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.

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.

Beacon-mediated exponential amplification reaction (BEAR) using a single enzyme and primer

Beacon-mediated Exponential Amplification Reaction (BEAR) enables isothermal, exponential signal amplification. BEAR uses only a single enzyme and a single primer. Detection of 0.2 amol of a mitochondrial DNA with a point mutation in less than an hour demonstrates an application of the BEAR technique for nucleic acid research.

Competitive fluorometric assay for the food toxin T-2 by using DNA-modified silver nanoclusters, aptamer-modified magnetic beads, and exponential isothermal amplification

The authors describe an aptamer based assay for the mycotoxin T-2. The method is making use of exponential isothermal amplification reaction (EXPAR) and fluorescent silver nanoclusters (AgNCs). Free T-2 and cDNA (which is a DNA that is partially complementary to the aptamer) compete for binding to aptamer-modified magnetic beads. The cDNA collected by magnetic separation can be used as a primer to trigger EXPAR to obtain ssDNA. The C-base-rich ssDNA binds and reduces Ag(I) ion to form fluorescent AgNCs. Fluorescence is measured at excitation/emission wavelengths of 480/525 nm. T-2 can be detected by fluorometry with a detection limit as low as 30 fg·mL^-1. The method was applied to analyse spiked oat and corn, and the average recoveries ranged from 97.3 to 102.3% and from 95.9 to 107.5%, respectively. The results were in good agreement with data of the commercial ELISA kit. The assay is highly sensitive, has a wide analytical range, good specificity and reliable operation. It provides a promising alternative for the standard method for quantitative detection of T-2. Graphical abstract Schematic presentation of fluorometric assay for T-2 based on aptamer-functionalized magnetic beads exponential, isothermal amplification reaction (EXPAR) and fluorescent silver nanoclusters (AgNCs).

A catalytic DNA circuit-programmed and enzyme-powered autonomous DNA machine for nucleic acid detection

A catalytic DNA circuit-programmed and enzyme-powered autonomous DNA machine was proposed for one-step, isothermal and dual-level amplified detection of nucleic acids.

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.