Categories
Tag: crRNA
Structure-guided discovery of anti-CRISPR and anti-phage defense proteins
Identification of putative anti-crispr proteins using structural features To identify Acrs in phage genomes, we began by retrieving ~66.5 million proteins from Integrated Microbial Genomes Virus database (IMG/VR)37. We excluded large proteins because over 90% of known Acrs contain less than 200 amino acids38 (Fig. 1A, Supplementary Data 1). To reduce computational…
Pharmaceutics | Free Full-Text | Natural Biopolymer-Based Delivery of CRISPR/Cas9 for Cancer Treatment
Cancer is one of the leading causes of disease-associated mortality, with a rising incidence worldwide [1]. Although many therapeutic methods have been used in cancer treatment, such as chemotherapy, radiotherapy, surgery, and targeted therapy, the overall therapeutic outcome remains unsatisfactory. Therefore, developing new therapeutic means is urgently needed. With advances…
Development and evaluation of a CRISPR-Cas13a system-based diagnostic for hepatitis E virus
Objectives: Hepatitis E virus (HEV) is the leading cause of acute viral hepatitis worldwide. HEV RNA detection is the gold standard for HEV infection diagnosis and PCR methods are commonly used but are usually time-consuming and expensive, resulting in low detection efficiency and coverage, especially in low-income areas. Here, we…
Based on CRISPR-Cas13a System, to Establish a Rapid Visual Detection Method for Avian Influenza Viruses
1Hebei Agricultural University, China 2Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, China 3Hebei Sanshi Biotechnology Co., Ltd, China The final, formatted version of the article will be published soon. Notify me Receive an email when it…
Summary of Genomics and Transcriptomics – DNA sequencing I. Goal II. Methodology A. Sanger DNA
DNA sequencing I. Goal II. Methodology A. Sanger DNA sequencing ● Up to 900 base pairs ● Primer extension with labeled ddNTPs (radioactive or fluorescent) ● Prior knowledge on target needed ● Difficult to detect variation in mixtures ● High accuracy + still in use for genotyping When it is…
Programmable Aptasensor for Regulating CRISPR/Cas12a Activity
CRISPR-mediated aptasensors have gained prevalence for detecting non-nucleic acid targets. However, there is an urgent need to develop an easily customizable design to improve the signal-to-noise ratio, enhance universality, and expand the detection range. In this article, we report a CRISPR-mediated programmable aptasensor (CPAS) platform. The platform includes single-stranded DNA…
Light-Triggered Signal Enhancement Strategy Integrated with a CRISPR/Cas13a-Based Assay for Ultrasensitive and Specific miRNA Detection
The development of facile, accurate, and affordable assays for microRNAs (miRNAs) in early cancer is greatly desirable but encounters an obstacle due to low cellular abundance in biofuids. In this study, we present a novel approach called a light-triggered exponential amplification strategy coupled with a CRISPR/Cas13a-based diagnostic system (LEXPA-CRISPR), which…
Foods | Free Full-Text | Isothermal Amplification and CRISPR/Cas12a-System-Based Assay for Rapid, Sensitive and Visual Detection of Staphylococcus aureus
1. Introduction Staphylococcus aureus [1], one of the top five foodborne pathogens, has a common and strong aggressiveness in humans and can secrete multiple toxic proteins (Pathogenic enterotoxins, Hemolysin, PVL) [1,2] which can cause bacteraemia, endocarditis, meningitis, toxic shock syndrome, pneumonia and other dangerous infectious diseases [3]. Moreover, the worldwide…
Biosensors | Free Full-Text | CRISPR/Cas12a-Based Detection Platform for Early and Rapid Diagnosis of Scrub Typhus
1. Introduction Orientia tsutsugamushi (OT) is an obligate intracellular parasite bacteria and the causative agent of scrub typhus (ST), which is associated with acute febrile illness (AFI) [1] and transmitted by mites through an infected chigger bite (in the larval stage). This disease, which was earlier believed to be endemic…
Solved A key revelation in the CASCADE-DNA structure is that
A key revelation in the CASCADE–DNA structure is that DNA is engaged with crRNAs in 5–base pair blocks, with every sixth base unpaired (MOVIE). It was proposed that the crRNA ‘seed’ containing the 5–nucleotide stretches are ‘pre–ordered’ for DNA pairing due to their proximity to the protospacer adjacent motif (PAM)….
CRISPR/Cas12a-Responsive Hydrogels for Conjugation-Free and Universal Indicator Release in Colorimetric Detection
Recent advances have demonstrated the significant potential and advantages to repurpose existing point-of-care reactions/devices to realize portable detection of nonoriginal targets, e.g., pathogen genes. However, pursuing this aim usually requires protein indicator-nucleic acid conjugation via a covalent bond, which may bring drawbacks such as high cost, complicated procedure, and annoying…
New FREM platform delivers 98% accuracy for malaria screening | The Guardian Nigeria News
Breakthrough has been recorded in malaria detection as the new FREM platform delivers 98 per cent accuracy for rapid screening, genotyping. In a recent study published in eBioMedicine, researchers developed the Flexible, Robust, Equipment-free Microfluidic (FREM) platform for malaria screening and Plasmodium species genotyping. Malaria, a worldwide health concern caused…
In what ways does the CRISPR-Cas13a system enable efficient phage genome editing?
