Simulation guided intramolecular orthogonal reporters for dissecting cellular oxidative stress and response

Pan, Yecan; Weng, Rui; Zhang, Linghao; Qiu, Jing; Wang, Xinlu; Liao, Guangqin; Qin, Zhaohui; Zhang, Lingpu; Xiao, Haihua; Qian, Yongzhong; Su, Xin

doi:10.1016/j.nantod.2022.101573

Cited by 13 publications

(17 citation statements)

References 35 publications

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“…It was reported that the studied biomarkers are abnormally expressed in NSCLC. [ 26–53 ] We collected 10 groups of clinical samples. Every group included tumor tissues, tumor‐adjacent tissues, and normal control tissues of NSCLC patients ( Figure A).…”

Section: Resultsmentioning

confidence: 99%

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Simulation‐Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging

Kou

Wang

Zhang

et al. 2022

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DNA‐based nanodevices equipped with localized modules have been promising probes for biomarker detection. Such devices heavily rely on the intramolecular hybridization reaction. However, there is a lack of mechanistic insights into this reaction that limits the sensing speed and sensitivity. A coarse‐grained model is utilized to simulate the intramolecular hybridization of localized DNA circuits (LDCs) not only optimizing the performance, but also providing mechanistic insights into the hybridization reaction. The simulation guided‐LDCs enable the detection of multiple biomarkers with high sensitivity and rapid speed showing good consistency with the simulation. Fluorescence assays demonstrate that the simulation‐guided LDC shows an enhanced sensitivity up to 9.3 times higher than that of the same probes without localization. The detection limits of ATP, miRNA, and APE1 reach 0.14 mM, 0.68 pM, and 0.0074 U mL−1, respectively. The selected LDC is operated in live cells with good success in simultaneously detecting the biomarkers and discriminating between cancer cells and normal cells. LDC is successfully applied to detect the biomarkers in cancer tissues from patients, allowing the discrimination of cancer/adjacent/normal tissues. This work herein presents a design workflow for DNA nanodevices holding great potential for expanding the applications of DNA nanotechnology in diagnostics and therapeutics.

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Section: Resultsmentioning

confidence: 99%

“…It was noteworthy that the LDC was resistant to the degradation of some nonspecific nucleases owing to the protective function of DNA nanostructures. [41,42] In the same conditions, the linear substrate could be rapidly digested by nonspecific nucleases (Figure S10, Supporting Information).…”

Section: Logic Gated Detection Of Biomarkers By Ldcsmentioning

confidence: 99%

Simulation‐Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging

Kou

Wang

Zhang

et al. 2022

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“…93 Modification of the nuclear localization signal (NLS) on DNA nanostructures is also a commonly used method to guide foreign materials into the nucleus. 94 Liang et al modified the NLS on DNA tetrahedra, which initially targeted lysosomes, to target the nuclei (Fig. 4(b)).…”

Section: Nuclear Targetingmentioning

confidence: 99%

Subcellular localization of DNA nanodevices and their applications

et al. 2023

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“…There is growing interest in the practical use of biomolecule interactions involving nucleic acids as affinity probes − for specific and sensitive detection of toxic heavy metals. , Aptamers, i.e., single-stranded DNA (ssDNA) and RNA, as affinity biomolecules, carry advantages such as high binding affinity, which can lead to high sensitivity and selectivity. It makes them ideal for constructing online assays for detecting heavy metals in environmental and food samples .…”

Section: Introductionmentioning

confidence: 99%

Exploration of the Interaction of Cadmium and Aptamer by Molecular Simulation and Development of Sensitive Capillary Zone Electrophoresis-Based Aptasensor

Irfan

Murtaza

Zhao

et al. 2023

J. Chem. Inf. Model.

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The presence of cadmium ions (Cd2+) in environmental samples demands a fast, sensitive, and selective analytical method that can measure toxic levels. Biosensors based on aptamers (aptasensors) have been developed, but some of them suffer from poor sensitivity and specificity due to the immobilization of aptamers. Here, we employed circular dichroism, molecular docking, and molecular dynamics simulation to reveal that the aptamer gradually undergoes significant conformational changes upon Cd2+ binding. This fact highlights the advantages of biosensors based on free aptamers. So, keeping these results, an analytical method was established for the detection of Cd2+ by utilizing capillary zone electrophoresis (CZE), which is adapted for the free aptamer. So, CZE equipped with aptamer as a detection probe can detect Cd2+ within 4 min in the range from 5 to 250 nM with R 2 = 0.994, limit of detection 5 nM (signal-to-noise ratio = 3), and recovery from 92.6 ± 1.6 to 107.4 ± 1.0% in river water samples. Furthermore, the detected concentration in water samples is below the harmful levels (267 nM) recommended by World Health Organization standards in drinking water. This method displays a high sensitivity and specificity for Cd2+. It is found to be superior to existing methods, which use immobilized aptamers, and can be readily expanded to design aptasensors for other targets.

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Simulation guided intramolecular orthogonal reporters for dissecting cellular oxidative stress and response

Cited by 13 publications

References 35 publications

Simulation‐Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging

Simulation‐Assisted Localized DNA Logical Circuits for Cancer Biomarkers Detection and Imaging

Subcellular localization of DNA nanodevices and their applications

Exploration of the Interaction of Cadmium and Aptamer by Molecular Simulation and Development of Sensitive Capillary Zone Electrophoresis-Based Aptasensor

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