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Label-free amplified fluorescence detection of DNA biomarker based on KFP polymerase-driven double strand displacement reactions and magnetic nanoprobe

Abstract

Developing a sensitive, low-cost and general sensing platform for the DNA biomarker and its mutation analysis is vital important for early cancer screening. In our work, the tumor suppressor gene-P53 DNA was chosen as the model of DNA biomarker due to its vital role in preventing oncogenes cancer-inhibiting activity through mediating cellular proliferation and apoptosis. Compared with the tumor biopsy, the quantification of P53 gene and its mutation in biofluids (such as urine) is more convenient due to its simple operation and non-invasive. Herein, a label-free amplified fluorescence assay has been developed for P53 DNA in urine samples through the KFP polymerase-driven double strand displacement reactions and magnetic nanoprobe. First, the ssDNA probe (RP) was designed with the antisense sequences for P53 DNA and the Nb.BbvCI endonuclease recognition site. In the presence of P53 DNA, the formed dsDNA between RP and P53 DNA performed as engaging primers to initiate the first strand displacement reaction (SDA) under the action of KFP DNA polymerase and Nb.BbvCI, generating abundant short ssDNA (primer). Subsequently, the resulted primers will initiate the downstream SDA through the primer-hairpin DNA (HPa) binding, opening up, and extension of HPb and HPc under the action of KFP DNA polymerase. In the process of this final DNA polymerization reaction, the primer hybridized on HPa is released and goes on to initiate another round, forming plenty of duplex Y-shaped DNA. With the integration of SYBR Green I (SG I) into these duplex DNA, the amplified label-free fluorescence detection platform for P53 DNA can be achieved. Moreover, the biotin modified nanoprobe (bio-CP) was used to capture the superfluous HP. Performing the separated function through the action between the bio-CP and streptavidin-magnetic nanobeads, the binding of superfluous HP and SG could be avoided and a low background was acquired. Benefit from the abundant SG intercalating sites of Y-shaped DNA and low background signal, this method showed excellent sensitivity with a detection limit of 0.012 nM, and the P53 DNA in urine samples has been evaluated, offering a powerful tool for biomedical research and clinical diagnosis.

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Supplementary files

Article information


Submitted
17 Feb 2020
Accepted
04 May 2020
First published
12 May 2020

Anal. Methods, 2020, Accepted Manuscript
Article type
Paper

Label-free amplified fluorescence detection of DNA biomarker based on KFP polymerase-driven double strand displacement reactions and magnetic nanoprobe

X. Sun, Y. Liu, L. Liu, F. Yin, R. Liu, X. Li and Q. Xue, Anal. Methods, 2020, Accepted Manuscript , DOI: 10.1039/D0AY00338G

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