The structure and unzipping behavior of dumbbell and hairpin DNA revealed by real-time nanopore sensing

Li, Xinqiong; Song, Guiqin; Dou, Linqin; Yan, Shuli; Zhang, Ming; Yuan, Weidan; Lai, Shaoyong; Jiang, Xin; Li, Kaiju; Sun, Kai; Zhao, Chengli; Geng, Jia

doi:10.1039/d0nr08729g

Cited by 11 publications

(13 citation statements)

References 60 publications

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“…Similar current fluctuations with both upward and downward spikes have been reported for hairpin DNA molecules trapped inside a biological nanopore. 34,35 In our nanocavity device, the trapped DNA can be formed either by DNA compaction into a globule shape 36 or by multiple DNA strands residing in the Si pore constriction at the same time. 37,38 The dominating DNA trapping mechanism in our nanocavity will be discussed later.…”

Section: Resultsmentioning

confidence: 99%

DNA compaction and dynamic observation in a nanopore gated sub-attoliter silicon nanocavity

et al. 2022

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Section: Resultsmentioning

confidence: 99%

DNA compaction and dynamic observation in a nanopore gated sub-attoliter silicon nanocavity

et al. 2022

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“…29,62 MspA remains stable under extreme pH value of 2-14 and high temperature up to 92 C. 63 It has a conical shape with a constriction region of 1.2 nm wide and 0.6 nm length, which makes MspA a superior candidate for DNA sensing and sequencing. 11,14,40,64 However, the constriction region of wild-type MspA is highly negative charged, preventing ssDNA from being translocated and detected. Then, Butler et al 40 65 Mucin 1 protein, 66 and rapid assay for carbapenemresistant Klebsiella pneumoniae.…”

Section: Mycobacterium Smegmatis Porin Amentioning

confidence: 99%

Biological nanopores for sensing applications

et al. 2022

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Biological nanopores are proteins with transmembrane pore that can be embedded in lipid bilayer. With the development of single-channel current measurement technologies, biological nanopores have been reconstituted into planar lipid bilayer and used for single-molecule sensing of various analytes and events such as single-molecule DNA sensing and sequencing. To improve the sensitivity for specific analytes, various engineered nanopore proteins and strategies are deployed. Here, we introduce the origin and principle of nanopore sensing technology as well as the structure and associated properties of frequently used protein nanopores. Furthermore, sensing strategies for different applications are reviewed, with focus on the alteration of buffer condition, protein engineering, and deployment of accessory proteins and adapterassisted sensing. Finally, outlooks for de novo design of nanopore and nanopore beyond sensing are discussed.

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“…For example, Li et al developed a nanopore sensing based on the interaction of hairpin DNA and dumbbell DNA with pore proteins, demonstrating the potential application of dumbbell DNA in clinical diagnostics. 22 Mathilde et al developed an antibody-free assay platform for thrombin detection using dumbbell-shaped DNA and loop-mediated isothermal amplification (LAMP). 23 nucleic acid signal amplification technology has recently attracted great attention for the early diagnosis of AD.…”

Section: Introductionmentioning

confidence: 99%

“…More recently, signal amplification sensors based on DNA aptamers , and dumbbell-shaped DNA structures were regarded as appealing analytical platforms for the detection of trace amounts of biomolecules. For example, Li et al developed a nanopore sensing based on the interaction of hairpin DNA and dumbbell DNA with pore proteins, demonstrating the potential application of dumbbell DNA in clinical diagnostics . Mathilde et al developed an antibody-free assay platform for thrombin detection using dumbbell-shaped DNA and loop-mediated isothermal amplification (LAMP) .…”

Section: Introductionmentioning

confidence: 99%

Dumbbell Aptamer Sensor Based on Dual Biomarkers for Early Detection of Alzheimer’s Disease

Zhou

Sun

Zhang

et al. 2023

ACS Appl. Mater. Interfaces

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Finding a timely, sensitive, and noninvasive detection method has become an urgent need for asymptomatic early diagnosis of Alzheimer’s disease (AD). MicroRNA-193b (miR-193b) and Aβ42 oligomers (AβO42) in neurogenic exosomes were confirmed to reflect pathological changes in the AD early stage. The combination of two biomarkers is promising for the earlier detection of AD. In this study, a detection system based on the principle of the entropy-driven strand displacement reaction (ESDR) was developed, including a dumbbell detection probe (H), an indicator probe (R), and graphene oxide (GO). In the detection system, the two hairpins of H were opened by the interaction of miR-193b (T1) and AβO42 (T2) with the aptamer. Then R hybridized with H and began to displace T, initiating the next round of ESDR to achieve sensitive detection of T. GO specifically adsorbed free R and quenched the fluorescence, further reducing the intensity of the background signal. Both of these points provided the system with a more sensitive analytical performance. The detection limit of miR-193b was 77 pM and the detection limit of AβO42 was 53 pM. This sensor detected the change of “one increase (AβO42) and one decrease (miR-193b)” in the exosome sample. Additionally, results showed that this detection system could distinguish the model of early AD from the non-AD control, which was sufficient for earlier and more sensitive detection of AD. This strategy has strong specificity, high sensitivity, and easy operation, which provides broad prospects for the early diagnosis of AD.

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The structure and unzipping behavior of dumbbell and hairpin DNA revealed by real-time nanopore sensing

Abstract: Hairpin structures play an essential role in replication, transcription and recombination. Single molecule studies enable real-time measurement and observation of energetics and dynamics of hairpin structures, including folding and DNA-protein...

Cited by 11 publications

References 60 publications

DNA compaction and dynamic observation in a nanopore gated sub-attoliter silicon nanocavity

DNA compaction and dynamic observation in a nanopore gated sub-attoliter silicon nanocavity

Biological nanopores for sensing applications

Dumbbell Aptamer Sensor Based on Dual Biomarkers for Early Detection of Alzheimer’s Disease

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