PAM-less conditional DNA substrates leverage trans-cleavage of CRISPR-Cas12a for versatile live-cell biosensing

The CRISPR-Cas system has been repurposed as a powerful live-cell imaging tool, but its utility is limited to genomic loci and mRNA imaging in living cells. Here, we demonstrated the potential of the CRISPR-Cas system as a generalizable live-cell biosensing tool by extending its applicability to monitor diverse intracellular biomolecules. In this work, we engineered a CRISPR-Cas12a system with a generalized stimulus-responsive switch mechanism based on PAM-less conditional DNA substrates (pcDNAs). The pcDNAs with stimulus-responsiveness toward a trigger were constructed from the DNA substrates featuring no requirement of a protospacer-adjacent motif (PAM) and a bubble structure. With further leveraging the trans-cleavage activity of CRISPR-Cas12a for signal reporting, we established a versatile CRISPR-based live-cell biosensing system. This system enabled the sensitive sensing of various intracellular biomolecules, such as telomerase, ATP, and microRNA-21, making it a helpful tool for basic biochemical research and disease diagnostics.

This work developed the PAM-less conditional DNA substrates that leverage the trans-cleavage effect of CRISPR-Cas12a to sense various biomolecules in living cells.     

2′-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR–Cas12a systems

The CRISPR–Cas12a system has been widely applied to genome editing and molecular diagnostics. However, off-target cleavages and false-positive results remain as major concerns in Cas12a practical applications. Herein, we propose a strategy by utilizing the 2′-O-methyl (2′-OMe) modified guide RNA (gRNA) to promote the Cas12a''s specificity. Gibbs free energy analysis demonstrates that the 2′-OMe modifications at the 3′-end of gRNA effectively suppress the Cas12a''s overall non-specific affinity while maintaining high on-target affinity. For general application illustrations, HBV genotyping and SARS-CoV-2 D614G mutant biosensing platforms are developed to validate the enhanced Cas12a''s specificity. Our results indicate that the 2′-OMe modified gRNAs could discriminate single-base mutations with at least two-fold enhanced specificity compared to unmodified gRNAs. Furthermore, we investigate the enhancing mechanisms of the 2′-OMe modified Cas12a systems by molecular docking simulations and the results suggest that the 2′-OMe modifications at the 3′-end of gRNA reduce the Cas12a''s binding activity to off-target DNA. This work offers a versatile and universal gRNA design strategy for highly specific Cas12a system development.

This study illustrates that 2′-O-methyl modified gRNAs improve the specificity of the CRISPR–Cas12a system (mg-CRISPR) via suppressing the Cas12a''s affinity to off-target DNA and provides an efficient strategy for high-specificity gRNA design.     

Universal and high-fidelity DNA single nucleotide polymorphism detection based on a CRISPR/Cas12a biochip

Single nucleotide polymorphisms (SNPs) are associated with many human diseases, so accurate and efficient SNP detection is of great significance for early diagnosis and clinical prognosis. This report proposes a universal and high-fidelity genotyping method in microfluidic point-of-care equipment based on the clustered regularly interspaced short palindromic repeat (CRISPR) system. Briefly, by systematically inserting the protospacer-adjacent-motif (PAM) sequence, we improved the universality of the CRISPR/Cas12a based SNP detection; by removing the complementary ssDNA and introducing an additional nucleotide mismatch, we improved the sensitivity and specificity. We preloaded the CRISPR/Cas12a reagents into the point-of-care biochip for automating the process, increasing the stability and long-term storage. This biochip enables us to rapidly and conveniently detect the genotypes within 20 min. In a practical application, the CRISPR/Cas12a biochip successfully distinguished three genotypes (homozygous wild type; the homozygous mutant type; and the heterozygous mutant type) of the CYP1A1*2 (A4889G, rs1048943), CYP2C19*2 (G681A, rs4244285), CYP2C9*3 (A1075C, rs1057910), and CYP2C19*3 (G636A, rs4986893) genes related to multiple cancers from 17 clinical blood samples. This CRISPR/Cas12a-based SNP genotyping method, being universal, accurate, and sensitive, will have broad applications in molecular diagnostics and clinical research.

A universal and high-fidelity genotyping method based on the clustered regularly interspaced short palindromic repeat (CRISPR) system was performed on the microfluidic point-of-care equipment.     

