Extension of duplex specific nuclease sensing application with RNA aptamer

Ghazala Ashraf; Zi-Tao Zhong; Muhammad Asif; Ayesha Aziz; Laibo Song; Shujie Zhang; Bo Liu; Wei Chen; Yuan-Di Zhao

doi:10.1016/j.talanta.2022.123314

Extension of duplex specific nuclease sensing application with RNA aptamer

Talanta. 2022 May 15:242:123314. doi: 10.1016/j.talanta.2022.123314. Epub 2022 Feb 15.

Authors

Ghazala Ashraf¹, Zi-Tao Zhong¹, Muhammad Asif², Ayesha Aziz¹, Laibo Song¹, Shujie Zhang¹, Bo Liu¹, Wei Chen³, Yuan-Di Zhao⁴

Affiliations

¹ Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, PR China.
² Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan, 430205, PR China.
³ Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, PR China. Electronic address: chen1980wei@hust.edu.cn.
⁴ Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, PR China; Key Laboratory of Biomedical Photonics (HUST), Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, PR China. Electronic address: zydi@mail.hust.edu.cn.

PMID: 35182839
DOI: 10.1016/j.talanta.2022.123314

Abstract

Duplex specific nuclease (DSN) that can precisely cleave DNA portion in double-stranded DNA or DNA-RNA hybrid has engrossed immense attention owing to its great potential in emerging bioanalytical applications. Here, we present a novel approach to extend DSN sensing application by coupling RNA aptamer. Specially designed RNA ligand sequences are used to capture the target and simultaneously provide complementary sequences of DNA for DSN aided fluorescent signal enhancement. A clotting enzyme, thrombin, has been used as a model analyte. One RNA aptamer combined with the target molecule can generate fluorescent signals through cleavage of hybridized TaqMan DNA probe (P2) by DSN. The proposed assay has achieved the lowest detection limit of 0.039 pM. The assay has been applied for real-time detection of thrombin release from live cells and other biotic media for early disease diagnosis. The developed method is versatile and can detect various other targets by choosing the relevant aptamer and probe sequences. This method is promising to be applied to medical diagnosis, biosensing, food safety, environmental monitoring, and other fields.

Keywords: Aptasensor; Duplex specific nuclease; Fluorescence; RNA aptamer; Signal amplification; Thrombin.

MeSH terms

Aptamers, Nucleotide*
Biosensing Techniques* / methods
DNA
DNA Probes
Endonucleases
Limit of Detection
Thrombin

Substances

Aptamers, Nucleotide
DNA Probes
DNA
Endonucleases
Thrombin