scholarly journals Biological Nanopores: Engineering on Demand

Life ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Ana Crnković ◽  
Marija Srnko ◽  
Gregor Anderluh
Keyword(s):  
Molecular Biology ◽  
Single Molecule ◽  
Enzymatic Reactions ◽  
Label Free ◽  
Natural Sources ◽  
On Demand ◽  
Label Free Detection ◽  
Long Read ◽  
Inorganic Molecules ◽  
Standard Molecular Biology

Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.

scholarly journals Capacitive Field-Effect EIS Chemical Sensors and Biosensors: A Status Report

Sensors ◽  
2020 ◽  
Vol 20 (19) ◽  
pp. 5639 ◽  
Author(s):  
Arshak Poghossian ◽  
Michael J. Schöning
Keyword(s):  
Chemical Sensors ◽  
Field Effect ◽  
Status Report ◽  
Enzymatic Reactions ◽  
Label Free ◽  
Ion Concentrations ◽  
Biochemical Sensing ◽  
Current Trends ◽  
Label Free Detection ◽  
New Generation

Electrolyte-insulator-semiconductor (EIS) field-effect sensors belong to a new generation of electronic chips for biochemical sensing, enabling a direct electronic readout. The review gives an overview on recent advances and current trends in the research and development of chemical sensors and biosensors based on the capacitive field-effect EIS structure—the simplest field-effect device, which represents a biochemically sensitive capacitor. Fundamental concepts, physicochemical phenomena underlying the transduction mechanism and application of capacitive EIS sensors for the detection of pH, ion concentrations, and enzymatic reactions, as well as the label-free detection of charged molecules (nucleic acids, proteins, and polyelectrolytes) and nanoparticles, are presented and discussed.

scholarly journals Single-Molecule Detection of DNA in a Nanochannel by High-Field Strength-Assisted Electrical Impedance Spectroscopy

Micromachines ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 189 ◽  
Author(s):  
Porpin Pungetmongkol ◽  
Takatoki Yamamoto
Keyword(s):  
Single Molecule ◽  
High Intensity ◽  
High Sensitivity ◽  
Electrical Impedance Spectroscopy ◽  
Random Coil ◽  
Label Free ◽  
Electrode Gap ◽  
Label Free Detection ◽  
Intensity Field ◽  
Nanogap Electrodes

Many researchers have fabricated micro and nanofluidic devices incorporating optical, chemical, and electrical detection systems with the aim of achieving on-chip analysis of macromolecules. The present study demonstrates a label-free detection of DNA using a nanofluidic device based on impedance measurements that is both sensitive and simple to operate. Using this device, the electrophoresis and dielectrophoresis effect on DNA conformation and the length dependence were examined. A low alternating voltage was applied to the nanogap electrodes to generate a high intensity field (>0.5 MV/m) under non-faradaic conditions. In addition, a 100 nm thick gold electrode was completely embedded in the substrate to allow direct measurements of a solution containing the sample passing through the gap, without any surface modification required. The high intensity field in this device produced a dielectrophoretic force that stretched the DNA molecule across the electrode gap at a specific frequency, based on back and forth movements between the electrodes with the DNA in a random coil conformation. The characteristics of 100 bp, 500 bp, 1 kbp, 5 kbp, 10 kbp, and 48 kbp λ DNA associated with various conformations were quantitatively analyzed with high resolution (on the femtomolar level). The sensitivity of this system was found to be more than about 10 orders of magnitude higher than that obtained from conventional linear alternating current (AC) impedance for the analysis of bio-polymers. This new high-sensitivity process is expected to be advantageous with regard to the study of complex macromolecules and nanoparticles.

scholarly journals Advances in Label-Free Detections for Nanofluidic Analytical Devices

Micromachines ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 885 ◽  
Author(s):  
Thu Le ◽  
Hisashi Shimizu ◽  
Kyojiro Morikawa
Keyword(s):  
Single Molecule ◽  
Detection Methods ◽  
Label Free ◽  
Practical Applications ◽  
Detection Techniques ◽  
Kinetic Information ◽  
Label Free Detection ◽  
Nanofluidic Devices ◽  
Nanofluidic Device ◽  
New Research

Nanofluidics, a discipline of science and engineering of fluids confined to structures at the 1–1000 nm scale, has experienced significant growth over the past decade. Nanofluidics have offered fascinating platforms for chemical and biological analyses by exploiting the unique characteristics of liquids and molecules confined in nanospaces; however, the difficulty to detect molecules in extremely small spaces hampers the practical applications of nanofluidic devices. Laser-induced fluorescence microscopy with single-molecule sensitivity has been so far a major detection method in nanofluidics, but issues arising from labeling and photobleaching limit its application. Recently, numerous label-free detection methods have been developed to identify and determine the number of molecules, as well as provide chemical, conformational, and kinetic information of molecules. This review focuses on label-free detection techniques designed for nanofluidics; these techniques are divided into two groups: optical and electrical/electrochemical detection methods. In this review, we discuss on the developed nanofluidic device architectures, elucidate the mechanisms by which the utilization of nanofluidics in manipulating molecules and controlling light–matter interactions enhances the capabilities of biological and chemical analyses, and highlight new research directions in the field of detections in nanofluidics.

scholarly journals Label-Free Detection of Single-Molecule Melting Kinetics with Laser Heated Nanopore

2018 ◽  
Vol 114 (3) ◽  
pp. 216a-217a
Author(s):  
Hirohito Yamazaki ◽  
Rui Hu ◽  
Robert Henley ◽  
Justin Halman ◽  
Kirill Afonin ◽  
...  
Keyword(s):  
Single Molecule ◽  
Label Free ◽  
Melting Kinetics ◽  
Label Free Detection ◽  
Laser Heated

