scholarly journals Single-Molecule Detection of SARS-CoV-2 by Plasmonic Sensing of Isothermally Amplified Nucleic Acids

2021 ◽  
Author(s):  
Haihang Ye ◽  
Chance Nowak ◽  
Yaning Liu ◽  
Yi Li ◽  
Tingting Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Hybridization ◽  
Single Molecule Detection ◽  
Colorimetric Sensing ◽  
Plasmonic Sensors ◽  
Plasmonic Sensing ◽  
Sequence Identification ◽  
Additional Sequence ◽  
Visible Wavelengths ◽  
Virus Testing

AbstractSingle-molecule detection of pathogens such as SARS-CoV-2 is key to combat infectious diseases outbreak and pandemic. Currently colorimetric sensing with loop-mediated isothermal amplification (LAMP) provides simple readouts but suffers from intrinsic non-template amplification. Herein, we report that plasmonic sensing of LAMP amplicons via DNA hybridization allows highly specific and single-molecule detection of SARS-CoV-2 RNA. Our work has two important advances. First, we develop gold and silver alloy (Au-Ag) nanoshells as plasmonic sensors that have 4-times stronger extinction in the visible wavelengths and give 20-times lower detection limit for oligonucleotides than Au nanoparticles. Second, we demonstrate that the diagnostic method allows cutting the complex LAMP amplicons into short repeats that are amendable for hybridization with oligonucleotide-functionalized nanoshells. This additional sequence identification eliminates the contamination from non-template amplification. The detection method is a simple and single-molecule diagnostic platform for virus testing at its early representation.Table of Content

scholarly journals Single-molecule detection of DNA hybridization

2003 ◽  
Vol 100 (13) ◽  
pp. 7605-7610 ◽  
Author(s):  
M. Singh-Zocchi ◽  
S. Dixit ◽  
V. Ivanov ◽  
G. Zocchi
Keyword(s):  
Single Molecule ◽  
Dna Hybridization ◽  
Single Molecule Detection

scholarly journals Label-free single-molecule detection of DNA-hybridization kinetics with a carbon nanotube field-effect transistor

2011 ◽  
Vol 6 (2) ◽  
pp. 126-132 ◽  
Author(s):  
Sebastian Sorgenfrei ◽  
Chien-yang Chiu ◽  
Ruben L. Gonzalez ◽  
Young-Jun Yu ◽  
Philip Kim ◽  
...  
Keyword(s):  
Carbon Nanotube ◽  
Single Molecule ◽  
Dna Hybridization ◽  
Field Effect ◽  
Field Effect Transistor ◽  
Single Molecule Detection ◽  
Label Free ◽  
Effect Transistor

scholarly journals A machine learning approach for accurate and real-time DNA sequence identification

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yiren Wang ◽  
Mashari Alangari ◽  
Joshua Hihath ◽  
Arindam K. Das ◽  
M. P. Anantram
Keyword(s):  
Real Time ◽  
Dna Sequence ◽  
Single Molecule ◽  
Identification Accuracy ◽  
Measuring System ◽  
Identification System ◽  
Genetic Sequencing ◽  
Sequence Identification ◽  
Tree Classifier ◽  
Single Mismatch

Abstract Background The all-electronic Single Molecule Break Junction (SMBJ) method is an emerging alternative to traditional polymerase chain reaction (PCR) techniques for genetic sequencing and identification. Existing work indicates that the current spectra recorded from SMBJ experimentations contain unique signatures to identify known sequences from a dataset. However, the spectra are typically extremely noisy due to the stochastic and complex interactions between the substrate, sample, environment, and the measuring system, necessitating hundreds or thousands of experimentations to obtain reliable and accurate results. Results This article presents a DNA sequence identification system based on the current spectra of ten short strand sequences, including a pair that differs by a single mismatch. By employing a gradient boosted tree classifier model trained on conductance histograms, we demonstrate that extremely high accuracy, ranging from approximately 96 % for molecules differing by a single mismatch to 99.5 % otherwise, is possible. Further, such accuracy metrics are achievable in near real-time with just twenty or thirty SMBJ measurements instead of hundreds or thousands. We also demonstrate that a tandem classifier architecture, where the first stage is a multiclass classifier and the second stage is a binary classifier, can be employed to boost the single mismatched pair’s identification accuracy to 99.5 %. Conclusions A monolithic classifier, or more generally, a multistage classifier with model specific parameters that depend on experimental current spectra can be used to successfully identify DNA strands.

scholarly journals A controlled T7 transcription-driven symmetric amplification cascade machinery for single-molecule detection of multiple repair glycosylases

2021 ◽  
Author(s):  
Li-juan Wang ◽  
Le Liang ◽  
Bing-jie Liu ◽  
BingHua Jiang ◽  
Chun-yang Zhang
Keyword(s):  
Single Molecule ◽  
Single Molecule Detection ◽  
Amplification Cascade

A controlled T7 transcription-driven symmetric amplification cascade machinery is developed for single-molecule detection of multiple repair glycosylases.

Highly Sensitive Detection of Paraquat with Pillar[5]arene as an aptamer in α-Hemolysin Nanopore

2021 ◽  
Author(s):  
Xiaojia Jiang ◽  
Mingsong Zang ◽  
Fei Li ◽  
Chunxi Hou ◽  
Quan Luo ◽  
...  
Keyword(s):  
Real Time ◽  
High Throughput ◽  
Single Molecule ◽  
Single Molecule Detection ◽  
Sensitive Detection ◽  
High Throughput Analysis ◽  
Throughput Analysis ◽  
The Real ◽  
Highly Sensitive ◽  
Highly Sensitive Detection

Biological nanopore-based techniques have attracted more and more attention recently in the field of single-molecule detection, because they allow the real-time, sensitive, high-throughput analysis. Herein, we report an engineered biological...

scholarly journals A Programmable DNA‐Silicification‐Based Nanocavity for Single‐Molecule Plasmonic Sensing

2021 ◽  
Vol 33 (7) ◽  
pp. 2005133
Author(s):  
Le Liang ◽  
Peng Zheng ◽  
Chi Zhang ◽  
Ishan Barman
Keyword(s):  
Single Molecule ◽  
Plasmonic Sensing
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