A fluorescent glucose bioassay based on the hydrogen peroxide-induced decomposition of a quencher system composed of MnO<Subscript>2</Subscript> nanosheets and copper nanoclusters

The authors describe a fluorometric glucose assay that is based on the use of MnO₂ nanosheets and copper nanoclusters (CuNCs) acting as nanoprobes. The CuNCs were synthesized by using bovine serum albumin as a template by chemical reduction of copper(II) sulfate. On addition of MnO₂ nanosheets to a colloidal solution of CuNCs, the fluorescence of CuNCs (measured at excitation/emission wavelengths of 335/410 nm) is quenched. However, in the presence of enzymatically generated H₂O₂, the MnO₂ nanosheets are reduced to form Mn(II) ions. As a result, fluorescence intensity recovers. The glucose assay is based on the enzymatic conversion of glucose by glucose oxidase to generate H₂O₂ and glucuronic acid. The calibration plot is linear in the 1 μM to 200 μM glucose concentration range, and the detection limit is 100 nM. The method was successfully applied to the determination of glucose in spiked human serum samples.

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Graphical abstract A sensitive fluorescent bioassay is reported for the detection of glucose based on the hydrogen peroxide-induced decomposition of a quencher system composed of MnO₂ nanosheets and copper nanoclusters (CuNCs).

     

An amplification-free ultra-sensitive electrochemical CRISPR/Cas biosensor for drug-resistant bacteria detection

Continued development of high-performance and cost-effective in vitro diagnostic tools is vital for improving infectious disease treatment and transmission control. For nucleic acid diagnostics, moving beyond enzyme-mediated amplification assays will be critical in reducing the time and complexity of diagnostic technologies. Further, an emerging area of threat, in which in vitro diagnostics will play an increasingly important role, is antimicrobial resistance (AMR) in bacterial infections. Herein, we present an amplification-free electrochemical CRISPR/Cas biosensor utilizing silver metallization (termed E-Si-CRISPR) to detect methicillin-resistant Staphylococcus aureus (MRSA). Using a custom-designed guide RNA (gRNA) targeting the mecA gene of MRSA, the Cas12a enzyme allows highly sensitive and specific detection when employed with silver metallization and square wave voltammetry (SWV). Our biosensor exhibits excellent analytical performance, with detection and quantitation limits of 3.5 and 10 fM, respectively, and linearity over five orders of magnitude (from 10 fM to 0.1 nM). Importantly, we observe no degradation in performance when moving from buffer to human serum samples, and achieve excellent selectivity for MRSA in human serum in the presence of other common bacteria. The E-Si-CRISPR method shows significant promise as an ultrasensitive field-deployable device for nucleic acid-based diagnostics, without requiring nucleic acid amplification. Finally, adjustment to a different disease target can be achieved by simple modification of the gRNA protospacer.

An amplification-free electrochemical CRISPR/Cas biosensor utilizing silver metallization (termed E-Si-CRISPR) allows detection of methicillin-resistant Staphylococcus aureus (MRSA) with excellent sensitivity and specificity.     

High-fidelity ATP imaging via an isothermal cascade catalytic amplifier

Artificial catalytic DNA circuits that can identify, transduce and amplify the biomolecule of interest have supplemented a powerful toolkit for visualizing various biomolecules in cancer cells. However, the non-specific response in normal tissues and the low abundance of analytes hamper their extensive biosensing and biomedicine applications. Herein, by combining tumor-responsive MnO₂ nanoparticles with a specific stimuli-activated cascade DNA amplifier, we propose a multiply guaranteed and amplified ATP-sensing platform via the successive cancer-selective probe exposure and stimulation procedures. Initially, the GSH-degradable MnO₂ nanocarrier, acting as a tumor-activating module, ensures the accurate delivery of the cascade DNA amplifier into GSH-rich cancer cells and simultaneously provides adequate Mn²⁺ cofactors for facilitating the DNAzyme biocatalysis. Then, the released cascade amplifier, acting as an ATP-monitoring module, fulfills the precise and sensitive analysis of low-abundance ATP in cancer cells where the catalyzed hairpin assembly (CHA) is integrated with the DNAzyme biocatalyst for higher signal gain. Additionally, the cascade catalytic amplifier achieved tumor-specific activated photodynamic therapy (PDT) after integrating an activatable photosensitizer into the system. This homogeneous cascade catalytic aptasensing circuit can detect low-abundance endogenous ATP of cancer cells, due to its intrinsically rich recognition repertoire and avalanche-mimicking hierarchical acceleration, thus demonstrating broad prospects for analyzing clinically important biomolecules and the associated physiological processes.