What are the molecular mechanisms of CRISPR-Cas immunity in bacteria?5 answersCRISPR-Cas systems in bacteria provide adaptive and hereditary immunity against foreign nucleic acids. The systems consist of CRISPR arrays containing short DNA fragments called spacers and Cas proteins that facilitate spacer acquisition, processing, and recognition of targeted nucleic acids. The…
new FREM platform delivers 98% accuracy for rapid screening and genotyping
In a recent study published in eBioMedicine, researchers developed the Flexible, Robust, Equipment-free Microfluidic (FREM) platform for malaria screening and Plasmodium species genotyping. Study: A versatile microfluidic platform for malaria infection screening and Plasmodium species genotyping. Image Credit: nechaevkon/Shutterstock.com Background Malaria, a worldwide health concern caused by Plasmodium species, needs precise detection and genotyping…
New Study Develops Innovative Microfluidic Platform for Malaria Screening and Genotyping
Researchers have made a breakthrough in malaria detection and genotyping with the development of the Flexible, Robust, Equipment-free Microfluidic (FREM) platform. The current diagnostic techniques for detecting and identifying malaria-causing Plasmodium species often face limitations in resource-limited settings. However, the FREM platform offers a versatile solution to these challenges. The…
Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a
doi: 10.1093/nar/gkad1127. Online ahead of print. Affiliations Expand Affiliations 1 Department of Bioengineering, University of California Riverside, Riverside, CA , 92521, USA. 2 Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA. 3 Center for RNA Biology, University of Rochester School of Medicine and…
Prime editing-mediated correction of the CFTR W1282X mutation in iPSCs and derived airway epithelial cells
Abstract A major unmet need in the cystic fibrosis (CF) therapeutic landscape is the lack of effective treatments for nonsense CFTR mutations, which affect approximately 10% of CF patients. Correction of nonsense CFTR mutations via genomic editing represents a promising therapeutic approach. In this study, we tested whether prime editing,…
New design strategies for ultra-specific CRISPR-Cas13a-based RNA detection with single-nucleotide mismatch sensitivity
doi: 10.1093/nar/gkad1132. Online ahead of print. Affiliations Expand Affiliations 1 Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. 2 Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA. 3 Department of Biomedical Genetics, School of Medicine…
MSL2 ensures biallelic gene expression in mammals
Materials Animals All of the mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics. The mice were maintained under specific-pathogen-free conditions, with 2 to 5 mice housed in individually ventilated cages (Techniplast). The cages were equipped with bedding material, nesting material, a paper…
CRISPR Gene Editing: Cas9 and Beyond
Scientists use the CRISPR-Cas9 system to target a DNA sequence of interest near a protospacer-adjacent motif (PAM). The PAM initiates Cas9-DNA binding, a guide RNA (yellow) invades the double helix (blue) and hybridizes with the target DNA, and Cas9 (red) breaks the unwound double-stranded target DNA. iStock Meletios Verras Stay…
Improved CRISPR Diagnostic Technology Enhances Efficacy and Efficiency for Nucleic Acid Detection
– Advertisement – Efficacy and Efficiency of CRISPR Diagnostic Technology Improved Researchers have developed a new method that improves existing diagnostic technology for a more rapid, sensitive, and deployable approach to molecular diagnostics. The research, published in Nature Communications, unravels new potential for simple and sensitive nucleic acid detection in…
In vivo imaging of mitochondrial DNA mutations using an integrated nano Cas12a sensor
Mutations in mitochondrial DNA (mtDNA) play critical roles in many human diseases. In vivo visualization of cells bearing mtDNA mutations is important for resolving the complexity of these diseases, which remains challenging. Here we develop an integrated nano Cas12a sensor (InCasor) and show its utility for efficient imaging of mtDNA…
Empowering optical tweezers with ‘biometric eyes’
a, The diagrammatic sketch of the three components in the solution: DNA@AuNS conjugate, CRISPR/Cas12a complex, and target ssDNA. b, Optical setup, the BS, SPF, and TL are beam splitter, short pass filter, and tube lens (f=200 mm), respectively. Additional details of the setup are provided in the Materials and Methods…
The new IP battleground in CRISPR-Cas
While much attention has been focused on the major IP battle affecting foundational patents covering CRISPR-Cas9 systems as gene modifiers, another battle has erupted concerning modified guide ribonucleic acids (RNAs) for use with Cas enzymes. The most visible recent sign of this was the invalidation of all claims of two…
New Breakthrough Enhances CRISPR Diagnostic Technology
Researchers at the University of Connecticut have made a significant breakthrough in improving the efficacy and efficiency of CRISPR diagnostic technology. Led by Professor Changchun Liu, the team has developed a new method that enhances the existing clustered regularly interspaced short palindromic repeats (CRISPR) technology, allowing for faster, more sensitive,…
Researchers Improve Efficacy and Efficiency of CRISPR Diagnostic Technology
Changchun Liu, professor of Biomedical Engineering at UConn Health, has developed a new method that improves existing diagnostic technology for a more rapid, sensitive, and deployable approach to molecular diagnostics. The research, published in Nature Communications, unravels new potential for simple and sensitive nucleic acid detection in various diagnostic settings—including…
