Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA DOI
Anya Kardailsky, Benjamín Durán‐Vinet, Georgia Nester

et al.

The CRISPR Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 30, 2024

Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA is limited by biases toward certain species the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics enables collection whole ecosystem data sequencing all molecules present, allowing characterization identification. Clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated proteins (Cas)-based methods have potential to improve efficiency metagenomic low-abundant target organisms simplify analysis enrichment or nontarget depletion before sequencing. Implementation CRISPR-Cas has been due lack interest support past. This perspective synthesizes approaches study underrepresented taxa advocate further application optimization CRISPR-Cas, holding promise biomonitoring.

Language: Английский

CRISPR-based electrochemical biosensors: an alternative for point-of-care diagnostics? DOI
Dagwin Wachholz, Lauro T. Kubota

Talanta, Journal Year: 2024, Volume and Issue: 278, P. 126467 - 126467

Published: June 28, 2024

Language: Английский

Citations

7
Paper-based CRISPR-Cas diagnostics: A comprehensive review of advances and applications in disease detection DOI

Vasita Lapee-e,

Suphachai Nuanualsuwan,

Lalitphan Hongtanee

et al.

Microchemical Journal, Journal Year: 2025, Volume and Issue: unknown, P. 113055 - 113055

Published: Feb. 1, 2025

Language: Английский

Citations

0
Advancing CRISPR/Cas Biosensing with Integrated Devices DOI Creative Commons
Guozhen Liu

ACS Sensors, Journal Year: 2025, Volume and Issue: 10(2), P. 575 - 576

Published: Feb. 28, 2025

InfoMetricsFiguresRef. ACS SensorsVol 10/Issue 2Article This publication is free to access through this site. Learn More CiteCitationCitation and abstractCitation referencesMore citation options ShareShare onFacebookX (Twitter)WeChatLinkedInRedditEmailJump toExpandCollapse EditorialFebruary 28, 2025Advancing CRISPR/Cas Biosensing with Integrated DevicesClick copy article linkArticle link copied!Guozhen Liu*Guozhen LiuIntegrated Devices Intelligent Diagnosis (ID2) Laboratory, School of Medicine, The Chinese University Hong Kong, Shenzhen 518172, China*Email: [email protected]More by Guozhen Liuhttps://orcid.org/0000-0002-0556-6404Open PDFACS SensorsCite this: Sens. 2025, 10, 2, 575–576Click citationCitation copied!https://pubs.acs.org/doi/10.1021/acssensors.5c00330https://doi.org/10.1021/acssensors.5c00330Published February 2025 Publication History Received 27 January 2025Published online 28 in issue 2025editorialCopyright © American Chemical Society. available under these Terms Use. Request reuse permissionsThis licensed for personal use PublicationsCopyright SocietySubjectswhat are subjectsArticle subjects automatically applied from the Subject Taxonomy describe scientific concepts themes article.AssaysBiosensingBiotechnologyGeneticsSensorsRather than being famous only gene editing field, revealing collateral cleavage activity Cas12a, Cas13a, Cas14 effectors, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR associated (Cas) systems (i.e., CRISPR/Cas) have received significant credit modern analytical science capability detecting versatile analytes superior sensitivity specificity. (1,2) A variety exciting biosensing now been developed successfully detection different varying nucleic acids non-nucleic (such as metabolites, proteins, exosomes, metal ions). Although most popular signal output biosensors fluorescence, various modalities such colorimetric, electrochemiluminescence, electrochemical, electrical systems. Furthermore, potential has demonstrated multiplex integration microfluidics or other devices enabling identification presence multiple targets. However, despite extensive efforts success develop diagnostic tools based on trans-cleavage enzymatic activity, encounter unavoidable challenges, including inadequate limit (near picomole level) clinically