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Journal ArticleDOI: 10.1021/ACS.ANALCHEM.1C00371

MXene Coupled with CRISPR-Cas12a for Analysis of Endotoxin and Bacteria.

02 Mar 2021-Analytical Chemistry (American Chemical Society (ACS))-Vol. 93, Iss: 10, pp 4676-4681
Abstract: With hydrophilic surface and high density of functional groups, MXene can efficiently adsorb single-stranded DNA to enhance target-induced strand release and quench the fluorescence. Herein, MXene is coupled with CRISPR-Cas12a to sensitively detect LPS and bacteria. Specifically, the aptamer is well designed to initiate the trans-cleavage activity of CRISPR-Cas12a to indiscriminately cleave single-stranded DNA, resulting it to be far away from MXene and the recovery of fluorescence. The target can effectually induce the release of the aptamer strand from the hybrid duplex with the assistance of MXene. The formed aptamer/target complex will inhibit the activation of CRISPR-Cas12a and its trans-cleavage on single-stranded DNA. The established method can selectively and sensitively quantify LPS and Gram-negative bacteria in different samples with detection limits of 11 pg/mL and 23 CFU/mL, respectively. Our study provides a new insight for exploration of universal analytical methods based on MXene coupled with CRISPR-Cas12a.

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Topics: Aptamer (51%)

7 results found

Journal ArticleDOI: 10.1016/J.MATLET.2021.130656
01 Dec 2021-Materials Letters
Abstract: The success of internet-of-things (IoT)-assisted wearable biomedical electronics demands novel high-performance biosensing prototypes which depend on smart opto-electric-nanosystems. In this direction, 2D MXenes (early transition metal carbides/nitrides) have recently emerged as materials of choice to investigate biosensors of desired performance due to high electro-conductivity, hydrophilicity, and versatile surface chemistry. This letter highlights recent advances and current challenges to project MXenes for next generation biosensing based on unfurled potentials and novel bio-analytical technologies.

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Topics: MXenes (58%)

7 Citations

Journal ArticleDOI: 10.1016/J.SNB.2021.130533
Yi Li1, Fei Deng1, Ewa M. Goldys1Institutions (1)
Abstract: The collateral cleavage function is only a corollary of programmable nuclease activity of certain Cas effectors, such as Cas12 and Cas13, but it can be utilised to amplify fluorescence signals in various CRISPR/Cas-based biosensing systems. In this work, this special signal amplification capability of CRISPR/Cas12a ribonucleoproteins has been employed to increase the sensitivity of a broad class of commercial ELISA systems with undisclosed chemistry except for the use of horseradish peroxidase (HRP), a common signal reporting molecule. We demonstrated that such ELISA systems with HRP on the detection antibody, can be amplified by 2 orders of magnitude using an example commercial IFN-γ ELISA kit where the detection limit was decreased from 312.5 pg/mL to 1.2 pg/mL. The detection range was simultaneously increased from 2 orders to 3 orders of magnitude. Our CRISPR/Cas12a-based ELISA Sensitivity Amplifier (CES-Amplifier) approach is based on a hybrid single strand DNA oligo and antibody conjugate targeting the HRP enzyme. The CES-Amplifier can be directly integrated into commercial ELISA kits to replace their original last step, without any additional changes of the ELISA kit reagents or setup. In this way, our CES-Amplifier provides a versatile and affordable approach for expanding CRISPR/Cas-based biosensing to a wide range of non-nucleic acid analytes.

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1 Citations

Journal ArticleDOI: 10.1016/J.SNB.2021.130586
Lijuan Yin1, Ninghui Duan1, Si Chen1, Yuan Yao1  +2 moreInstitutions (1)
Abstract: Foodborne diseases, caused by pathogenic bacteria, severely threaten global human health and cause a financial burden. Rapid, sensitive and on-site detection of pathogenic bacteria is significant. The existing methods have different defects, such as time-consuming and inconvenient. In this study, we developed a G-quadruplex-based CRISPR-Cas12a bioassay for pathogenic bacteria detection with high sensitivity and visualization capability. Salmonella was used as the detection model. Simply, the amplicons of Salmonella specific invA gene activated the trans-cleavage activity of Cas12a and triggered CRISPR-Cas12a based indiscriminate degradation of single-stranded DNAs (ssDNAs). The ssDNAs were designed with the guanine-rich sequence and formed a stable G-quadruplex DNAzyme by adding K+. This DNAzyme could catalyze the TMB-H2O2 reaction in the presence of hemin, leading to an increase in absorbance at 454 nm and a color change. This change can be readily differentiated by the naked eyes as well as a smartphone with a Color Picker App. With this strategy, the limit of detection (LOD) for Salmonella was 1 CFU/mL with no cross-reactivity. A linear relationship (R2 = 0.993) between the absorbance and the concentration of Salmonella was obtained. Furthermore, G-quadruplex-based CRISPR-Cas12a bioassay was successfully applied for sensing Salmonella in real food samples. This work not only expands the reach of CRISPR-Cas based biosensing but also provides a novel pathogenic bacteria detection method with high sensitivity, specificity and on-site capability.