CRISPR therapies Pipeline Insights 2023: Therapies, Latest
CRISPR therapies Pipeline (New York, USA) “CRISPR therapies Pipeline Insight, 2023” report by DelveInsight outlines comprehensive insights into the present clinical development scenario and growth prospects across the CRISPR therapies Market. The CRISPR therapies Pipeline report embraces in-depth commercial and clinical assessment of the pipeline products from the pre-clinical developmental…
An ultrasensitive Cd2+ detection biosensor based on DNAzyme and CRISPR/Cas12a coupled with hybridization chain reaction
. 2023 Dec 1:1283:341950. doi: 10.1016/j.aca.2023.341950. Epub 2023 Oct 23. Affiliations Expand Affiliations 1 Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing, 210037, China. 2 Jiangsu Key Laboratory for…
CRISPR/Cas12a trans-cleavage triggered by cleavage ligation of dumbbell DNA for specific detection of human 8-oxoguanine DNA glycosylase activity
Poetsch AR (2020) The genomics of oxidative DNA damage, repair, and resulting mutagenesis. Comput Struct Biotechnol J 18:207–219. doi.org/10.1016/j.csbj.2019.12.013 Article CAS PubMed PubMed Central Google Scholar Ba X, Aguilera-Aguirre L, Rashid QT, Bacsi A, Radak Z, Sur S, Hosoki K, Hegde ML, Boldogh I (2014) The role of 8-oxoguanine DNA…
Primate-specific ZNF808 is essential for pancreatic development in humans
Subjects The study was conducted in accordance with the Declaration of Helsinki and all subjects or their parents/guardian gave informed written consent for genetic testing. DNA testing and storage in the Beta Cell Research Bank was approved by the Wales Research Ethics Committee 5 Bangor (REC 17/WA/0327, IRAS project ID…
Detection of Clostridium perfringens Using Novel Methods Based on Recombinase-Aided Amplification Assay-Assisted CRISPR/Cas12a System
Clostridium perfringens is a highly versatile pathogen of humans and animals. Rapid and sensitive detection methods for C. perfringens are urgently needed for the timely implementation of control. In this study, to provide novel promising methods for the detection of C. perfringens, two rapid, sensitive, and instrument-free C. perfringens detection…
Rapid detection of avian influenza virus based on CRISPR-Cas12a
Background: Avian influenza (AI) is a disease caused by the avian influenza virus (AIV). These viruses spread naturally among wild aquatic birds worldwide and infect domestic poultry, other birds, and other animal species. Currently, real-time reverse transcription polymerase chain reaction (rRT-PCR) is mainly used to detect the presence of pathogens…
IJMS | Free Full-Text | CRISPR/Cas9-Mediated Genome Editing in Cancer Therapy
1. Introduction Recently, the morbidity and mortality rates of cancer have been increasing rapidly, posing a significant threat to human health. Cancer, a refractory and multifaceted disease, fundamentally originates from a cumulative series of mutations in the cellular genome and epigenome. These mutations activate oncogenes and deactivate tumor suppressors, leading…
Rapid detection of avian influenza virus based on CRISPR-Cas12a | Virology Journal
Materials Escherichia coli strains expressing the LbCas12a protein, plasmids containing the AIV M and NP genes, and H1–H16 subtypes of AIV, newcastle disease virus (NDV), infectious bursal disease virus (IBDV), and infectious bronchitis virus (IBV) were conserved in the State Key Laboratory of Harbin Veterinary Research Institute (HVRI), Chinese Academy…
Establishment of RT-RPA-Cas12a assay for rapid and sensitive detection of human rhinovirus B | BMC Microbiology
Clinical samples Thirty nasopharyngeal aspirates were collected from individuals with symptoms of respiratory tract infections, and tested positive for HRV-A (5 clinical samples), HRV-B (20 clinical samples), or HRV-C-positive (5 clinical samples) based on the method, as previously described [27]. Ten other specimens were tested negative for HRV-B, including human…
IJMS | Free Full-Text | CRISPR/Cas9 Landscape: Current State and Future Perspectives
1. Introduction Genome editing has taken a leading position among genome modification technologies in a short time and is now widely used in gene therapy. To date, there are three main systems for genome editing: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas nucleases. Genome editing has…
Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction | Nucleic Acids Research
Abstract RNA In situ imaging through DNA self-assembly is advantaged in illustrating its structures and functions with high-resolution, while the limited reaction efficiency and time-consuming operation hinder its clinical application. Here, we first proposed a new strand displacement reaction (SDR) model (Cas12a thrusting SDR, CtSDR), in which Cas12a could overcome…
RPA biosensors for rapid zoonoses screening
Introduction Since the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 2019, this coronavirus has spread to more than 200 countries, cumulatively infecting 672 million people and causing 6.84 million deaths. Moreover, the emergence of numerous variant strains (α, β, γ, δ, and Omicron) presents a serious challenge for…
One-Step Reverse-Transcription Recombinase-Aided Amplification CRISPR/Cas12a-Based Lateral Flow Assay for Fast Field Screening and Accurate Differentiation of Four Major Tobamoviruses Infecting Tomato and Pepper
doi: 10.1021/acs.jafc.3c05268. Online ahead of print. Affiliations Expand Affiliations 1 Chinese Academy of Inspection and Quarantine, Beijing 100176, China. 2 State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, Department of Plant Pathology, China Agricultural University, 100193 Beijing, China. Item in Clipboard Zhenxing Zhao et al….
