Palm-Sized Lab-In-A-Magnetofluidic Tube Platform for Rapid and Sensitive Virus Detection.

Simple, sensitive, and accurate molecular diagnostics are critical for preventing rapid spread of infection and initiating early treatment of diseases. However, current molecular detection methods typically rely on extensive nucleic acid sample preparation and expensive instrumentation. Here, a simple, fully integrated, lab-in-a-magnetofluidic tube (LIAMT) platform is presented for "sample-to-result" molecular detection of virus. By leveraging magnetofluidic transport of micro/nano magnetic beads, the LIAMT device integrates viral lysis, nucleic acid extraction, isothermal amplification, and CRISPR detection within a single engineered microcentrifuge tube. To enable point-of-care molecular diagnostics, a palm-sized processor is developed for magnetofluidic separation, nucleic acid amplification, and visual fluorescence detection. The LIAMT platform is applied to detect SARS-CoV-2 and HIV viruses, achieving a detection sensitivity of 73.4 and 63.9 copies µL-1, respectively. Its clinical utility is further demonstrated by detecting SARS-CoV-2 and HIV in clinical samples. This simple, affordable, and portable LIAMT platform holds promise for rapid and sensitive molecular diagnostics of infectious diseases at the point-of-care.

Intrinsic RNA Targeting Triggers Indiscriminate DNase Activity of CRISPR-Cas12a.

The CRISPR-Cas12a system has emerged as a powerful tool for next-generation nucleic acid-based molecular diagnostics. However, it has long been believed to be effective only on DNA targets. Here, we investigate the intrinsic RNA-enabled trans-cleavage activity of AsCas12a and LbCas12a and discover that they can be directly activated by full-size RNA targets, although LbCas12a exhibits weaker trans-cleavage activity than AsCas12a on both single-stranded DNA and RNA substrates. Remarkably, we find that the RNA-activated Cas12a possesses higher specificity in recognizing mutated target sequences compared to DNA activation. Based on these findings, we develop the "Universal Nuclease for Identification of Virus Empowered by RNA-Sensing" (UNIVERSE) assay for nucleic acid testing. We incorporate a T7 transcription step into this assay, thereby eliminating the requirement for a protospacer adjacent motif (PAM) sequence in the target. Additionally, we successfully detect multiple PAM-less targets in HIV clinical samples that are undetectable by the conventional Cas12a assay based on double-stranded DNA activation, demonstrating unrestricted target selection with the UNIVERSE assay. We further validate the clinical utility of the UNIVERSE assay by testing both HIV RNA and HPV 16 DNA in clinical samples. We envision that the intrinsic RNA targeting capability may bring a paradigm shift in Cas12a-based nucleic acid detection and further enhance the understanding of CRISPR-Cas biochemistry.

CRISPR-powered quantitative keyword search engine in DNA data storage.

Despite the growing interest of archiving information in synthetic DNA to confront data explosion, quantitatively querying the data stored in DNA is still a challenge. Herein, we present Search Enabled by Enzymatic Keyword Recognition (SEEKER), which utilizes CRISPR-Cas12a to rapidly generate visible fluorescence when a DNA target corresponding to the keyword of interest is present. SEEKER achieves quantitative text searching since the growth rate of fluorescence intensity is proportional to keyword frequency. Compatible with SEEKER, we develop non-collision grouping coding, which reduces the size of dictionary and enables lossless compression without disrupting the original order of texts. Using four queries, we correctly identify keywords in 40 files with a background of ~8000 irrelevant terms. Parallel searching with SEEKER can be performed on a 3D-printed microfluidic chip. Overall, SEEKER provides a quantitative approach to conducting parallel searching over the complete content stored in DNA with simple implementation and rapid result generation.

CRISPR-Powered DNA Computing and Digital Display.

Clustered regularly interspaced short palindromic repeats (CRISPR) technology has unique specificity for recognizing and cleaving target DNA complementary to the CRISPR guide sequence. Here, we report on a CRISPR-powered DNA computing and digital display system in which programmed DNA targets serve as the input and an ON/OFF fluorescence signal indicates a TRUE/FALSE output. This system allows the establishment of a one-to-one relationship between input and output, enabling multilevel DNA logic computing. Applying pre-CRISPR reactions that selectively maintain or inhibit CRISPR reactivity can further improve the computing capability by expanding input size. In particular, we present a paper-based microfluidic chip with freeze-dried CRISPR reaction mixtures that are programmed to digitally display the results of functional operations, including square, cube, and square-root operations. This strategy allows information decoding and displaying as well, which brings potential in next-generation DNA steganography and cryptography. We envision that the intrinsic orthogonality of CRISPR provides a new paradigm for DNA computing and molecular programming.

Electrochemical biotoxicity detection on a microfluidic paper-based analytical device via cellular respiratory inhibition.

A novel microfluidic paper-based analytical device (µPAD) was developed with benzoquinone (BQ)-mediated E. coli respiration method to measure the biotoxicities of pollutants. Functional units including sample injection, fluid-cell separation, all-carbon electrode-enabled electrochemical detection, were integrated on a piece of chromatography paper. The three-electrode, working electrode, counter electrode and reference electrode, were simultaneously screen-printed on the µPAD with conductive carbon ink. The satisfying electrochemical performance of the paper-based carbon three-electrode was confirmed by cyclic voltammetry detecting K3 [Fe(CN)6]. The process of cell toxication was considered that toxicants inhibited cell respiration and diminished the electrons on E. coli respiratory chain. It was quantitatively reflected by measuring oxidation current of hydroquinone (HQ) as a reduced state of the redox mediator BQ after the incubation of cells with pollutants. The current detection time, BQ concentration and E. coli incubation time were carefully optimized to establish the systematic optimized operations of BQ-mediated E. coli respiration method. Using the fabricated µPAD the half inhibitory concentration (IC50) were Cu2+ solution 13.5 µg mL-1, Cu2+-soil 21.4 mg kg-1, penicillin sodium-soil 85.1 mg kg-1, and IC30 of Pb2+ solution was 60.0 µg mL-1. Detection of pesticide residues in vegetable juices were accomplished in a similar way. The proposed method is fascinating on three points; 1) The generality in the biotoxicity detection depends on toxicants inducing cellular respiratory inhibition; 2) The portability and affordability make it convenient for practical applications, because of replacing incubators and centrifuges; 3) There is potential applicability in less-developed areas due to its simple operation and low-cost.