Label-free detection of biotoxins via a photo-induced force infrared spectrum at the single-molecular level

The Analyst ◽  
2019 ◽  
Vol 144 (20) ◽  
pp. 6108-6117 ◽  
Author(s):  
Bin Ji ◽  
Ahmad Kenaan ◽  
Shan Gao ◽  
Jin Cheng ◽  
Daxiang Cui ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Infrared Spectrum ◽  
Single Molecule ◽  
Molecular Level ◽  
Principal Component ◽  
Component Analysis ◽  
Label Free ◽  
Force Microscopy ◽  
Label Free Detection

Schematic illustration of photo-induced force microscopy combine principal component analysis detected and distinguish single molecule particles of biotoxins AT, RT/ETX with label-free.

scholarly journals A large size-selective DNA nanopore with sensing applications

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Rasmus P. Thomsen ◽  
Mette Galsgaard Malle ◽  
Anders Hauge Okholm ◽  
Swati Krishnan ◽  
Søren S.-R. Bohr ◽  
...  
Keyword(s):  
Lipid Bilayers ◽  
Single Molecule ◽  
Detection System ◽  
Optical Methods ◽  
Label Free ◽  
Sensing Applications ◽  
Large Size ◽  
Transmission Electron ◽  
Label Free Detection ◽  
External Signals

AbstractTransmembrane nanostructures like ion channels and transporters perform key biological functions by controlling flow of molecules across lipid bilayers. Much work has gone into engineering artificial nanopores and applications in selective gating of molecules, label-free detection/sensing of biomolecules and DNA sequencing have shown promise. Here, we use DNA origami to create a synthetic 9 nm wide DNA nanopore, controlled by programmable, lipidated flaps and equipped with a size-selective gating system for the translocation of macromolecules. Successful assembly and insertion of the nanopore into lipid bilayers are validated by transmission electron microscopy (TEM), while selective translocation of cargo and the pore mechanosensitivity are studied using optical methods, including single-molecule, total internal reflection fluorescence (TIRF) microscopy. Size-specific cargo translocation and oligonucleotide-triggered opening of the pore are demonstrated showing that the DNA nanopore can function as a real-time detection system for external signals, offering potential for a variety of highly parallelized sensing applications.

scholarly journals PCR-free, label-free detection of sequence-specific DNA with single-molecule sensitivity using in vitro N-hybrid system in microfluidic drops

2022 ◽  
Author(s):  
Yizhe Zhang ◽  
David A Weitz
Keyword(s):  
Single Molecule ◽  
High Specificity ◽  
Label Free ◽  
Hybrid Strategy ◽  
Single Molecule Level ◽  
Target Dna ◽  
Label Free Detection ◽  
Novel Method ◽  
Picoliter Droplet

We propose a novel method that can detect DNA with high specificity at the single-molecule level by employing the in vitro N-hybrid strategy realized in sub-picoliter microfluidic drops. It detects target DNA based on the specific interactions of the target-encoded proteins with their partner molecules, and achieves single-molecule sensitivity via signal-transduction and signal-amplification during gene-expression processes in a sub-picoliter droplet, therefore effectively avoiding complicated procedures in labeling-based methods or biases and artifacts in PCR-based methods.

scholarly journals DNA nanotechnology assisted nanopore-based analysis

2020 ◽  
Vol 48 (6) ◽  
pp. 2791-2806 ◽  
Author(s):  
Taoli Ding ◽  
Jing Yang ◽  
Victor Pan ◽  
Nan Zhao ◽  
Zuhong Lu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Nanotechnology ◽  
Clinical Diagnostics ◽  
Dna Assembly ◽  
Label Free ◽  
One Pot ◽  
Dna Strand Displacement ◽  
Label Free Detection ◽  
Target Molecules ◽  
Dna Strand

Abstract Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.

Label-free, mass-sensitive single-molecule imaging using interferometric scattering microscopy

2020 ◽  
Author(s):  
Nikolas Hundt
Keyword(s):  
Single Molecule ◽  
Cellular Systems ◽  
Single Molecule Imaging ◽  
Label Free ◽  
Measurement Sensitivity ◽  
Mass Distributions ◽  
Quantitative Measurements ◽  
Contrast Mechanism ◽  
Cellular Components ◽  
Scattering Signal

Abstract Single-molecule imaging has mostly been restricted to the use of fluorescence labelling as a contrast mechanism due to its superior ability to visualise molecules of interest on top of an overwhelming background of other molecules. Recently, interferometric scattering (iSCAT) microscopy has demonstrated the detection and imaging of single biomolecules based on light scattering without the need for fluorescent labels. Significant improvements in measurement sensitivity combined with a dependence of scattering signal on object size have led to the development of mass photometry, a technique that measures the mass of individual molecules and thereby determines mass distributions of biomolecule samples in solution. The experimental simplicity of mass photometry makes it a powerful tool to analyse biomolecular equilibria quantitatively with low sample consumption within minutes. When used for label-free imaging of reconstituted or cellular systems, the strict size-dependence of the iSCAT signal enables quantitative measurements of processes at size scales reaching from single-molecule observations during complex assembly up to mesoscopic dynamics of cellular components and extracellular protrusions. In this review, I would like to introduce the principles of this emerging imaging technology and discuss examples that show how mass-sensitive iSCAT can be used as a strong complement to other routine techniques in biochemistry.

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