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Topics: Pathogenic bacteria (53%)

Journal ArticleDOI: 10.1016/J.ACA.2021.338747
Pei Wang1, Yamei Liu1, Ying Yu2, Yuan Zhang1  +3 moreInstitutions (3)
Abstract: In this work, hydrazone ligation assisted DNAzyme walking nanomachine is explored to couple with CRISPR-Cas12a trans-cleavage. Hydrazone ligation with high efficiency can mediate signal input which can be induced by target binding, thereby regulating the performance of DNAzyme walking nanomachine. The product strand from DNAzyme walking nanomachine can further activate the trans-cleavage of Cas12a. So, cascade signal amplification can be achieved to enhance the sensitivity for target detection. Subsequently, hydrazone ligation assisted DNAzyme walking nanomachine coupled with CRISPR-Cas12a has been further developed as a biosensor to analyze lipopolysaccharides. The developed biosensor exhibits a linear range from 0.05 ng/mL to 106 ng/mL and a lowest limit of detection of 7.31 fg/mL. This research provides a new mode for the signal output of DNAzyme walking nanomachine, so as to sensitively analyze different biomolecules.

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Open accessJournal ArticleDOI: 10.1016/J.JHAZMAT.2021.127690
Pian Wu1, Xiaosheng Ye1, Danqi Wang1, Fangjie Gong1  +5 moreInstitutions (1)
Abstract: Selective and sensitive detection of microcystin-LR (MC-LR) is of vital importance because of its high toxicity and broad distribution. Herein, a novel and versatile fluorescence sensor (Cas14-pMOFs fluorescence sensor) was developed by combining the CRISPR/Cas14a system with a 2D porphyrin metal-organic framework nanosheets (2D-pMOFs) for MC-LR determination. The designed CRISPR/Cas14a system was activated by the unbound complementary DNA (cDNA), which was positively correlated with MC-LR concentration. Furthermore, the activated Cas14a protein was utilized to indiscriminately cleave the FAM-labeled single-stranded DNA (ssDNA-FAM), which was pre-absorbed on Cu-TCPP(Fe) nanosheets. Because of the desorption of the cleaved ssDNA-FAM, the pre-quenched fluorescence signal was recovered. Owing to the excellent performance in quantifying cDNA using this Cas14-pMOFs fluorescence sensor with a limit of detection (LOD) of 0.12 nM, this Cas14-pMOFs fluorescence sensor was able to detect MC-LR in a range from 50 pg/mL to 1 μg/mL with the LOD of 19 pg/mL. This work not only provided a new insight for the exploration of fluorescence sensors based on 2D-pMOFs coupled with CRISPR/Cas14a, but also, demonstrated its universality in both nucleic acid and non-nucleic acid targets determination.

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42 results found

Open accessJournal ArticleDOI: 10.1038/NATURE06536
21 Feb 2008-Nature
Abstract: Emerging infectious diseases (EIDs) are a significant burden on global economies and public health. Their emergence is thought to be driven largely by socio-economic, environmental and ecological factors, but no comparative study has explicitly analysed these linkages to understand global temporal and spatial patterns of EIDs. Here we analyse a database of 335 EID 'events' (origins of EIDs) between 1940 and 2004, and demonstrate non-random global patterns. EID events have risen significantly over time after controlling for reporting bias, with their peak incidence (in the 1980s) concomitant with the HIV pandemic. EID events are dominated by zoonoses (60.3% of EIDs): the majority of these (71.8%) originate in wildlife (for example, severe acute respiratory virus, Ebola virus), and are increasing significantly over time. We find that 54.3% of EID events are caused by bacteria or rickettsia, reflecting a large number of drug-resistant microbes in our database. Our results confirm that EID origins are significantly correlated with socio-economic, environmental and ecological factors, and provide a basis for identifying regions where new EIDs are most likely to originate (emerging disease 'hotspots'). They also reveal a substantial risk of wildlife zoonotic and vector-borne EIDs originating at lower latitudes where reporting effort is low. We conclude that global resources to counter disease emergence are poorly allocated, with the majority of the scientific and surveillance effort focused on countries from where the next important EID is least likely to originate.