An on-site activated aptasensing platform is constructed for highly reliable ATP monitoring in cancer cells both in vitro and in vivo by combining tumor-specific activatable MnO₂ with the stimuli-responsive cascade DNA amplifier.     

Element coding based accurate evaluation of CRISPR/Cas9 initial cleavage

As a powerful gene editing tool, the kinetic mechanism of CRISPR/Cas9 has been the focus for its further application. Initial cleavage events as the first domino followed by nuclease end trimming significantly affect the final on-target rate. Here we propose EC-CRISPR, element coding CRISPR, an accurate evaluation platform for initial cleavage that directly characterizes the cleavage efficiency and breaking sites. We benchmarked the influence of 19 single mismatch and 3 multiple mismatch positions of DNA-sgRNA on initial cleavage, as well as various reaction conditions. Results from EC-CRISPR demonstrate that the PAM-distal single mismatch is relatively acceptable compared to the proximal one. And multiple mismatches will not only affect the cleavage efficiency, but also generate more non-site #3 cleavage. Through in-depth research of kinetic behavior, we uncovered an abnormally higher non-#3 proportion at the initial stage of cleavage by using EC-CRISPR. Together, our results provided insights into cleavage efficiency and breaking sites, demonstrating that EC-CRISPR as a novel quantitative platform for initial cleavage enables accurate comparison of efficiencies and specificities among multiple CRISPR/Cas enzymes.

Initial cleavage events as the first domino of CRISPR/Cas9 kinetic behaviors. To accurately evaluate the initial cleavage of Cas9, element coding CRISPR platform-enabled direct characterization of the cleavage efficiency and cleavage sites was proposed.     

Sensitive fluorescent light-up probe for enzymatic determination of glucose using carbon dots modified with MnO<Subscript>2</Subscript> nanosheets

We describe a highly sensitive glucose probe based on carbon dots modified with MnO₂. A strong reduction of the green fluorescence of the carbon dots (CDs) happened due to the surface energy transfer (SET) from CDs to the deposited MnO₂. In the presence of H₂O₂ (formed via enzymatic oxidation of glucose), fluorescence is restored because the MnO₂ nanosheets are reduced to form colorless Mn(II) ions. These findings were used to design a fluorometric glucose assay that has a detection limit as low as 44 nM (at an S/N ratio of 3).

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Graphical Abstract A strong reduction of the green fluorescence of the carbon dots (CDs) occurs due to surface energy transfer (SET) from CDs to the deposited MnO₂. In the presence of H₂O₂ (formed by enzymatic action of glucose oxidase) the MnO₂ nanosheets are reduced to form colorless Mn(II) ions, and glucose can be quantified by the fluorescence restored.

     

Aptasensor for ATP based on analyte-induced dissociation of ferrocene-aptamer conjugates from manganese dioxide nanosheets on a screen-printed carbon electrode

The authors report on a new electrochemical aptasensing strategy for the determination of adenosine - 5’-triphosphate (ATP) at picomolar levels. First, manganese dioxide (MnO₂) nanosheets with an average size of ~70 nm were synthesized via a hot-injection method on the basis of reaction between potassium permanganate and the cationic detergent cetyltrimethylammonium bromide. The resulting MnO₂ nanosheets were then immobilized onto a pretreated screen-printed carbon electrode which readily binds the ferrocene-labeled ATP aptamer through the van der Waals force between the nucleobases and the basal plane of the nanoflakes. The immobilized ferrocene-aptamer conjugates activates the electrical contact with the electrode and produces a strong signal in the potentials scanned (0.0 to 1.0 V vs. Ag/AgCl). Upon addition of ATP, it will react with the aptamer and cause the dissociation of the ferrocene-aptamer from the nanosheets, this resulting in a decrease in the electrical signal. Under optimal conditions, this platform exhibits a detection limit as low as 0.32 nM of ATP. The repeatability and intermediate precision is below 10.7 % at a 10 nM concentration level. The method was applied to analyze blank fetal calf serum spiked with ATP, and the recoveries (at 3 concentration levels) ranged between 91.3 and 118 %. This detection scheme is rapid, simple, cost-effective, and does not require extensive sample preparation or multiple washing steps.