relevant biomarkers at subpicomolar levels limited catalytic efficiency DNA cleavage. These limitations significantly hinder widespread adoption clinical diagnostics point-of-care testing.To further enhance avoid necessity sophisticated costly equipment, acids-based preamplification techniques, thermal-dependent amplification, polymerase chain reaction (PCR), thermal-independent rolling circle amplification (RCA), recombinase (RPA), loop-mediated isothermal (LAMP), frequently integrated assays. techniques increase sensitivity, they inevitably overshadow Cas effectors neglect intrinsic effectors. Preamplification also extends time reduces subsequent due nonspecific primer interference, while substantially increasing risk aerosol contamination. sensitive acid strategies employ exponential formats which amplicons (amplification products) recycled primers templates. because format, background products that lead false-positive results inevitable after long times can be caused by, example, contaminants, off-template products, secondary structures Therefore, evaluated controlled practice generation unwanted signals. Consequently, amplification-based always determined resolution between true- signals generated diluted standard samples blank/negative controls, respectively.Development preamplification-free aims achieve rapid one-pot high (attomolar single-molecule levels) adaptability. achieved optimizing key components reporters), employing cascade adopting microfluidic droplet analysis, integrating readout patterns. Conventional single-strand reporters replaced a range nanoparticle-based reporters, (3) gold nanoparticle (AuNP) quantum dot platinum nanoparticles, aggregation-induced emission agent reporters. AuNPs were used CRISPR/Cas12a biosensor surface enhanced Raman spectroscopy (SERS) low 10 aM. (4) By utilizing autocatalytic circuits, enabled attomolar without need preamplification. (5) ability detect acids, immunoassays into system abundance. (6)CRISPR/Cas technologies promise beyond simple assay. (7) CRISPR technology engineering led advances molecular biology healthcare vitro diagnosis vivo monitoring, tube assays devices. (8−10) lateral flow assay, face mask incorporated lyophilized sensor was noninvasive SARS-CoV-2 room temperature 90 min requires no user intervention press button. (11) Microfluidic paper-based realize supersensitive pathogenic bacteria foods. (10) wearable microneedle patch uses CRISPR-activated graphene biointerfaces reported extraction long-term monitoring universal cell-free DNA. It enables real-time over days vivo, highlighting its early disease screening prognosis. (12) single-step monkeypox virus 15 vest-pocket device 0.5 copies μL–1 100% concordance PCR validation, (13) adaptable resource-limited settings. Multiplex challenging certain enzymes, resulting interference possible cross-reactivity among analytes. (14) Solutions, high-fidelity variants, coupling optimal crRNA designs, using orthogonal technologies, allow simultaneous targets interference. We recently CRISPR-Cas12a immunosensing glass fiber portable fluorescence reader proteins pM limit, cytokines synovial joint fluids scenario. (6) eliminating expensive instrument tedious sample preparation, CRISPR/Cas-mediated provide sample-to-answer will continue bring about breakthrough diagnosis. (10,11)CRISPR/Cas-based much away maturation. editorial encourages submissions demonstrate advancements existing address growing quick, cost-effective, sensitive, accurate field-deployable vivo. With nanotechnologies, microfluidics, enzyme-based systems, artificial intelligence, our aim facilitate comprehensive reliable analyte detection. (15) And it throughput biomarker discovery (16) designing "all-in-one" combine processing, readout. Real-time target bioimaging another highlight research biomedical field if novel discovered integrate continuous corresponding typically involve steps, extraction, readout, become time-consuming prone In addition integration, respond innovations enzyme reagent assay