scholarly journals Single-Entity Detection With TEM-Fabricated Nanopores

2021 ◽  
Vol 9 ◽  
Author(s):  
Hongcheng Yang ◽  
Muhammad Saqib ◽  
Rui Hao
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Low Cost ◽  
Ionic Current ◽  
High Sensitivity ◽  
Protein Sequencing ◽  
Next Generation Sequencing Technology ◽  
Single Entity ◽  
Nanoparticle Detection ◽  
The Future

Nanopore-based single-entity detection shows immense potential in sensing and sequencing technologies. Solid-state nanopores permit unprecedented detail while preserving mechanical robustness, reusability, adjustable pore size, and stability in different physical and chemical environments. The transmission electron microscope (TEM) has evolved into a powerful tool for fabricating and characterizing nanometer-sized pores within a solid-state ultrathin membrane. By detecting differences in the ionic current signals due to single-entity translocation through the nanopore, solid-state nanopores can enable gene sequencing and single molecule/nanoparticle detection with high sensitivity, improved acquisition speed, and low cost. Here we briefly discuss the recent progress in the modification and characterization of TEM-fabricated nanopores. Moreover, we highlight some key applications of these nanopores in nucleic acids, protein, and nanoparticle detection. Additionally, we discuss the future of computer simulations in DNA and protein sequencing strategies. We also attempt to identify the challenges and discuss the future development of nanopore-detection technology aiming to promote the next-generation sequencing technology.

scholarly journals Comparing current noise in biological and solid-state nanopores

2019 ◽  
Author(s):  
A. Fragasso ◽  
S. Schmid ◽  
C. Dekker
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Signal To Noise Ratio ◽  
Low Cost ◽  
Ionic Current ◽  
Low Noise ◽  
Signal To Noise ◽  
Experimental Conditions ◽  
High Frequencies ◽  
Noise Ratio

AbstractNanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the signal-to-noise ratio (SNR), the important figure of merit, by measuring free translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR >160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.

scholarly journals Application of Solid-State Nanopore in Protein Detection

2020 ◽  
Vol 21 (8) ◽  
pp. 2808 ◽  
Author(s):  
Yuhan Luo ◽  
Linlin Wu ◽  
Jing Tu ◽  
Zuhong Lu
Keyword(s):  
Solid State ◽  
Chemical Modification ◽  
Single Molecule ◽  
Protein Detection ◽  
High Sensitivity ◽  
Protein Sequencing ◽  
Its Sequence ◽  
Sequence Structure ◽  
Single Molecule Level ◽  
Protein Molecules

A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.

scholarly journals Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Itaru Yanagi ◽  
Rena Akahori ◽  
Ken-ichi Takeda
Keyword(s):  
Solid State ◽  
Dielectric Breakdown ◽  
Ionic Current ◽  
High Sensitivity ◽  
Fabrication Method ◽  
High Ph ◽  
Target Molecule ◽  
Sin Membrane ◽  
Total Dna ◽  
Ph Conditions

Abstract For nanopore sensing of various-sized molecules with high sensitivity, the size of the nanopore should be adjusted according to the size of each target molecule. For solid-state nanopores, a simple and inexpensive nanopore fabrication method utilizing dielectric breakdown of a membrane is widely used. This method is suitable for fabricating a small nanopore. However, it suffers two serious problems when attempting to fabricate a large nanopore: the generation of multiple nanopores and the non-opening failure of a nanopore. In this study, we found that nanopore fabrication by dielectric breakdown of a SiN membrane under high-pH conditions (pH ≥ 11.3) could overcome these two problems and enabled the formation of a single large nanopore up to 40 nm in diameter within one minute. Moreover, the ionic-current blockades derived from streptavidin-labelled and non-labelled DNA passing through the fabricated nanopore were clearly distinguished. The current blockades caused by streptavidin-labelled DNA could be identified even when its concentration is 1% of the total DNA.