Will Alphabet Achieve With Isomorphic Labs What It Couldn’t With DeepMind?
In 2018, when DeepMind unveiled AlphaFold to the public, a pivotal discovery in medical technology that could predict single-chain protein structures, it disrupted biology, giving new direction to structural biology, in particular. Two years later, DeepMind announced AlphaFold 2, which cracked half-a-century-old puzzle of protein folding, a defining moment for…
The latest AlphaFold model now covers a variety of biological molecules
The protein folding problem, or at least one of its iterations, consists of reliably determining the 3D structure of a protein from the sequence of its amino acids alone. There is a variety of amino acids serving different purposes, the best known of these molecules being the 22 proteinogenic (protein-creating)…
CRISPR/Cas9 bioluminescence-based assay for monitoring CFTR trafficking to the plasma membrane
Introduction Cystic fibrosis (CF) is a lethal, autosomal recessive disorder caused by mutations in the CFTR gene that results in aberrant transport of chloride, bicarbonate, and sodium ions (Kerem et al, 1989; Riordan et al, 1989; Rommens et al, 1989; Tabcharani et al, 1991; Poulsen et al, 1994; Stutts et…
CRISPR screening in hematology research: from bulk to single-cell level | Journal of Hematology & Oncology
Transcriptomics CROP-seq [46] Jurkat Poly-A CRISPRko Cas9 119 – 5798 (+ 1320 cells with NT gRNA) Lentiviral DROP-seq RNA Perturb-seq [43, 44] K562 Barcode CRISPRi dCas9-KRAB UPR epistasis screen: 9 triplet combinations UPR Perturb-seq experiment: 91 Up to 3 gRNAs in a single vector UPR epistasis screen: 15006 UPR Perturb-seq experiment:…
CRISPR-Cas9 gene editing in liver disease
Introduction to CRISPR-Cas9 Gene EditingLiver disease: the need for innovative treatmentsCRISPR-Cas9 applications in liver diseasePrecision medicine and personalized treatmentFuture prospects and research directionsrefer to further reading CRISPR-Cas9 gene editing has great potential in the field of precision medicine for liver diseases. This innovative technology allows researchers to precisely modify genes…
Harnessing the Power of CRISPR-Cas9 Gene Editing for Liver Diseases
Liver diseases continue to pose significant challenges to global health, necessitating the exploration of innovative treatment approaches. One technology that shows immense promise is CRISPR-Cas9 gene editing, which enables precise modifications to genes associated with liver conditions, offering hope for targeted therapies. CRISPR-Cas9 gene editing, a revolutionary technique in genetic…
CRISPR: Positive Exa-Cel AdCom Opens Door For Historic Approval (CRSP)
Prostock-Studio/iStock via Getty Images Investment Overview Swiss gene therapy specialist CRISPR Therapeutics AG (NASDAQ:CRSP) and partner Vertex Pharmaceuticals Incorporated (VRTX), the >$90bn market cap, Boston-based Pharma giant, took a step closer to a historic first approval for a CRISPR/Cas9 gene editing therapy yesterday, after an FDA Advisory Committee raised few…
CRISPR-Cas9 Gene Editing in Liver Diseases
Liver diseases: The need for innovative treatmentsFuture prospects and research directions This innovative technology permits researchers to precisely modify genes linked to liver conditions, ultimately offering hope for targeted treatments.Introduction to CRISPR-Cas9 gene editing The science of genetic engineering has been revolutionized by the groundbreaking CRISPR-Cas9 gene-editing technique. This system…
Google Teases Next Generation of AlphaFold, Expanding AI Structure Prediction Beyond Proteins
In 2020, DeepMind’s AlphaFold AI system shocked researchers by predicting protein structures with unprecedented accuracy. Now, Google and biotech startup Isomorphic Labs have previewed AlphaFold’s next generation, showing dramatically expanded capabilities beyond proteins to model complexes containing DNA, RNA, small molecule ligands, and post-translational modifications (PTMs). This progress solidifies AlphaFold…
A glimpse of the next generation of AlphaFold
Progress update: Our latest AlphaFold model shows significantly improved accuracy and expands coverage beyond proteins to other biological molecules, including ligands Since its release in 2020, AlphaFold has revolutionised how proteins and their interactions are understood. Isomorphic Labs and Google DeepMind have been working together to build the foundations…
Animals | Free Full-Text | RPA-CRISPR/Cas12a-Based Detection of Haemophilus parasuis
H. parasuis is a common pathogenic bacterium in the respiratory tract of pigs, which can cause widespread cellulose inflammation (also called Glässer’s disease) when the immunity of pigs is decreased. H. parasuis has fifteen serovars, and some clinical strains remain indistinguishable from serotypes. The vaccine’s cross-protection is poor among different…
Intrinsic Targeting of Host RNA by Cas13: Implications and Challenges
A recent study published in Nature Biomedical Engineering sheds light on the previously unknown ability of Cas13 to intrinsically target host RNA in mammalian cells. Cas13 is a member of the type-VI CRISPR-Cas13 systems, which have been widely utilized for various RNA-targeting applications. Cas13 is known to require a single…
Amerigo Scientific Unveils CRISPR/Cas Enzymes to Expand
