanomachine biosensor is capable of discriminating single-base mismatch lower than 3.5 pM. The results showed that this DNA nanomachine biosensor has the potential for biomedical studies and clinical applications.

Exponential Isothermal Amplification of Nucleic Acids and Assays for Proteins, Cells, Small Molecules, and Enzyme Activities: An EXPAR Example

Isothermal exponential amplification techniques, such as strand-displacement amplification (SDA), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence based amplification (NASBA), helicase-dependent amplification (HDA), and recombinase polymerase amplification (RPA), have great potential for on-site, point-of-care, and in situ assay applications. These amplification techniques eliminate the need for temperature cycling, as required for the polymerase chain reaction (PCR), while achieving comparable amplification yields. We highlight here recent advances in the exponential amplification reaction (EXPAR) for the detection of nucleic acids, proteins, enzyme activities, cells, and metal ions. The incorporation of fluorescence, colorimetric, chemiluminescence, Raman, and electrochemical approaches enables the highly sensitive detection of a variety of targets. Remaining issues, such as undesirable background amplification resulting from nonspecific template interactions, must be addressed to further improve isothermal and exponential amplification techniques.

Click Chemical Ligation-Initiated On-Bead DNA Polymerization for the Sensitive Flow Cytometric Detection of 3'-Terminal 2'-O-Methylated Plant MicroRNA

A versatile flow cytometric strategy is developed for the sensitive detection of plant microRNA (miRNA) by coupling the target-templated click nucleic acid ligation (CNAL) with on-bead terminal enzymatic DNA polymerization (TEP). Unlike ligase-catalyzed ligation reaction, the plant miRNA-templated enzyme-free CNAL between two single-stranded DNA (ssDNA) probes, respectively modified with Aza-dibenzocyclooctyne (Aza-DBCO) and N₃, can not only simplify the operation, but also achieve a much higher ligation efficiency. More importantly, the undesirable nonspecific ligation between the Aza-DBCO- and N₃-modified ssDNA, can be effectively eliminated by adding Tween-20, which allows the use of cycling CNAL (CCNAL) in a background-free manner. So each plant miRNA can template many rounds of CNAL reaction to produce numerous ligation products, forming efficient signal amplification. The ligated ssDNA can be anchored on the magnetic beads (MBs) with the 3'-OH termini exposed outside. Then terminal deoxynucleotidyl transferase (TdT), a sequence-independent and template-free polymerase, would specifically catalyze the DNA polymerization along these 3'-OH termini on the MBs, forming poly(T) tails up to thousands of nucleotides long. Each poly(T) tail allows specific binding of numerous 6-carboxyfluorescein (FAM)-labeled poly(A)25 oligonucleotides to accumulate a lot of fluorophores on the MBs, leading to the second step of signal amplification. By integrating the advantages of CCNAL-TEP for highly efficient signal amplification and robust MBs signal readout with powerful flow cytometer, high sensitivity is achieved and the detection limit of plant miRNA has been pushed down to a low level of 5 fM with high specificity to well discriminate even single-base difference between miRNA targets.

Imaging multiple microRNAs in living cells using ATP self-powered strand-displacement cascade amplification

Herein, we design a smart autonomous ATP self-powered strand-displacement cascade amplification (SDCA) system for highly sensitive multiple intracellular miRNA detection. Rationally engineered Y-motif DNA structures are functionalized on mesoporous silica-coated copper sulfide nanoparticles loaded with numerous ATPs (CuS@mSiO2-Y/ATP) through pH stimulus-responsive disulfide bonds. The SDCA system is implemented by endogenous specific miRNA as a trigger and ATP as fuel released from the nanocarrier at acidic pH and photothermal stimuli-responsive CuS. The ATP self-powered SDCA process presents higher sensitivity compared to that without amplification for intracellular miRNA imaging. Two-color simultaneous and sensitive imaging of multiple cancer-related miRNAs in living cells is also confirmed. This enables facile and accurate differentiation between normal cells and different types of cancer cell using intracellular miRNA imaging, which improves the veracity and timeliness for early cancer diagnosis.

Imaging of intracellular-specific microRNA in tumor cells by symmetric exponential amplification-assisted fluorescence in situ hybridization

A symmetric exponential amplification-assisted fluorescence in situ hybridization (SEXPAR-FISH) strategy was reported for imaging intracellular-specific microRNAs.