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Graphic abstract MnO₂ nanosheets are used as the sensing platform for electrochemical detection of ATP based on target-induced dissociation of ferrocene-labeled aptamer.

     

Intra Q-body: an antibody-based fluorogenic probe for intracellular proteins that allows live cell imaging and sorting

Although intracellular biomarkers can be imaged with fluorescent dye(s)-labeled antibodies, the use of such probes for precise imaging of intracellular biomarkers in living cells remains challenging due to background noise from unbound probes. Herein, we describe the development of a conditionally active Fab-type Quenchbody (Q-body) probe derived from a monoclonal antibody (DO-1) with the ability to both target and spatiotemporally visualize intracellular p53 in living cells with low background signal. p53 is a key tumor suppressor and validated biomarker for cancer diagnostics and therapeutics. The Q-body displayed up to 27-fold p53 level-dependent fluorescence enhancement in vitro with a limit of detection of 0.72 nM. In fixed and live cells, 8.3- and 8.4-fold enhancement was respectively observed. Furthermore, we demonstrate live-cell sorting based on p53 expression. This study provides the first evidence of the feasibility and applicability of Q-body probes for the live-cell imaging of intrinsically intracellular proteins and opens a novel avenue for research and diagnostic applications on intracellular target-based live-cell sorting.

A fluorescent immunosensor that lights up tumor biomarker p53 in living cells was developed based on the Q-body technology. The technology was further applied to the live cell monitoring of p53 levels, and live cell sorting based on p53 expression.     

Engineering CRISPR/Cas-based nanosystems for therapeutics,diagnosis and bioimaging

CRISPR/Cas system has been utilized to rationally manipulate intracellular genes, and it has been engineered as versatile and efficient gene editing tools with precise site-specificity and excellent targeting ability for therapeutics, diagnostics, and bioimaging. Here, the evolution and application of CRISPR/Cas systems were sketched chronologically. Landmark works were exemplified to illustrate the design principles of CRISPR/Cas systems. Furthermore, the delivery vectors of CRISPR/Cas system especially DNA nanomaterials-based vectors were categorized and illuminated. DNA nanomaterials are suitable for CRISPR/Cas system delivery via base pairing due to its sequence programmability and biocompatibility. Then the applications of CRISPR/Cas in diagnosis and genomic imaging were highlighted. At the end of the review, the challenges and opportunities of CRISPR/Cas systems were deeply discussed. We envision that the grant advances on CRISPR/Cas systems will promote the development of interdisciplinary fields in chemistry, biology and medicine.     

Amplified detection of nucleic acids and proteins using an isothermal proximity CRISPR Cas12a assay

Herein, we describe an isothermal proximity CRISPR Cas12a assay that harnesses the target-induced indiscrimitive single-stranded DNase activity of Cas12a for the quantitative profiling of gene expression at the mRNA level and detection of proteins with high sensitivity and specificity. The target recognition is achieved through proximity binding rather than recognition by CRISPR RNA (crRNA), which allows for flexible assay design. A binding-induced primer extension reaction is used to generate a predesigned CRISPR-targetable sequence as a barcode for further signal amplification. Through this dual amplification protocol, we were able to detect as low as 1 fM target nucleic acid and 100 fM target protein isothermally. The practical applicability of this assay was successfully demonstrated for the temporal profiling of interleukin-6 gene expression during allergen-mediated mast cell activation.

Herein, we develop an isothermal proximity CRISPR Cas12a assay that harnesses the target-induced collateral cleavage activity of Cas12a for the quantitative profiling of gene expression and detection of proteins with high sensitivity and specificity.     