Amerigo Scientific, as a distributor focused on providing critical products and services to biomedical and life science communities, announced the release of a groundbreaking selection of CRISPR/Cas enzymes to its extensive life science portfolio, aimed at further expanding the vast potential of the CRISPR toolbox. This addition brings cutting-edge genetic…
Cas13’s Intrinsic Targeting of Host RNA Limits Its Utility
Cas13 is capable of intrinsically targeting host RNA in mammalian cells through mechanisms that were not previously understood. Through transcript-specific mechanisms that are independent of the CRISPR RNA sequence and dynamically dependent on the conformational state of Cas13, Cas13 can also cleave host RNA. This effect is demonstrated by a…
Antiviral type III CRISPR signalling via conjugation of ATP and SAM
Cloning Supplementary Table 1 shows the synthetic gene, DNA and RNA oligonucleotide sequences used in this study. The synthetic genes encoding B.fragilis Cas6, CorA, NrN and C. botulinum SAM lyase purchased as g-blocks (IDT) were codon-optimized for expression in E. coli C43 (DE3) via the vector pEhisV5TEV, which encodes eight…
Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice
Mouse strains All mouse procedures were approved by the Institutional Animal Care and Use Committees at Binghamton or Stanford University; and were conducted in accordance with the National Institute of Health Guide for Care and Use of Laboratory Animals, Eighth Edition. All mice were originally obtained from Jackson Laboratories, and…
Mitigating a TDP-43 proteinopathy by concentrating on ataxin-2 utilizing
Concentrating on ataxin-2 with RfxCas13d Due to its potential to affect TDP-43-associated toxicity20,25,26, ataxin-2 has emerged as a doubtlessly broadly relevant goal for ALS-FTD, as TDP-43 pathology is noticed in ~97% of ALS instances1,4,5 and ~45% FTD occurrences1,2,4. Given this, we sought to find out if RNA-targeting CRISPR effector proteins…
QUESTION 11 11 What key components of Type 2 CRISPR systems were adapted for use
Other answer: ●The two elements of the CRISPR system that were modified were the crRNA + tracer RNA, and the Cas9 protein. The crispr RNA are the shot palindromic sequences adjacent to the integrated viral genome segments that act as the target for the tacer RNA. Tracer RNA is the…
CRISPR-Cas12a test strip (CRISPR/CAST) package: In-situ detection of Brucella from infected livestock | BMC Veterinary Research
Infections caused by Brucella have emerged as a considerable threat worldwide, particularly in vast amounts of livestock. It is essential to eradicate and control Brucella infections in livestock from the source. In addition, earlier detection and timely culling are equally important. Consequently, the screening used for livestock must be accurate, sensitive, specific, simple,…
CRISPR and CRISPR-Associated (Cas) Genes market was valued
CRISPR and CRISPR-Associated (Cas) Genes market was valued at US$ 1863.6 million in 2022 and is anticipated to reach US$ 9813.2 million by 2029, witnessing a CAGR of 31.9% during the forecast period 2023-2029. Get sample report – reports.valuates.com/request/sample/QYRE-Auto-39I6706/China_CRISPR_and_CRISPR_Associated_Cas_Genes_Market_Report_Forecast_2021_2027 This report studies the CRISPR And CRISPR-Associated (Cas) Genes market. Clustered…
Foods | Free Full-Text | Qualitative and Quantitative Detection of CRISPR-Associated Cas Gene in Gene-Edited Foods
1. Introduction Gene editing technology can effectively edit target genes and is therefore a valuable tool in biological research [1,2,3]. The third-generation gene editing technology, namely clustered regularly interspaced short palindromic repeats (CRISPR), is a defense system in bacteria. The presence of these repeats was first discovered in Escherichia coli…
Programmable RNA detection with CRISPR-Cas12a
Santosh R. Rananaware, Emma K. Vesco, Grace M. Shoemaker, Swapnil S. Anekar, Luke Samuel W. Sandoval, Katelyn S. Meister, Nicolas C. Macaluso, Long T. Nguyen and Piyush K. Jain () Additional contact information Santosh R. Rananaware: University of Florida Emma K….
Atomistic understanding of the RNA-mediated allosteric crosstalk in Cas13a
Cas13a is the one of the latest additions in the CRISPR-Cas library that exclusively targets RNA, a remarkable property being leveraged for the development of tools for RNA detection, regulation and imaging. Cas13a uses a CRISPR RNA (crRNA) sequence as a guide to target RNA sequences, which are then cleaved…
A thermostable type I-B CRISPR-Cas system for orthogonal and multiplexed genetic engineering
A thermostable type I-B CRISPR-Cas system from P. thermoglucosidasius Geobacillus and Parageobacillus are ubiquitous in a wide range of environments, growing at temperatures ranging from 35–80 °C29. To survey the distribution of thermostable type I CRISPR-Cas systems in these genera, we extracted all available genomes from CRISPRCasFinder database30, and identified Type…
A versatile regulatory toolkit of arabinose-inducible artificial transcription factors for Enterobacteriaceae
Design of arabinose-inducible artificial transcription factors A core objective of our work was to develop inducible, heterologous regulators capable of genetically reprogramming gene regulatory networks in Enterobacteriaceae, specifically Salmonella and E. coli. To achieve this, we designed arabinose-inducible ATFs incorporating diverse DBDs originating from CRISPR/dCas9 and plant heterologous TFs (Fig. 1)….