Design and Characterization of a Singly Labeled Fluorescent Smart Probe for In Vitro Detection of miR-21

A sensitive hairpin smart probe (SP) has been developed and tested for its sequence-specificity and sensitivity for detecting microRNAs (miRNAs). The loop sequence of this SP is perfectly complementary to microRNA-21 (miR-21) sequence. This miRNA regulates certain biological processes and has been implicated in certain forms of cancer. The stem of the new SP consists of a fluorophore on one end and multiple guanine bases on the opposing end are used as quenchers. The fluorescence of the SP is significantly quenched by the guanine bases at room temperature and in the absence of the miR-21 target. The presence of miR-21 switches on the fluorescence due to spontaneous hybridization of the SP with this target, which also forces the stem hybrid of the SP apart. This new SP successfully discriminated between the perfect miR-21 target and two closely similar single-base mismatch sequences. When the SP was incubated with the miR-21 at 37 ℃, the hybridization kinetics increased seven times, compared to room temperature hybridization. Overall, this new SP shows good detection sensitivity and gives a limit of detection and limit of quantitation of 14.0 nM and 46.7 nM, respectively. This detection platform represents a simple, fast, mix-and-read homogeneous assay for sequence-specific detection of miR-21, and it can be adapted for other related diagnostic applications.

Single-step, homogeneous and sensitive detection for microRNAs with dual-recognition steps based on luminescence resonance energy transfer (LRET) using upconversion nanoparticles

A single-step, homogeneous and sensitive LRET assay is presented for the detection of miRNAs. The amplification-free assay provides a unique combination of high specificity with dual-recognition approach of different hybridization and ligation steps and preventing background auto-fluorescence in biological samples using upconversion nanoparticles (UCNPs) as signal-producing nanoprobes. The assay probe is composed of signal-producing unit (a pair of homogeneous upconversion luminescence resonance energy transfer (UC-LRET)-based oligonucleotides) and recognition unit (two adaptor oligonucleotides). In the presence of target miRNAs, the probe and target miRNAs leads to the formation of stable double-strands and semi-stable adaptor-miRNAs complexes with an adaptor nick. Ligation of the nick using ligase cause the formation of stable double-strands, resulting in UCNPs-to-dye UC-LRET for detection of the miRNAs with near-infrared radiation (980nm). Sensitive detection of miRNA-21 at concentrations of 200pM to 1.4nM and detection limits of 0.095nM with good precision of 3.9% (RSD) for seven repeated measurements of 500pM miRNAs demonstrate the feasibility of both high throughput and point-of-care clinical diagnostics. The homogeneous UC-LRET assay without any washing can be extended to the application in other important types of nucleic acid analysis.

Mimicking an Enzyme-Based Colorimetric Aptasensor for Antibiotic Residue Detection in Milk Combining Magnetic Loop-DNA Probes and CHA-Assisted Target Recycling Amplification

A mimicking-enzyme-based colorimetric aptasensor was developed for the detection of kanamycin (KANA) in milk using magnetic loop-DNA-NMOF-Pt (m-L-DNA) probes and catalytic hairpin assembly (CHA)-assisted target recycling for signal amplification. The m-L-DNA probes were constructed via hybridization of hairpin DNA H1 (containing aptamer sequence) immobilized magnetic beads (m-H1) and signal DNA (sDNA, partial hybridization with H1) labeled nano Fe-MIL-88NH₂-Pt (NMOF-Pt-sDNA). In the presence of KANA and complementary hairpin DNA H2, the m-L-DNA probes decomposed and formed an m-H1/KANA intermediate, which triggered the CHA reaction to form a stable duplex strand (m-H1-H2) while releasing KANA again for recycling. Consequently, numerous NMOF-Pt-sDNA as mimicking enzymes can synergistically catalyze 3,3',5,5'-tetramethylbenzidine (TMB) for color development. The aptasensor exhibited high selectivity and sensitivity for KANA in milk with a detection limit of 0.2 pg mL^-1 within 30 min. The assay can be conveniently extended for on-site screening of other antibiotics in foods by simply changing the base sequence of the probes.

Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification

LS-MMB based intra-SDA and inter-SDA for amplified gene signaling.

Multiplexed detection of microRNAs by a competitive DNA microarray-based resonance light scattering assay

A competitive DNA microarray-based resonance light scattering assay is developed for the selective and sensitive detection of multiple microRNAs.

Label-free detection of microRNA based on coupling multiple isothermal amplification techniques

MicroRNA (miRNA) was a promising class of cancer biomarkers. Here we developed a label-free method for sensitive measurement of let-7d miRNA based on multiple amplification techniques. The primer will bind to the duplex strand DNA that was formed by stem-loop template and target let-7d to initiate strand displacement amplification (SDA) in tandem. The released single strand DNA will be a primer to bind the circular template to initiate rolling circle amplification (RCA). The products based on multiple amplifications will be detected by a standard fluorimeter with N-methyl mesoporphyrin IX (NMM) as the fluorescent indicator. The proposed method exhibited excellent selectivity and high sensitivity with a detection limit of as low as 1.5 × 10⁻¹³ M. Moreover, this methodology was used for the determination of biomolecules in real serum samples with satisfying results.