Theranostics 2022; 12(13):5914-5930. doi:10.7150/thno.75816 This issue Cite

Research Paper

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

Bohan Yin1, Qin Zhang1, Xinyue Xia2, Chuanqi Li1, Willis Kwun Hei Ho1, Jiaxiang Yan1, Yingying Huang1, Honglian Wu1, Pui Wang3, Changqing Yi4, Jianhua Hao5, Jianfang Wang2, Honglin Chen3, Siu Hong Dexter Wong1,6✉, Mo Yang1✉

1. Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China.
2. Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China.
3. Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong 999077, China.
4. Key Laboratory of Sensing Technology and Biomedical Instruments (Guangdong Province), School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, P. R. China.
5. Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China.
6. Research Institute for Sports Science and Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China.

Citation:
Yin B, Zhang Q, Xia X, Li C, Ho WKH, Yan J, Huang Y, Wu H, Wang P, Yi C, Hao J, Wang J, Chen H, Wong SHD, Yang M. A CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection. Theranostics 2022; 12(13):5914-5930. doi:10.7150/thno.75816. https://www.thno.org/v12p5914.htm
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Abstract

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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: gold nanoparticles, magnetic manipulation, surface-enhanced Raman spectroscopy, CRISPR-Cas12a, nucleic acid detection


Citation styles

APA
Yin, B., Zhang, Q., Xia, X., Li, C., Ho, W.K.H., Yan, J., Huang, Y., Wu, H., Wang, P., Yi, C., Hao, J., Wang, J., Chen, H., Wong, S.H.D., Yang, M. (2022). A CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection. Theranostics, 12(13), 5914-5930. https://doi.org/10.7150/thno.75816.

ACS
Yin, B.; Zhang, Q.; Xia, X.; Li, C.; Ho, W.K.H.; Yan, J.; Huang, Y.; Wu, H.; Wang, P.; Yi, C.; Hao, J.; Wang, J.; Chen, H.; Wong, S.H.D.; Yang, M. A CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection. Theranostics 2022, 12 (13), 5914-5930. DOI: 10.7150/thno.75816.

NLM
Yin B, Zhang Q, Xia X, Li C, Ho WKH, Yan J, Huang Y, Wu H, Wang P, Yi C, Hao J, Wang J, Chen H, Wong SHD, Yang M. A CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection. Theranostics 2022; 12(13):5914-5930. doi:10.7150/thno.75816. https://www.thno.org/v12p5914.htm

CSE
Yin B, Zhang Q, Xia X, Li C, Ho WKH, Yan J, Huang Y, Wu H, Wang P, Yi C, Hao J, Wang J, Chen H, Wong SHD, Yang M. 2022. A CRISPR-Cas12a integrated SERS nanoplatform with chimeric DNA/RNA hairpin guide for ultrasensitive nucleic acid detection. Theranostics. 12(13):5914-5930.

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