desirable reduced time. Realizing full platforms sustained interdisciplinary collaboration scientists, biologists, engineers, clinicians, policy makers. Continued innovation components, regulatory standardization essential translate cutting-edge laboratory bedside beyond, although there challenges. confident match proudly not but affordable globally accessible, driving improvements precision medicine sustainability science.Author InformationClick section linkSection copied!Corresponding AuthorGuozhen Liu, China, https://orcid.org/0000-0002-0556-6404, Email: protected]NotesViews expressed those author necessarily views ACS.ReferencesClick copied! references 16 publications. 1Chertow, D. S. Next-generation CRISPR. Science 2018, 360, 381– 382, DOI: 10.1126/science.aat4982 Google Scholar1Next-generation CRISPRChertow Daniel S.Science (Washington, DC, United States) (2018), 360 (6387), 381-382CODEN: SCIEAS; ISSN:0036-8075. (American Association Advancement Science) There expanded reference. >> SciFinder ®https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXpt1Witbs%253D&md5=b83cc13b01ff95f5b9dba8b21ee480c02Li, Y.; Li, S.; Wang, J.; G. towards next-generation biosensing. Trends Biotechnol. 2019, 37, 730– 743, 10.1016/j.tibtech.2018.12.005 Scholar2CRISPR/Cas Systems Next-Generation BiosensingLi, Yi; Shiyuan; Jin; GuozhenTrends Biotechnology (2019), 37 (7), 730-743CODEN: TRBIDM; ISSN:0167-7799. (Elsevier Ltd.) review. Beyond remarkable genome ability, CRISPR/Cas9 effector utilized applications. recent RNA Cas13a sparked even greater interest developing promised diagnostics. Now, along Cas12 activities single-stranded (ssDNA), several established targets, bacteria, viruses, cancer mutations, others. Based we detailed classification propose their future utility. As continues mature, promising candidates platforms. ®https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXksVyntQ%253D%253D&md5=99d745d312b053b1c9582bcbd832ab923Ki, J. CRISPR/Cas-assisted colorimetric point-of-use testing African swine fever virus. 2022, 7, 3940– 3946, 10.1021/acssensors.2c02007 Scholar3CRISPR/Cas-Assisted Colorimetric Biosensor Point-of-Use Testing Swine Fever VirusKi, Jisun; Na, Hee-Kyung; Yoon, Sun Woo; Le, Van Phan; Lee, Tae Geol; Lim, Eun-KyungACS Sensors (2022), 7 (12), 3940-3946CODEN: ASCEFJ; ISSN:2379-3694. Society) (ASFV) causes highly contagious fatal affecting both domesticated wild pigs. Substandard therapies vaccinations cause severe economic damages pig culling removal infected carcasses. an urgent approach assists avoiding spread ASFV reducing loss. study, sensing platform dual enzymic combined clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-assocd. protein 12a (Cas12a) urease ASFV. mechanism involves magnetic bead-anchored urease-conjugated oligodeoxynucleotide (MB@urODN), dsDNA cleaved activated CRISPR/Cas12a. After magnetically sepg. urease, confirmed measuring change soln. advantage method undergoing complex duplication process. detected three clin. specimens collected porcine tissue samples. proposed designed adequate, simple, robust, selective anal. technique zoonotic vast specialized tools. ®https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XivFSgsrbJ&md5=192b3a94a2eeda9308c22970296517d24Yin, B. SERS nanoplatform chimeric DNA/RNA hairpin guide ultrasensitive Theranostics 12, 5914, 10.7150/thno.75816 Scholar4A detectionYin, Bohan; Zhang, Qin; Xia, Xinyue; Chuanqi; Ho, Willis Kwun Hei; Yan, Jiaxiang; Huang, Yingying; Wu, Honglian; Pui; Yi, Changqing; Hao, Jianhua; Jianfang; Chen, Honglin; Wong, Siu Dexter; Yang, MoTheranostics 12 (13), 5914-5930CODEN: THERDS; ISSN:1838-7640. (Ivyspring International Publisher) nanomaterial-based optical surface-enhanced scattering (SERS), formulate powerful amplification-free system. nanomaterials impose steric hindrance accessibility narrow gaps (SERS hot spots) nanoparticles (NPs) producing To overcome restriction, specifically design hairpins (displacers) destabilized DNA, liberating excessive disintegrate core-satellite