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4,911 Citations

Open accessJournal ArticleDOI: 10.1002/ADMA.201102306
Michael Naguib1, Murat Kurtoglu1, Volker Presser1, Jun Lu2  +5 moreInstitutions (2)
04 Oct 2011-Advanced Materials
Abstract: Currently, however, there are relatively few such atomically layered solids. [ 2–5 ] Here, we report on 2D nanosheets, composed of a few Ti 3 C 2 layers and conical scrolls, produced by the room temperature exfoliation of Ti 3 AlC 2 in hydrofl uoric acid. The large elastic moduli predicted by ab initio simulation, and the possibility of varying their surface chemistries (herein they are terminated by hydroxyl and/or fl uorine groups) render these nanosheets attractive as polymer composite fi llers. Theory also predicts that their bandgap can be tuned by varying their surface terminations. The good conductivity and ductility of the treated powders suggest uses in Li-ion batteries, pseudocapacitors, and other electronic applications. Since Ti 3 AlC 2 is a member of a 60 + group of layered ternary carbides and nitrides known as the MAX phases, this discovery opens a door to the synthesis of a large number of other 2D crystals. Arguably the most studied freestanding 2D material is graphene, which was produced by mechanical exfoliation into single-layers in 2004. [ 1 ] Some other layered materials, such as hexagonal BN, [ 2 ] transition metal oxides, and hydroxides, [ 4 ] as well as clays, [ 3 ] have also been exfoliated into 2D sheets. Interestingly, exfoliated MoS 2 single layers were reported as early as in 1986. [ 5 ] Graphene is fi nding its way to applications ranging from supercapacitor electrodes [ 6 ] to reinforcement in composites. [ 7 ] Although graphene has attracted more attention than all other 2D materials combined, its simple chemistry and the weak van der Waals bonding between layers in multilayer structures limit its use. Complex, layered structures that contain more than one element may offer new properties because they

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Topics: Exfoliation joint (61%)

4,043 Citations

Journal ArticleDOI: 10.1002/ADMA.201304138
01 Feb 2014-Advanced Materials
Abstract: Recently a new, large family of two-dimensional (2D) early transition metal carbides and carbonitrides, called MXenes, was discovered. MXenes are produced by selective etching of the A element from the MAX phases, which are metallically conductive, layered solids connected by strong metallic, ionic, and covalent bonds, such as Ti2AlC, Ti3AlC2, and Ta4AlC3. MXenes ­combine the metallic conductivity of transition metal carbides with the hydrophilic nature of their hydroxyl or oxygen terminated surfaces. In essence, they behave as “conductive clays”. This article reviews progress—both ­experimental and theoretical—on their synthesis, structure, properties, intercalation, delamination, and potential applications. MXenes are expected to be good candidates for a host of applications. They have already shown promising performance in electrochemical energy storage systems. A detailed outlook for future research on MXenes is also presented.

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Topics: MXenes (76%)

2,716 Citations

Open accessJournal ArticleDOI: 10.1016/J.CELL.2015.09.038
22 Oct 2015-Cell
Abstract: The microbial adaptive immune system CRISPR mediates defense against foreign genetic elements through two classes of RNA-guided nuclease effectors. Class 1 effectors utilize multi-protein complexes, whereas class 2 effectors rely on single-component effector proteins such as the well-characterized Cas9. Here, we report characterization of Cpf1, a putative class 2 CRISPR effector. We demonstrate that Cpf1 mediates robust DNA interference with features distinct from Cas9. Cpf1 is a single RNA-guided endonuclease lacking tracrRNA, and it utilizes a T-rich protospacer-adjacent motif. Moreover, Cpf1 cleaves DNA via a staggered DNA double-stranded break. Out of 16 Cpf1-family proteins, we identified two candidate enzymes from Acidaminococcus and Lachnospiraceae, with efficient genome-editing activity in human cells. Identifying this mechanism of interference broadens our understanding of CRISPR-Cas systems and advances their genome editing applications.

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Topics: CRISPR/Cpf1 (72%), Cas9 (66%), Trans-activating crRNA (65%) ... read more

2,617 Citations

Open accessJournal ArticleDOI: 10.1126/SCIENCE.AAM9321
28 Apr 2017-Science
Abstract: Rapid, inexpensive, and sensitive nucleic acid detection may aid point-of-care pathogen detection, genotyping, and disease monitoring. The RNA-guided, RNA-targeting clustered regularly interspaced short palindromic repeats (CRISPR) effector Cas13a (previously known as C2c2) exhibits a “collateral effect” of promiscuous ribonuclease activity upon target recognition. We combine the collateral effect of Cas13a with isothermal amplification to establish a CRISPR-based diagnostic (CRISPR-Dx), providing rapid DNA or RNA detection with attomolar sensitivity and single-base mismatch specificity. We use this Cas13a-based molecular detection platform, termed Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK), to detect specific strains of Zika and Dengue virus, distinguish pathogenic bacteria, genotype human DNA, and identify mutations in cell-free tumor DNA. Furthermore, SHERLOCK reaction reagents can be lyophilized for cold-chain independence and long-term storage and be readily reconstituted on paper for field applications.

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1,065 Citations