The isothermal amplification detection of double-stranded DNA based on a double-stranded fluorescence probe

Label-free DNA quantification using isothermal amplification on an exposed core optical fiber microfluidic platform

Isothermal amplification technology has triggered a surge in research due to its compatibility with small and portable equipment, simplicity, and high efficiency, especially in light of the COVID-19 pandemic where reliable widescale testing is critical to outbreak management. In this paper, a label-free isothermal deoxyribonucleic acid (DNA) amplification method based on refractive index (RI) quantification is proposed and demonstrated for the first time by combining optical fiber sensing, microfluidics, and isothermal amplification. A highly RI-sensitive Mach-Zehnder (MZ) interference is formed by splicing a short length of an exposed-core fiber between two lengths of a single-mode fiber while the microfluidic liquid channel on the exposed side of the ECF is filled with target DNA and the amplification solution. Real-time quantitative measurement of the target DNA is then realized by monitoring the change in RI of the solution during the isothermal DNA amplification process. The experimental results show that the platform successfully realizes real-time label-free monitoring of isothermal amplification of 0.16 aM DNA samples. This method is a breakthrough for applications in the fields of DNA detection and quantification where simple operation, rapid detection, portability, small size, high selectivity, and high sensitivity are required.

Simulation-Guided Rational Design of DNA Probe for Accurate Discrimination of Single-Nucleotide Variants Based on "Hill-Type" Cooperativity

The accurate discrimination of single-nucleotide variants is of great interest for disease diagnosis and clinical treatments. In this work, a unique DNA probe with "Hill-type" cooperativity was first developed based on toehold-mediated strand displacement processes. Under simulation, this probe owns great thermodynamics advantage for specificity due to two mismatch bubbles formed in the presence of single-nucleotide variants. Besides, the strategies of ΔG' = 0 and more competitive strands are also beneficial to discriminate single-nucleotide variants. The feasibility of this probe was successfully demonstrated in consistent with simulation results. Due to "Hill-type" cooperativity, the probe allows a steeper dynamic range compared with previous probes. With simulation-guided rational design, the resulting probe can accurately discriminate single-nucleotide variants including nucleotide insertions, mutation, and deletions, which are arbitrarily distributed in target sequence. Two specificity parameters were calculated to quantitatively evaluate its good discrimination ability. Hence, "Hill-type" cooperativity can serve as a novel strategy in DNA probe's design for accurate discrimination of single-nucleotide variants.

Isothermal Background-Free Nucleic Acid Quantification by a One-Pot Cas13a Assay Using Droplet Microfluidics

High sensitivity and specificity nucleic acid detection has been achieved by the Cas13a collateral effect in combination with a separate recombinase polymerase amplification (RPA). However, these emerging methods cannot provide accurate quantification of nucleic acids because the two-step assay performance may be compromised if the RPA and Cas13a reactions are simply unified in a single step. In this work, we first addressed the challenges associated with enzymatic incompatibility and the macromolecular crowding effect in the one-pot assay development, making the consolidated RPA-Cas13a assay a facile and robust diagnostic tool. Next, we found that the one-pot reaction cannot precisely quantify the targets at low concentrations. Thus, by leveraging droplet microfluidics, we converted the one-pot assay to a digital quantification format, termed Microfluidics-Enabled Digital Isothermal Cas13a Assay (MEDICA). Due to the droplet compartmentation, MEDICA greatly accelerates the reaction and enables relative detection in 10 min and the end-point quantification in 25 min. Moreover, MEDICA facilitates the droplet binarization for counting because of background-free signals generated by trans-cleavage reporting of Cas13a. Our clinical validation highlights that CRISPR-based isothermal assays are promising for the next generation of nucleic acid quantification methods.

Ultrasensitive competitive detection of patulin toxin by using strand displacement amplification and DNA G-quadruplex with aggregation-induced emission

A novel sensitive assay was established by using strand displacement amplification (SDA) and DNA G-quadruplex with aggregation-induced emission (AIE) for the detection of patulin (PAT) toxin. The complementary DNA (cDNA) of the aptamer and PAT competed for binding to aptamer-modified magnetic beads. The cDNA was obtained by magnetic separation and used as a primer in SDA to produce a large amount of G-base single-stranded DNA (ssDNA). They can form the G-quadruplex to be combined with the AIE of TTAPE dye, which features a special combination of G-quadruplex that amplify the fluorescent signals. This work can reach a lower detection limit of 0.042 pg mL^-1 with a wide linear range of 0.001-100 ng mL^-1 for PAT detection than other methods. The results also showed good recoveries of 97.8%-104% and 101.7%-105.3% in spiked apple and grape juices, respectively. The assay used for the detection of PAT exhibits high sensitivity and good specificity. It also provides a stable and reliable platform for detecting other small-molecule toxins.

Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Triggered Isothermal Amplification for Site-Specific Nucleic Acid Detection

A novel CRISPR/Cas9 triggered isothermal exponential amplification reaction (CAS-EXPAR) strategy based on CRISPR/Cas9 cleavage and nicking endonuclease (NEase) mediated nucleic acids amplification was developed for rapid and site-specific nucleic acid detection. CAS-EXPAR was primed by the target DNA fragment produced by cleavage of CRISPR/Cas9, and the amplification reaction performed cyclically to generate a large number of DNA replicates which were detected using a real-time fluorescence monitoring method. This strategy that combines the advantages of CRISPR/Cas9 and exponential amplification showed high specificity as well as rapid amplification kinetics. Unlike conventional nucleic acids amplification reactions, CAS-EXPAR does not require exogenous primers, which often cause target-independent amplification. Instead, primers are first generated by Cas9/sgRNA directed site-specific cleavage of target and accumulated during the reaction. It was demonstrated this strategy gave a detection limit of 0.82 amol and showed excellent specificity in discriminating single-base mismatch. Moreover, the applicability of this method to detect DNA methylation and L. monocytogenes total RNA was also verified. Therefore, CAS-EXPAR may provide a new paradigm for efficient nucleic acid amplification and hold the potential for molecular diagnostic applications.

New nucleic acid testing devices to diagnose infectious diseases in resource-limited settings

Point-of-care diagnosis based on nucleic acid testing aims to incorporate all the analytical steps, from sample preparation to nucleic acid amplification and detection, in a single device. This device needs to provide a low-cost, robust, sensitive, specific, and easily readable analysis. Microfluidics has great potential for handling small volumes of fluids on a single platform. Microfluidic technology has recently been applied to paper, which is already used in low-cost lateral flow tests. Nucleic acid extraction from a biological specimen usually requires cell filtration and lysis on specific membranes, while affinity matrices, such as chitosan or polydiacetylene, are well suited to concentrating nucleic acids for subsequent amplification. Access to electricity is often difficult in resource-limited areas, so the amplification step needs to be equipment-free. Consequently, the reaction has to be isothermal to alleviate the need for a thermocycler. LAMP, NASBA, HDA, and RPA are examples of the technologies available. Nucleic acid detection techniques are currently based on fluorescence, colorimetry, or chemiluminescence. For point-of-care diagnostics, the results should be readable with the naked eye. Nowadays, interpretation and communication of results to health professionals could rely on a smartphone, used as a telemedicine device. The major challenge of creating an "all-in-one" diagnostic test involves the design of an optimal solution and a sequence for each analytical step, as well as combining the execution of all these steps on a single device. This review provides an overview of available materials and technologies which seem to be adapted to point-of-care nucleic acid-based diagnosis, in low-resource areas.

Self-primed isothermal amplification for genomic DNA detection of human papillomavirus

Rolling circle amplification (RCA) is an isothermal amplification technique with high efficiency and perfect accuracy for nucleic acids detection. However, RCA technique suffers the limitation to detect short DNA or RNA molecules. For long nucleic acid molecules, enzymatic restriction as well as heat denaturation process is usually required, which makes the amplification not effective and strictly isothermal. In this article, a simple and efficient one-pot self-primed isothermal amplification (SIA) was developed for detection of genomic DNA directly based on the combination of nicking endonuclease assisted strand displacement amplification (SDA) and exponential RCA. In virtue of numerous nicking sites on the genome, a pre-amplification of the whole genome was performed through SDA with the specific cleaving of nicking endonuclease. Meanwhile, the single strand DNA with HPV target sequence generated from SDA could hybrid with the circle probe as a primer and trigger the exponential RCA as a result of the existence of nicking endonuclease. As the reaction temperature and enzyme were the same, the amplification could be operated in one pot. The reaction solution after amplification was added on the electrode for hybridization with the sulfydryl probe to achieve the electrochemical signal. Based on the isothermal amplification, genotyping of HPV 11, 16, 18 and the detection of HPV 18 in Hela cell line were attempted with satisfied results. This approach should be a promising tool for pathogene detection in clinical diagnostics and research.

Fluorescence recognition of double-stranded DNA based on the quenching of gold nanoparticles to a fluorophore labeled DNA probe

This work described an ultrasensitive fluorescent sensor for sequence-specific recognition of dsDNA based on the quenching of gold nanoparticles (AuNPs) to a fluorophore labeled DNA probe.