nanocluster via toehold-mediated strand displacement orchestrating "on-off" biosensor. comprises large core surrounded small tags hybridization ultrabright reporter, disassembly leads drastic decrease intensity readouts. introduce sepn. disassembled nanostructures suppress improving sensitivity. proof-of-concept findings showed application displacers more effective decreasing attained better (LOD, aM) directly CRISPR-Cas12a, selectivity stability Introducing magnetic-responsive functionality improves LOD 1 Our work offers sensitively selectively probe pre-amplification provides new insights CRISPR-Cas12a/SERS resolve constructing biosensors. ®https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xit12nurzK&md5=33e4d73cf233e629bd2c56718062532c5Shi, K. CRISPR-Cas autocatalysis-driven feedback network Sci. Adv. 2021, eabc7802 10.1126/sciadv.abc7802 ScholarThere record reference.6Zou, quantification inflammation osteoarthritis. Device 2024, 100319, 10.1016/j.device.2024.100319 reference.7Shi, R.; Zhong, L.; G.; Mak, W. C. Technology: From Lab Assays Portable Wearables. TrAC Anal. Chem. 177, 117796, 10.1016/j.trac.2024.117796 reference.8Broughton, P. CRISPR–Cas12-based SARS-CoV-2. Nat. 2020, 38, 870– 874, 10.1038/s41587-020-0513-4 Scholar8CRISPR-Cas12-based SARS-CoV-2Broughton, James P.; Deng, Xianding; Yu, Guixia; Fasching, Clare Servellita, Venice; Singh, Jasmeet; Miao, Xin; Streithorst, Jessica A.; Granados, Andrea; Sotomayor-Gonzalez, Alicia; Zorn, Kelsey; Gopez, Allan; Hsu, Elaine; Gu, Wei; Miller, Steve; Pan, Chao-Yang; Guevara, Hugo; Wadford, Debra Janice Chiu, Charles Y.Nature (2020), 38 870-874CODEN: NABIF9; ISSN:1087-0156. (Nature Research) Abstr.: An outbreak betacoronavirus acute respiratory syndrome (SARS)-CoV-2 began Wuhan, China Dec. 2019. COVID-19, assocd. infection, rapidly produce global pandemic. report development (<40 min), easy-to-implement CRISPR-Cas12-based swab exts. validated contrived ref. patients States, 36 COVID-19 infection 42 viral infections. CRISPR-based DETECTR visual faster alternative US Centers Disease Control Prevention RT-PCR 95% pos. predictive agreement neg. agreement. ®https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXntlejt7w%253D&md5=a1ccd699e2945474307f349518da37e59Lee, I.; Kwon, S.-J.; Heeger, Dordick, Ultrasensitive ImmunoMag-CRISPR Lateral Flow Assay Point-of-Care Urinary Biomarkers. 9, 92– 100, 10.1021/acssensors.3c01694 reference.10Nguyen, Q. Wearable materials embedded synthetic sensors biomolecule 39, 1366– 1374, 10.1038/s41587-021-00950-3 Scholar10Wearable detectionNguyen, Peter Q.; Soenksen, Luis Donghia, Nina M.; Angenent-Mari, Nicolaas de Puig, Helena; Ally; Rose; Slomovic, Shimyn; Galbersanini, Tommaso; Lansberry, Geoffrey; Sallum, Hani Zhao, Evan Niemi, B.; Collins, J.Nature (2021), 39 (11), 1366-1374CODEN: Portfolio) Integrating biol. wearables could expand opportunities physiol. status, states exposure pathogens toxins. operation circuits generally living, engineered wearables. Here lightwt., flexible substrates textiles functionalized freeze-dried, tools, chems. pathogen signatures. upon rehydration aq. events specific mol. changes detects fluorescent luminescent outputs. limits rival current lab. methods quant. PCR. wearable, temp. within min, requiring ®https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhsVenurnK&md5=70c78eaf02d067096407bd97d4ceb1ea11Dai, Gooding, mediated toward understanding cellular Angew. Chem., Int. Ed. 59, 20754– 20766, 10.1002/anie.202005398 Scholar11CRISPR Mediated Toward Understanding Cellular Biology DiagnosisDai, Yifan; Yanfang; Guozhen; JustinAngewandte Chemie, Edition 59 (47), 20754-20766CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA) Recent biotechnologies greatly authors' capabilities repurpose biomol. diagnosing diseases pathways. attribute allows widely programmable mechanism. Minireview, authors first illustrate principle functioning process actuating. Next, mols. summarized. some applications biomols. imaging networks. Finally, challenges with, prospects of, developments discussed. ®https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhs1Oks7nP&md5=0119652222aa5d39b8f64ccb8aceb96f12Yang, Fang, X. Programmable CRISPR-Cas9 capture Commun. 