A CRISPR/Cas12a-SERS platform for amplification-free detection of African swine fever virus genes
African swine fever virus (ASFV) is a highly infectious and lethal agent in pigs and is classified as a “notifiable disease” by the World Organization for Animal Health (OIE) [1,2]. Although ASFV cannot infect humans, it is extremely difficult to prevent and control due to its multiple infection paths, which…
Unmodificated stepless regulation of CRISPR/Cas12a multi-performance
As CRISPR technology is promoted to more fine-divided molecular biology applications, its inherent performance finds it increasingly difficult to cope with diverse needs in these different fields, and how to more accurately control the performance has become a key issue to develop CRISPR technology to a new stage. Herein, we…
Innovative strategies of reprograming immune system cells
Introduction Cancer is well characterized by genomic instability resulting in structural alterations that build up with tumor progression.1,2 A subpopulation of undifferentiated cancer cells, known as cancer stem cells (CSCs) are found within the tumor bulk. These cells are responsible for cancer initiation, recurrence and show therapeutic resistance and these…
Detection of Salmonella DNA and drug-resistance mutation by PCR-based CRISPR-lbCas12a system | AMB Express
Establishment of PCR-lbCas12 DETECTR The whole detection process is illustrated in Fig. 1a. According to the data of infected persons from the Medical Laboratory of Shenzhen Luohu People’s Hospital, Salmonella is always among the top 5 positive Gram-negative (G−) bacilli in both 2021 and 2020 (Fig. 1b). To obtain efficient and specific…
Highly sensitive and rapid point-of-care testing for HIV-1 infection based on CRISPR-Cas13a system | BMC Infectious Diseases
Selection of RT-RAA amplification primers and HIV-1 RNA nucleic acid target, development of ERASE detection method for HIV-1 RNA In this study, a rapid nucleic acid detection assay for HIV-1 RNA was developed based on the ERASE method for COVID-19 detection established by our collaborator (Fig. 1A). First, HIV-1 RNA extracted…
capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements
Cell culture All cell lines were grown in 6 cm dishes at 37 °C in a 5% CO2 incubator. The K562, MDA-MB-231 and HCT 116 cell lines were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics (pen-strep). NCM460 cells were cultured in RPMI 1640 medium supplemented…
A CRISPR-Cas12a-based platform facilitates the detection and serotyping of Streptococcus suis serotype 2
Streptococcus suis is a facultative anaerobic Gram-positive bacterium responsible for substantial economic losses in the worldwide swine industry. It can cause meningitis, septicemia, endocarditis, and sudden death in pigs. The bacterium can colonize the tonsil and nasal cavities of healthy pigs, with single or multiple serotypes possible in an individual…
Rapid Detection of blaKPC in Carbapenem-Resistant Enterobacterales Based on CRISPR/Cas13a
Materials and Instruments Clinical Strains and Sputum Samples Collection A total of 117 bacterial strains were isolated and collected from sputum samples of individual patients with suspected intestinal infection treated at our hospital during the first half of 2021. Carbapenemase production was confirmed by the Modified Carbapenem Inactivation Method (mCIM)…
CRISPR/Cas12a-Loaded intelligent DNA hydrogel for Universal and Ultrasensitive Exosome Assay
CRISPR/Cas12a-Loaded intelligent DNA hydrogel for Universal and Ultrasensitive Exosome Assay Abstract Tumor-derived exosomes are crucial for early non-invasive and accurate tumor diagnosis in clinical. The development of highly sensitive, simple and intuitive exosome assays has sparked a research upsurge in clinical diagnostics. Here, we develop a bio-responsive the intelligent DNA…
CRISPR-Cas12a mediated combinatorial knock-out of multiple epigenetically silenced genes promotes pro-tumorigenic properties in colon cancer evolution
Abstract Genome-wide epigenetic alterations are important for the development of cancers. In any given cancer tissue, multiple important developmental regulators undergo epigenetic silencing. Similar epigenetic alterations are observed in normal physiological aging. The cumulative effects of multiple epigenetically silenced genes (ESGs) on tumor development remains an unaddressed aspect of cancer…
New Point-of-Care Assay for Rapid Detection of Monkeypox Virus
A proof-of-concept study published in The Lancet Microbe introduces a promising point-of-care assay for the rapid detection of monkeypox virus (MPXV). The researchers from Australia developed the assay based on isothermal amplification and CRISPR-Cas technology. With its high sensitivity and specificity, the assay performed well when compared to the gold-standard…
Transgene-free genome editing of vegetatively propagated and perennial plant species in the T0 generation via a co-editing strategy
Zhang, Y. et al. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA. Nat. Commun. 7, 12617 (2016). Article CAS PubMed PubMed Central Google Scholar Woo, J. W. et al. DNA-free genome editing in plants with preassembled CRISPR–Cas9 ribonucleoproteins. Nat. Biotechnol. 33, 1162–1164 (2015)….
