Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations

Takeuchi, Nanami; Hiratani, Moe; Kawano, Ryuji

doi:10.1021/jacsau.2c00117

Cited by 16 publications

(13 citation statements)

References 56 publications

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“…Therefore, most other methods for detecting e.g. microRNA involve deep bioinformatics or base modification to increase the signal [26, 50, 51]. The wavy pattern of our signal in the density plot results from the three different current interruptions at 60, 80, or 100 mV during aptamer translocation.…”

Section: Resultsmentioning

confidence: 98%

Ready-to-use nanopore platform for ethanolamine quantification using an aptamer-based strand displacement assay

Quint

Simantzik

Kaiser

et al. 2023

Preprint

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In recent decades, nanopores have become a promising diagnostic tool. Protein and solid-state nanopores are increasingly used for both RNA/DNA sequencing and small molecule detection. The latter is of great importance because small molecules are difficult or expensive to detect using available methods such as HPLC or LC-MS. Moreover, DNA aptamers are an excellent detection element for sensitive and specific detection of small molecules. Here, we describe a method for the quantification of ethanolamine using Oxford Nanopore's ready-to-use sequencing platform. To this end, we have developed a strand displacement assay using a binding ethanolamine aptamer and magnetic beads. The displaced aptamer can be detected using the MinION nanopores and analysed/quantified using our in-house developed analysis software.

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Section: Resultsmentioning

confidence: 98%

Ready-to-use nanopore platform for ethanolamine quantification using an aptamer-based strand displacement assay

Quint

Simantzik

Kaiser

et al. 2023

Preprint

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“…Bilayer lipid membranes (BLMs) were prepared using the drop contact method in the microdevice. In the drop contact method as we have been developing, − the two lipid monolayers containing the aqueous droplets come into contact in a small hole punched in the parylene film to form lipid bilayers (Figure S1D). Lipid bilayers were formed as follows: first, 0.6 μL of DOPC:Cholesterol = 4:1 (w/w) dissolved in n -decane was added into both chambers.…”

Section: Methodsmentioning

confidence: 99%

Cell-Free Expression of De Novo Designed Peptides That Form β-Barrel Nanopores

2023

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Nanopore sensing has attracted much attention as a rapid, simple, and label-free single-molecule detection technology. To apply nanopore sensing to extensive targets including polypeptides, nanopores are required to have a size and structure suitable for the target. We recently designed a de novo β-barrel peptide nanopore (SVG28) that constructs a stable and monodispersely sized nanopore. To develop the sizes and functionality of peptide nanopores, systematic exploration is required. Here we attempt to use a cell-free synthesis system that can readily express peptides using transcription and translation. Hydrophilic variants of SVG28 were designed and expressed by the PURE system. The peptides form a monodispersely sized nanopore, with a diameter 1.1 or 1.5 nm smaller than that of SVG28. Such cell-free synthesizable peptide nanopores have the potential to enable the systematic custom design of nanopores and comprehensive sequence screening of nanopore-forming peptides.

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“…Takeuchi et al developed a miRNA classifier based on a 5‐input DNA AND gate and a nanopore readout. [ 114 ] The gate simply consists of the 5 microRNA binding sites and a 5′ hairpin structure to guide the direction of the gate inside the nanopore (α‐hemolysin) from the 3’ end. The binding of all 5 miRNAs to the gate leads to a distinct nanopore signal subsequently decoded in silico.…”

Section: Molecular Computers For Sample Classificationmentioning

confidence: 99%

Molecular Computation for Molecular Classification

et al. 2023

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DNA as an informational polymer has, for the past 30 years, progressively become an essential molecule to rationally build chemical reaction networks endowed with powerful signal‐processing capabilities. Whether influenced by the silicon world or inspired by natural computation, molecular programming has gained attention for diagnosis applications. Of particular interest for this review, molecular classifiers have shown promising results for disease pattern recognition and sample classification. Because both input integration and computation are performed in a single tube, at the molecular level, this low‐cost approach may come as a complementary tool to molecular profiling strategies, where all biomarkers are quantified independently using high‐tech instrumentation. After introducing the elementary components of molecular classifiers, some of their experimental implementations are discussed either using digital Boolean logic or analog neural network architectures.

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Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations

Cited by 16 publications

References 56 publications

Ready-to-use nanopore platform for ethanolamine quantification using an aptamer-based strand displacement assay

Ready-to-use nanopore platform for ethanolamine quantification using an aptamer-based strand displacement assay

Cell-Free Expression of De Novo Designed Peptides That Form β-Barrel Nanopores

Molecular Computation for Molecular Classification

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