A protein enzyme-free strategy for fluorescence detection of single nucleotide polymorphisms using asymmetric MNAzymes

Zhang, Xuanhao; Li, Qian; Chao, Qiqi; Zhang, Yuxi; Sun, Xufeng; Fan, Gao-Chao; Song, Zhiling; Kong, Rongmei; Liu, Xiang

doi:10.1016/j.aca.2023.340811

Cited by 7 publications

(2 citation statements)

References 42 publications

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“…We have confirmed that this biosensor enabled specific and sensitive SNP detection, showing a linear response ranging from 1 fM to 100 nM with a detection limit of 0.4 fM. This sensing performance is superior to the previously reported methods shown in Supplementary Table S2 (Zhou et al, 2018;Wolfe et al, 2019;Song et al, 2021;Zhang et al, 2023a). Moreover, we also executed anti-interference and real sample analysis with this biosensor, which exhibited superior detection performance.…”

Section: Discussionsupporting

confidence: 78%

A FEN 1-driven DNA walker-like reaction coupling with magnetic bead-based separation for specific SNP detection

Xu,

Chen,

Yang

et al. 2023

Front. Bioeng. Biotechnol.

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Single-nucleotide polymorphism (SNP) plays a key role in the carcinogenesis of the human genome, and understanding the intrinsic relationship between individual genetic variations and carcinogenesis lies heavily in the establishment of a precise and sensitive SNP detection platform. Given this, a powerful and reliable SNP detection platform is proposed by a flap endonuclease 1 (FEN 1)-driven DNA walker-like reaction coupling with a magnetic bead (MB)-based separation. A carboxyfluorescein (FAM)-labeled downstream probe (DP) was decorated on a streptavidin magnetic bead (SMB). The target DNA, as a walker strand, was captured by hybridization with DP and an upstream probe (UP) to form a three-base overlapping structure and execute the walking function on the surface of SMB. FEN 1 was employed to specifically recognize the three-base overlapping structure and cut the 5′flap at the SNP site to report the walking event and signal amplification. Considering the fact that the fluorescence was labeled on the cleavage and uncleavage sequences of DP and the target DNA-triggered walking event was undistinguishable from the mixtures, magnetic separation came in handy for cleavage probe (CP) isolation and discrimination of the amplified signal from the background signal. In comparison with the conventional DNA walker reaction, this strategy was coupling with SMB-based separation, thus promising a powerful and reliable method for SNP detection and signal amplification.

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Section: Discussionsupporting

confidence: 78%

A FEN 1-driven DNA walker-like reaction coupling with magnetic bead-based separation for specific SNP detection

Xu,

Chen,

Yang

et al. 2023

Front. Bioeng. Biotechnol.

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show abstract

“…The method was compared with others for the detection of ctDNA SNPs. As can be seen from Table , some conventional detection methods, , such as fluorescence ,− and electrochemical methods, ,− also expressed a characteristic of high sensitivity. Nevertheless, they still have some limitations, for instance, the comparatively complicated procedures of manufacturing the material, the inability to detect multiple ctDNA SNPs in a single detection, and the inability to detect both WT and MT of multiple SNPs at the same time.…”

Section: Resultsmentioning

confidence: 99%

Detection of Single Nucleotide Polymorphisms of Circulating Tumor DNA by Strand Displacement Amplification Coupled with Liquid Chromatography

Ma,

Xu,

Hou

et al. 2024

Anal. Chem.

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The detection of multiple single nucleotide polymorphisms (SNPs) of circulating tumor DNA (ctDNA) is still a great challenge. In this study, we designed enzyme-assisted nucleic acid strand displacement amplification combined with high-performance liquid chromatography (HPLC) for the simultaneous detection of three ctDNA SNPs. First, the trace ctDNA could be hybridized to the specially designed template strand, which initiated the strand displacement nucleic acid amplification process under the synergistic action of DNA polymerase and restriction endonuclease. Then, the targets would be replaced with G-quadruplex fluorescent probes with different tail lengths. Finally, the HPLC-fluorescence assay enabled the separation and quantification of multiple signals. Notably, this method can simultaneously detect both the wild type (WT) and mutant type (MT) of multiple ctDNA SNPs. Within a linear range of 0.1 fM–0.1 nM, the detection limits of BRAF V600E-WT, EGFR T790M-WT, and KRAS 134A-WT and BRAF V600E-MT, EGFR T790M-MT, and KRAS 134A-MT were 29, 31, and 11 aM and 22, 29, and 33 aM, respectively. By using this method, the mutation rates of multiple ctDNA SNPs in blood samples from patients with lung or breast cancer can be obtained in a simple way, providing a convenient and highly sensitive analytical assay for the early screening and monitoring of lung cancer.

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A bulged-type enzyme-free recognition strategy designed for single nucleotide polymorphisms integrating with label-free electrochemical biosensor

Ye,

Liang,

Tan

et al. 2024

Biosensors and Bioelectronics

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A protein enzyme-free strategy for fluorescence detection of single nucleotide polymorphisms using asymmetric MNAzymes

Cited by 7 publications

References 42 publications

A FEN 1-driven DNA walker-like reaction coupling with magnetic bead-based separation for specific SNP detection

A FEN 1-driven DNA walker-like reaction coupling with magnetic bead-based separation for specific SNP detection

Detection of Single Nucleotide Polymorphisms of Circulating Tumor DNA by Strand Displacement Amplification Coupled with Liquid Chromatography

A bulged-type enzyme-free recognition strategy designed for single nucleotide polymorphisms integrating with label-free electrochemical biosensor

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