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Article: A CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection

TitleA CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection
Authors
KeywordsCRISPR-Cas12a
gold nanoparticles
magnetic manipulation
nucleic acid detection
surface-enhanced Raman spectroscopy
Issue Date8-Aug-2022
PublisherIvyspring International Publisher
Citation
Theranostics, 2022, v. 12, n. 13, p. 5914-5930 How to Cite?
Abstract

Background: CRISPR-Cas12a has been integrated with nanomaterial-based optical techniques, such as surface-enhanced Raman scattering (SERS), to formulate a powerful amplification-free nucleic acid detection system. However, nanomaterials impose steric hindrance to limit the accessibility of CRISPR-Cas12a to the narrow gaps (SERS hot spots) among nanoparticles (NPs) for producing a significant change in signals after nucleic acid detection. Methods: To overcome this restriction, we specifically design chimeric DNA/RNA hairpins (displacers) that can be destabilized by activated CRISPR-Cas12a in the presence of target DNA, liberating excessive RNA that can disintegrate a core-satellite nanocluster via toehold-mediated strand displacement for orchestrating a promising "on-off" nucleic acid biosensor. The core-satellite nanocluster comprises a large gold nanoparticle (AuNP) core surrounded by small AuNPs with Raman tags via DNA hybridization as an ultrabright Raman reporter, and its disassembly leads to a drastic decrease of SERS intensity as signal readouts. We further introduce a magnetic core to the large AuNPs that can facilitate their separation from the disassembled nanostructures to suppress the background for improving detection sensitivity. Results: As a proof-of-concept study, our findings showed that the application of displacers was more effective in decreasing the SERS intensity of the system and attained a better limit of detection (LOD, 10 aM) than that by directly using activated CRISPR-Cas12a, with high selectivity and stability for nucleic acid detection. Introducing magnetic-responsive functionality to our system further improves the LOD to 1 aM. Conclusion: Our work not only offers a platform to sensitively and selectively probe nucleic acids without pre-amplification but also provides new insights into the design of the CRISPR-Cas12a/SERS integrated system to resolve the steric hindrance of nanomaterials for constructing biosensors.

Keywords: CRISPR-Cas12a; gold nanoparticles; magnetic manipulation; nucleic acid detection; surface-enhanced Raman spectroscopy.


Persistent Identifierhttp://hdl.handle.net/10722/331487
ISSN
2023 Impact Factor: 12.4
2023 SCImago Journal Rankings: 2.912
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorYin, BH-
dc.contributor.authorZhang, Q-
dc.contributor.authorXia, XY-
dc.contributor.authorLi, CQ-
dc.contributor.authorHo, WKH-
dc.contributor.authorYan, JX-
dc.contributor.authorHuang, YY-
dc.contributor.authorWu, HL-
dc.contributor.authorWang, P-
dc.contributor.authorYi, CQ-
dc.contributor.authorHao, JH-
dc.contributor.authorWang, JF-
dc.contributor.authorChen, HL-
dc.contributor.authorWong, SHD-
dc.contributor.authorYang, M-
dc.date.accessioned2023-09-21T06:56:16Z-
dc.date.available2023-09-21T06:56:16Z-
dc.date.issued2022-08-08-
dc.identifier.citationTheranostics, 2022, v. 12, n. 13, p. 5914-5930-
dc.identifier.issn1838-7640-
dc.identifier.urihttp://hdl.handle.net/10722/331487-
dc.description.abstract<p><strong>Background:</strong> CRISPR-Cas12a has been integrated with nanomaterial-based optical techniques, such as surface-enhanced Raman scattering (SERS), to formulate a powerful amplification-free nucleic acid detection system. However, nanomaterials impose steric hindrance to limit the accessibility of CRISPR-Cas12a to the narrow gaps (SERS hot spots) among nanoparticles (NPs) for producing a significant change in signals after nucleic acid detection. <strong>Methods:</strong> To overcome this restriction, we specifically design chimeric DNA/RNA hairpins (displacers) that can be destabilized by activated CRISPR-Cas12a in the presence of target DNA, liberating excessive RNA that can disintegrate a core-satellite nanocluster via toehold-mediated strand displacement for orchestrating a promising "on-off" nucleic acid biosensor. The core-satellite nanocluster comprises a large gold nanoparticle (AuNP) core surrounded by small AuNPs with Raman tags via DNA hybridization as an ultrabright Raman reporter, and its disassembly leads to a drastic decrease of SERS intensity as signal readouts. We further introduce a magnetic core to the large AuNPs that can facilitate their separation from the disassembled nanostructures to suppress the background for improving detection sensitivity. <strong>Results:</strong> As a proof-of-concept study, our findings showed that the application of displacers was more effective in decreasing the SERS intensity of the system and attained a better limit of detection (LOD, 10 aM) than that by directly using activated CRISPR-Cas12a, with high selectivity and stability for nucleic acid detection. Introducing magnetic-responsive functionality to our system further improves the LOD to 1 aM. <strong>Conclusion:</strong> Our work not only offers a platform to sensitively and selectively probe nucleic acids without pre-amplification but also provides new insights into the design of the CRISPR-Cas12a/SERS integrated system to resolve the steric hindrance of nanomaterials for constructing biosensors.</p><p><strong>Keywords: </strong>CRISPR-Cas12a; gold nanoparticles; magnetic manipulation; nucleic acid detection; surface-enhanced Raman spectroscopy.</p>-
dc.languageeng-
dc.publisherIvyspring International Publisher-
dc.relation.ispartofTheranostics-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectCRISPR-Cas12a-
dc.subjectgold nanoparticles-
dc.subjectmagnetic manipulation-
dc.subjectnucleic acid detection-
dc.subjectsurface-enhanced Raman spectroscopy-
dc.titleA CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection-
dc.typeArticle-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.7150/thno.75816-
dc.identifier.scopuseid_2-s2.0-85136837925-
dc.identifier.volume12-
dc.identifier.issue13-
dc.identifier.spage5914-
dc.identifier.epage5930-
dc.identifier.eissn1838-7640-
dc.identifier.isiWOS:000842078500001-
dc.identifier.issnl1838-7640-

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