Drug delivery systems for CRISPR-based genome editors
Li, Y., Glass, Z., Huang, M., Chen, Z. Y. & Xu, Q. Ex vivo cell-based CRISPR/Cas9 genome editing for therapeutic applications. Biomaterials 234, 119711 (2020). Article CAS PubMed PubMed Central Google Scholar Dong, W. & Kantor, B. Lentiviral vectors for delivery of gene-editing systems based on CRISPR/Cas: current state and…
The Potential for Groundbreaking Discoveries With CRISPR Screening
Since its discovery over 30 years ago, the potential therapeutic and diagnostic applications of the CRISPR-Cas system have continued to evolve. Found only in archaea and some bacteria – two of the three domains of life – the CRISPR-Cas system functions as a sort of adaptive immunity for prokaryotes, which,…
Researchers uncover novel physiological functions of CRISPR-Cas guard RNA
Graphical abstract. Credit: Cell Host & Microbe (2023). DOI: 10.1016/j.chom.2023.08.005 How the expression of Cas proteins in bacterial CRISPR-Cas immune system adapts to the constantly changing CRISPR structures and crRNA expression levels has been a long-standing unresolved question. Prof. Li Ming and Prof. Xiang Hua’s lab at Institute of Microbiology…
Programmable RNA detection with CRISPR-Cas12a,Nature Communications
Cas12a, a CRISPR-associated protein complex, has an inherent ability to cleave DNA substrates and is utilized in diagnostic tools to identify DNA molecules. We demonstrate that multiple orthologs of Cas12a activate trans-cleavage in the presence of split activators. Specifically, the PAM-distal region of the crRNA recognizes RNA targets provided that…
Healthcare and Nursing Community
CRISPR-based diagnostics offer numerous advantages, shifting clinical testing from lab settings to a patient-centric approach. Yet, until now, tests have only targeted DNA. Here, we share how our lab developed SAHARA, a method for RNA detection. Over the last decade, molecular diagnostics have undergone a transformative revolution with the help…
Rapid detection of Pseudomonas aeruginosa by recombinase polymerase amplification combined with CRISPR-Cas12a biosensing system
Front Cell Infect Microbiol . 2023 Aug 10;13:1239269. doi: 10.3389/fcimb.2023.1239269. eCollection 2023. Shuang Liu 1 , Siyuan Huang 1 , Fang Li 1 , Yuanyuan Sun 1 , Jin Fu 2 , Fei Xiao 2 , Nan Jia 2 , Xiaolan Huang 2 , Chunrong Sun 2 , Juan Zhou 2 , Yi Wang 2 , Dong Qu 1 Affiliations Expand…
Hybridization chain reaction circuit controller: CRISPR/Cas12a conversion amplifier for miRNA-21 sensitive detection
MicroRNA (miRNA) acts as a biomarker, reflecting the occurrence and development of many diseases by regulating human metabolic pathways and gene expression regulating [[1], [2], [3], [4], [5]]. Consequently, miRNA has been studied in clinical diagnosis, treatment, prognosis and drug development [[6], [7], [8], [9]]. Particularly, miRNA-21 (miR-21) is one…
Dual CRISPR-Cas3 is a promising tool to induce a gigantic genomic deletion and restore dystrophin protein
In a recent study published in Stem Cell Reports, researchers evaluated the use of a dual clustered regularly interspaced short palindromic repeats (CRISPR)-Cas3 system for inducing multi-exon skipping (MES) among Duchenne muscular dystrophy (DMD)-patient-derived induced pluripotent stem cells (iPSCs). Study: Dual CRISPR-Cas3 system for inducing multi-exon skipping in DMD patient-derived iPSCs. Image…
CVC Files Response and Reply Brief in Interference No. 106,115 Appeal | McDonnell Boehnen Hulbert & Berghoff LLP
In its appeal from an adverse decision on priority by the Patent Trial and Appeal Board (PTAB) in Interference No. 106,115 (directed to CRISPR-mediated gene editing), Junior Party the University of California/Berkeley, the University of Vienna, and Emmanuelle Charpentier (collectively, “CVC”) filed on May 19th its Response and Reply Brief…
2.1. Materials and r…
2.1. Materials and reagents All oligonucleotides (Table S1) were synthesized and purified by Sangon Biotech (Shanghai, China). Apurinic/apyrimidinic endonuclease 1 (APE1), T4 DNA ligase, Bst DNA polymerase (large fragment), Exonuclease III (Exo III), Exonuclease I (Exo I), T4 polynucleotide kinase (T4 PNK), Uracil DNA glycosylase (UDG), formamidopyrimidine DNA glycosylase (Fpg),…
A universal all-in-one RPA-Cas12a strategy with de novo autodesigner and its application in on-site ultrasensitive detection of DNA and RNA viruses
Revolutionary all-in-one RPA-CRISPR assays are rapidly becoming the most sought-after tools for point-of-care testing (POCT) due to their high sensitivity and ease of use. Despite the availability of one-pot methods for specific targets, the development of more efficient methods for new targets remains a significant challenge. In this study, we…
Transient naive reprogramming corrects hiPS cells functionally and epigenetically
Cell culture All cell lines used and derived by different approaches in this study are listed in Supplementary Table 1. Detailed information about the experimental design, materials and reagents is presented in the Reporting Summary. Primary human adult dermal fibroblasts (HDFa) from three different female donors were obtained from Gibco…
