Issue

Vol. 17 (2025)

Universal Amplification-Free RNA Detection by Integrating CRISPR-Cas10 with Aptameric Graphene Field-Effect Transistor

https://doi.org/10.1007/s40820-025-01730-3
Mingyuan Sun
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Zhenxiao Yu
CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology and Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Shuai Wang
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Jiaoyan Qiu
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Yuzhen Huang
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Xiaoshuang Chen
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Yunhong Zhang
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Chao Wang
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Xue Zhang
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Yanbo Liang
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Hong Liu
State Key Laboratory of Crystal Materials, Shandong University, Jinan, Shandong 250100, People’s Republic of China
Qunxin She
CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology and Microbial Technology Institute, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Yu Zhang
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China
Lin Han
Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, People’s Republic of China

Corresponding Author: Yu Zhang

yuzhang@sdu.edu.cn

Nano-Micro Letters, Vol. 17 (2025), Article Number: 242

Abstract

Amplification-free, highly sensitive, and specific nucleic acid detection is crucial for health monitoring and diagnosis. The type III CRISPR-Cas10 system, which provides viral immunity through CRISPR-associated protein effectors, enables a new amplification-free nucleic acid diagnostic tool. In this study, we develop a CRISPR-graphene field-effect transistors (GFETs) biosensor by combining the type III CRISPR-Cas10 system with GFETs for direct nucleic acid detection. This biosensor exploits the target RNA-activated continuous ssDNA cleavage activity of the dCsm3 CRISPR-Cas10 effector and the high charge density of a hairpin DNA reporter on the GFET channel to achieve label-free, amplification-free, highly sensitive, and specific RNA detection. The CRISPR-GFET biosensor exhibits excellent performance in detecting medium-length RNAs and miRNAs, with detection limits at the aM level and a broad linear range of 10−15 to 10−11 M for RNAs and 10−15 to 10−9 M for miRNAs. It shows high sensitivity in throat swabs and serum samples, distinguishing between healthy individuals (N = 5) and breast cancer patients (N = 6) without the need for extraction, purification, or amplification. This platform mitigates risks associated with nucleic acid amplification and cross-contamination, making it a versatile and scalable diagnostic tool for molecular diagnostics in human health.


Highlights:
1 A collaborative biosensing system is developed for amplification-free RNA/miRNA detection by integrating Type III CRISPR-Cas10 system with a graphene field-effect transistor (GFET).
2 Continuous cleavage of ssDNA by the mutant CRISPR-Cas10 effector complexes and high charge density of hairpin DNA reporters on the GFET channel enable the detection limit to reach the level of aM.
3 A universal sensing detection platform is established to directly detect the medium-length RNAs and miRNAs in clinical samples with the recognition capability of single nucleic acid.

Keywords

CRISPR Cas10; Graphene effect Field transistor; Biosensor; RNA/miRNA detection; Amplification Free
Sun, Mingyuan, Zhenxiao Yu, Shuai Wang, Jiaoyan Qiu, Yuzhen Huang, Xiaoshuang Chen, Yunhong Zhang, Chao Wang, Xue Zhang, Yanbo Liang, Hong Liu, Qunxin She, Yu Zhang, and Lin Han. 2025. “Universal Amplification-Free RNA Detection by Integrating CRISPR-Cas10 With Aptameric Graphene Field-Effect Transistor”. Nano-Micro Letters 17 (April):242. https://doi.org/10.1007/s40820-025-01730-3.
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