13, 3999, 10.1038/s41467-022-31740-3 Scholar12Programmable DNAYang, Bin; Jilie; XueenNature Communications 13 (1), 3999CODEN: NCAOBW; ISSN:2041-1723. health. modules, microneedles ext. interstitial fluid minimally invasive fashion. perform extn. macromol. simultaneously. show synergetic effect biointerfaces, Epstein-Barr virus, sepsis, kidney transplantation anti-interference 60% fetal bovine serum, satisfactory stable exptl. immunodeficient mouse models shows feasibility practicability method. holds great potentially ®https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XhvVChtr3N&md5=1e4c4fdfe726801050f38a8fda03c78d13Wang, Y. minutes device. 15, 3279, 10.1038/s41467-024-47518-8 reference.14Li, multiplexed biosensing: challenge insurmountable obstacle?. 792– 795, 10.1016/j.tibtech.2019.04.012 Scholar14CRISPR/Cas Multiplexed Biosensing: Challenge Insurmountable Obstacle?Li, Linyang; (8), 792-795CODEN: Performing still elusive goal CRISPR/Cas-based Instead obstacle, realistic successful Strategic considerations required fully explore ®https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXpsVOrsL4%253D&md5=414b5e06e7ed5c55a528e930054e0b8815Song, Amplifying mutational profiling extracellular vesicle mRNA SCOPE. 10.1038/s41587-024-02426-6 reference.16Rahimi, Balusamy, Perumalsamy, H.; Ståhlberg, Mijakovic, I. recognition biomarkers. Nucleic Acids Res. 52, 10040– 10067, 10.1093/nar/gkae736 reference.Cited Click copied!This yet cited publications.Download PDFFiguresReferences Get e-AlertsGet e-AlertsACS copied!https://doi.org/10.1021/acssensors.5c00330Published 2025Copyright permissionsArticle Views-Altmetric-Citations-Learn metrics closeArticle Views COUNTER-compliant sum text downloads since November 2008 (both PDF HTML) across all institutions individuals. updated reflect usage leading up last few days.Citations number articles citing article, calculated Crossref daily. Find information counts.The Altmetric Attention Score quantitative measure attention online. Clicking donut icon load page altmetric.com additional details score social media given article. how calculated.Recommended Articles FiguresReferencesThis figures.References 1Next-generation 2CRISPR/Cas 3CRISPR/Cas-Assisted 4A 8CRISPR-Cas12-based 10Wearable 11CRISPR 12Programmable 14CRISPR/Cas

Language: Английский

Citations

0
CRISPR revolution: Unleashing precision pathogen detection to safeguard public health and food safety DOI
Jacob Tizhe Liberty, Sabri Bromage,

Endurance Peter

et al.

Methods, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
A self-actuated CRISPR/Cas12a feedback amplification platform for ultrasensitive detection of exosome DOI

Meili Yang,

Huan Pan,

Pang Qiao

et al.

Microchemical Journal, Journal Year: 2025, Volume and Issue: unknown, P. 113477 - 113477

Published: March 1, 2025

Language: Английский

Citations

0
Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA DOI
Anya Kardailsky, Benjamín Durán‐Vinet, Georgia Nester

et al.

The CRISPR Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 30, 2024

Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA is limited by biases toward certain species the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics enables collection whole ecosystem data sequencing all molecules present, allowing characterization identification. Clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated proteins (Cas)-based methods have potential to improve efficiency metagenomic low-abundant target organisms simplify analysis enrichment or nontarget depletion before sequencing. Implementation CRISPR-Cas has been due lack interest support past. This perspective synthesizes approaches study underrepresented taxa advocate further application optimization CRISPR-Cas, holding promise biomonitoring.

Language: Английский

Citations

0