Screw dislocation-induced pyramidal crystallization of dendron-like macromolecules featuring asymmetric geometry

We report herein that dendron-shaped macromolecules AB_n crystallize into well-ordered pyramid-like structures from mixed solvents, instead of spherical motifs with curved structures, as found in the bulk. The design of the asymmetric molecular architecture and the choice of mixed solvents are applied as strategies to manipulate the crystallization process. In mixed solvents, the solvent selection for the Janus macromolecule and the existence of dominant crystalline clusters contribute to the formation of flat nanosheets. Whereas during solvent evaporation, the bulkiness of the asymmetric macromolecules easily creates defects within 2D nanosheets which lead to their spiral growth through screw dislocation. The size of the nanosheets and the growth into 2D nanosheets or 3D pyramidal structures can be regulated by the solvent ratio and solvent compositions. Moreover, macromolecules of higher asymmetry generate polycrystals of lower orderliness, probably due to higher localized stress.

The dendron-shaped macromolecules AB_n crystallize into well-ordered pyramid-like structures from mixed solvents, which is on the contrary to spherical motifs with curved structures in bulk.     

Hexagonal perovskite-intergrowth manganates: Ln2Ca2MnO7 (Ln=La, Nd and Sm)

Two structures, all consisting of alternative stacking of hexagonal perovskite layer and graphite-like Ca₂O layer, were identified in Ln₂Ca₂MnO₇ systems (Ln=La, Nd and Sm). La₂Ca₂MnO₇ (1), crystallizing in the space group with the lattice constants a=5.62231(7)  Å and c=17.3192(4) Å, contains almost ideal close packed [LnO₃] arrays. While for the smaller rare earth cations, e.g., Nd₂Ca₂MnO₇ (2) and Sm₂Ca₂MnO₇ (3), the structure distorts to large unit cell (a′=2a and c′=c). Study of the substituted systems, LnLn′Ca₂MnO₇ (Ln or Ln′=La, Ce, Pr, Nd, Sm, Eu, Gd) and La_2−xSm_xCa₂MnO₇, shows a phase transformation from (1) to (2) at certain value of cation size. The MnO₆ octahedra in these compounds are isolated, thus the magnetic property is mainly paramagnetic.     

A CRISPR/Cas12a-responsive dual-aptamer DNA network for specific capture and controllable release of circulating tumor cells

The separation and detection of circulating tumor cells (CTCs) have a significant impact on clinical diagnosis and treatment by providing a predictive diagnosis of primary tumors and tumor metastasis. But the responsive release and downstream analysis of live CTCs will provide more valuable information about molecular markers and functional properties. To this end, specific capture and controllable release methods, which can achieve the highly efficient enrichment of CTCs with strong viability, are urgently needed. DNA networks create a flexible, semi-wet three-dimensional (3D) microenvironment for cell culture, and have the potential to minimize the loss of cell viability and molecular integrity. More importantly, responsive DNA networks can be reasonably designed as smart sensors and devices to change shape, color, disassemble, and giving back to external stimuli. Here, a strategy for specifically collecting cells using a dual-aptamer DNA network is designed. The proposed strategy enables effective capture, 3D encapsulation, and responsive release of CTCs with strong viability, which can be used for downstream analysis of live cells. The programmability of CRISPR/Cas12a, a powerful toolbox for genome editing, is used to activate the responsive release of captured CTCs from the DNA network. After activation by a specified double-strand DNA (dsDNA) input, CRISPR/Cas12a cleaves the single-stranded DNA regions in the network, resulting in molecular to macroscopic changes in the network. Accompanied by the deconstruction of the DNA network into fragments, controllable cell release is achieved. The viability of released CTCs is well maintained and downstream cell analysis can be performed. This strategy uses the enzymatic properties of CRISPR/Cas12a to design a platform to improve the programmability and versatility of the DNA network, providing a powerful and effective method for capturing and releasing CTCs from complex physiological samples.

The separation and detection of circulating tumor cells (CTCs) have a significant impact on clinical diagnosis and treatment by providing a predictive diagnosis of primary tumors and tumor metastasis.     

Structural investigation of Ca2MnO4 by neutron powder diffraction and electron microscopy

The first member of the Ruddlesden-Popper family, Ca₂MnO₄, has been revisited. Coexistence of two structures has been shown from electron microscopy at room temperature and neutron diffraction data have evidenced two antiferromagnetic structures at low temperature. Two forms, with an orthorhombic Aba2 ( and c≈12 Å) and a tetragonal I4₁/cad ( and c≈24 Å) symmetries, were found to coexist coherently within the same matrix.     