Applications of CRISPR/Cas9 in the Synthesis of Bioactive Compounds from Medicinal Plants
Allgaier C, Franz S (2015) Risk assessment on the use of herbal medicinal products containing pyrrolizidine alkaloids. Regul Toxicol Pharmacol 73:494–500 CrossRef CAS PubMed Google Scholar Barrangou R (2015) Diversity of CRISPR-Cas immune systems and molecular machines. Genome Biol 16:247 CrossRef PubMed PubMed Central Google Scholar Barrangou R, Fremaux C,…
Single-Molecule Quantification of Protein-DNA Interactions Using Nanopores
Proteins and nucleic acids interact through specific binding, which plays a critical role in various biological processes. Understanding these interactions is crucial for developing biosensing tools, molecular engineering techniques, and therapies. Scientists have found that nanopores, specifically solid-state nanopores, can be used for resistive pulse sensing to analyze binding events…
Sensing the DNA-mismatch tolerance of catalytically inactive Cas9 via barcoded DNA nanostructures in solid-state nanopores
DNA-nanostructure barcodes To observe that the CRISPR–dCas9 system is specific enough to detect the single base pair, DNA constructs with different ‘barcodes’ plus an overhang sequence for dCas9 was created. The DNA construct was synthesized from pairing a linearized 7.2 kbp single-stranded (ss) M13mp18 DNA (GuildBiosciences) with 190 complementary oligonucleotides via…
CRISPR Cas12a-mediated amplification-free digital DNA assay improves the diagnosis and surveillance of Nasopharyngeal carcinoma
. 2023 Jul 23;237:115546. doi: 10.1016/j.bios.2023.115546. Online ahead of print. Affiliations Expand Affiliations 1 State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China. 2 School of Medicine, South China University of Technology, Guangzhou, 510180,…
ToolGen unsuccessful in landmark CRISPR patent appeal – Patent
To print this article, all you need is to be registered or login on Mondaq.com. The Federal Court of Australia has delivered judgement in Australia’s landmark CRISPR patent dispute, finding that none of the claims in ToolGen Inc.’s patent application for platform CRISPR technologies are valid. The proceeding is…
CRISPR/Cas12a combined with RPA for detection of T. gondii in mouse whole blood | Parasites & Vectors
Mice and parasites The strains RH, Pru, wh3, and wh6, utilized in the present investigation, were generously provided by the Anhui Key Laboratory of Zoonoses, Anhui Medical University. The DNA of C. parvum and Babesia were procured from Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences. Furthermore, Plasmodium was…
RNA-mediated Allosteric Activation in CRISPR-Cas13a
Abstract Cas13a is a recent addition to the CRISPR-Cas toolkit that exclusively targets RNA, which makes it a promising tool for RNA detection. The protein uses a CRISPR RNA (crRNA) to target RNA sequences, which are cleaved by a composite active site formed by two Higher Eukaryotes and Prokaryotes Nucleotide…
A predicted CRISPR-mediated symbiosis between uncultivated archaea
Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67 (2010). Article CAS PubMed Google Scholar Andersson, A. F. & Banfield, J. F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320, 1047–1050 (2008). Article CAS PubMed Google…
Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a
Abstract CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by Cas12a in vitro, and we measured the contributions of distinct regions of the pre-crRNA to this reaction. We find that…
Self-primer exponential Cas12a tandem reaction-amplified and [Cu(tz)] nanosheets based neoteric biosensing platform for quantifying multiple mTBI-related miRNAs
Head injuries are a globally widespread problem, particularly among children and teenagers, who may be more susceptible to long-term sequelae during brain development. Concussion, a sign of mild traumatic brain injury (mTBI), affects an estimated 20% of teenagers [1], [2]. Unfortunately, due to delayed onset of symptoms and strong subjectivity…
CPA-Cas12a-based lateral flow strip for portable assay of Methicillin-resistant Staphylococcus aureus in clinical sample | Journal of Nanobiotechnology
Principle of CPA-Cas 12a lateral flow assay strategy CPA and CPA-Cas 12a sensing strategies were proposed for detection of nuc and mecA genes in MRSA respectively. According to the sequence of the target gene, we designed two PAM sites and four pairs of primer according to the principles of double-crossing…
Insertion sequence transposition inactivates CRISPR-Cas immunity
Primers, plasmids, bacterial strains, and growth conditions Primers, plasmids, and strains used in this study are listed in Tables S1–S3, respectively. Escherichia coli strains MG1655, DH10B, MDS42, and their derivates were cultured in LB medium at 37 °C, with shaking at 220 rpm. All the recombinants containing the temperature-sensitive pSC101-derived plasmid were cultured…