Phase equilibrium in the system Ln-Mn-O VI: Ln=Ho and Tb at 1100°C

Phase equilibria were established in Ho-Mn-O and Tb-Mn-O systems at 1100°C by varying the oxygen partial pressure from −log(P_O2/atm)=0-13.00, and phase diagrams for the corresponding Ln₂O₃-MnO-MnO₂ systems at 1100°C were presented. Stable Ln₂O₃, MnO, Mn₃O₄, LnMnO₃, and LnMn₂O₅ phases were found at 1100°C, whereas Ln₂Mn₂O₇, Ln₂MnO₄, Mn₂O₃, and MnO₂ were not found to be stable. Small nonstoichiometric ranges were found in the LnMnO₃ phase, with the composition of LnMnO₃ represented as functions of log(P_O2/atm), and . Activities of the components in the solid solution were calculated from these equations. The composition of LnMnO₃ may range from Ln₂O₃ rich to Ln₂O₃ poor, while MnO is slightly nonstoichiometric, being oxygen rich and LnMn₂O₅ seems to be nonstoichiometric. Lattice constants of LnMnO₃ quenched at different oxygen partial pressures and of LnMn₂O₅ quenched in air were determined. The standard Gibbs energy changes of the reactions appearing in the phase diagrams were also calculated. The relationship between the tolerance factor of LnMnO₃ and ΔG⁰of reaction, (1/2)Ln₂O₃+MnO+(1/4)O₂=LnMnO₃, is shown graphically.     

Synergistic effects of CH3CO2H and Ca2+ on C–H bond activation by MnO4−

The activation of metal-oxo species with Lewis acids is of current interest. In this work, the effects of a weak Brønsted acid such as CH₃CO₂H and a weak Lewis acid such as Ca²⁺ on C–H bond activation by KMnO₄ have been investigated. Although MnO₄⁻ is rather non-basic (pK_a of MnO₃(OH) = −2.25), it can be activated by AcOH or Ca²⁺ to oxidize cyclohexane at room temperature to give cyclohexanone as the major product. A synergistic effect occurs when both AcOH and Ca²⁺ are present; the relative rates for the oxidation of cyclohexane by MnO₄⁻/AcOH, MnO₄⁻/Ca²⁺ and MnO₄⁻/AcOH/Ca²⁺ are 1 : 73 : 198. DFT calculations show that in the active intermediate of MnO₄⁻/AcOH/Ca²⁺, MnO₄⁻ is H-bonded to 3 AcOH molecules, while Ca²⁺ is bonded to 3 AcOH molecules as well as to an oxo ligand of MnO₄⁻. Our results also suggest that these synergistic activating effects of a weak Brønsted acid and a weak Lewis acid should be applicable to a variety of metal-oxo species.

The activation of metal-oxo species with Lewis acids is of current interest.     

Sensitive detection of hydrogen peroxide in foodstuff using an organic�Cinorganic hybrid multilayer-functionalized graphene biosensing platform

We report on a new electrochemical biosensing strategy for the sensitive detection of hydrogen peroxide (H₂O₂) in foodstuff samples. It is based on a gold electrode modified with layer of graphene patterned with a multilayer made from an organic?Cinorganic hybrid nanomaterial. Initially, a layer of thionine (Th) was assembled on the surface of the graphene nanosheets, and these were then cast on the surface of the electrode for the alternate assembly of gold nanoparticles and horseradish peroxidase. The large surface-to-volume ratio and high conductivity of the nanosheets provides a benign microenvironment for the construction of the biosensor. The use of such a multilayer not only shortens the electron transfer pathway of the active center of the enzyme due to the presence of gold nanoparticles, but also enhances the electrocatalytic efficiency of the biosensor toward the reduction of H₂O₂. The electrochemical characteristics of the biosensor were studied by cyclic voltammetry and chronoamperometry. The number of layers, the operating potential, and the pH of the supporting electrolyte were optimized. Linear response is obtained for the range from 0.5???M to 1.8?mM of H₂O₂, the detection limit is 10 nM (at S/N?=?3), and 95% of the steady-state current is reached within 2?s. The method was applied to sense H₂O₂ in spiked sterilized milk and correlated excellently with the permanganate titration method.