scholarly journals Field effect control of translocation dynamics in surround-gate nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Makusu Tsutsui ◽  
Sou Ryuzaki ◽  
Kazumichi Yokota ◽  
Yuhui He ◽  
Takashi Washio ◽  
...  
Keyword(s):  
Solid State ◽  
Water Flow ◽  
Single Molecule ◽  
Ionic Current ◽  
Critical Issue ◽  
Hydrodynamic Drag ◽  
Single Particles ◽  
Drag Forces ◽  
Fine Control ◽  
Controllable Motion

AbstractControlling the fast electrophoresis of nano-objects in solid-state nanopores is a critical issue for achieving electrical analysis of single-particles by ionic current. In particular, it is crucial to slow-down the translocation dynamics of nanoparticles. We herein report that a focused electric field and associated water flow in a surround-gate nanopore can be used to trap and manipulate a nanoscale object. We fine-control the electroosmosis-induced water flow by modulating the wall surface potential via gate voltage. We find that a nanoparticle can be captured in the vicinity of the conduit by balancing the counteracting electrophoretic and hydrodynamic drag forces. By creating a subtle force imbalance, in addition, we also demonstrate a gate-controllable motion of single-particles moving at an extremely slow speed of several tens of nanometers per second. The present method may be useful in single-molecule detection by solid-state nanopores and nanochannels.

The Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore

2018 ◽  
Author(s):  
Xin Shi ◽  
Qiao Li ◽  
Rui Gao ◽  
Wei Si ◽  
Shao-Chuang Liu ◽  
...  
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Conformational Changes ◽  
Ionic Current ◽  
Observation Time ◽  
Random Coil ◽  
Dna Complexes ◽  
Dna Complex ◽  
Identification And Characterization

<a></a><a>Docking of a protein-DNA complex onto a nanopore can provide ample observation time for a detailed inspection of the complex, enabling collection of biophysical data for detection, identification, and characterization of the biomolecules. While docking of a protein-DNA complex onto a biological nanopore has enabled analytic applications of nanopores including DNA sequencing, the application of the same principle to solid-state nanopores is tempered by poor understanding of the docking process. Here, we elucidate the behaviour of individual protein-DNA complexes docked onto a solid-state nanopore by monitoring the nanopore ionic current. </a><a>Repeat docking of monovalent streptavidin-DNA complexes is found to produce ionic current blockades that fluctuate between discrete levels within the same current blockade. </a>We elucidate the roles of the protein plug and the DNA tether in the docking process, finding the docking configurations to determine the multitude of the current blockade levels whereas the frequency of the current level switching to be determined by the interactions between the molecules and the solid-state membrane. Finally, we prove the feasibility of using the nanopore docking principle for single molecule sensing using solid-state nanopores by detecting conformational changes of a tethered DNA molecule from a random coil to an i-motif states.

The Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore

2018 ◽  
Author(s):  
Xin Shi ◽  
Qiao Li ◽  
Rui Gao ◽  
Wei Si ◽  
Shao-Chuang Liu ◽  
...  
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Conformational Changes ◽  
Ionic Current ◽  
Observation Time ◽  
Random Coil ◽  
Dna Complexes ◽  
Dna Complex ◽  
Identification And Characterization

<a></a><a>Docking of a protein-DNA complex onto a nanopore can provide ample observation time for a detailed inspection of the complex, enabling collection of biophysical data for detection, identification, and characterization of the biomolecules. While docking of a protein-DNA complex onto a biological nanopore has enabled analytic applications of nanopores including DNA sequencing, the application of the same principle to solid-state nanopores is tempered by poor understanding of the docking process. Here, we elucidate the behaviour of individual protein-DNA complexes docked onto a solid-state nanopore by monitoring the nanopore ionic current. </a><a>Repeat docking of monovalent streptavidin-DNA complexes is found to produce ionic current blockades that fluctuate between discrete levels within the same current blockade. </a>We elucidate the roles of the protein plug and the DNA tether in the docking process, finding the docking configurations to determine the multitude of the current blockade levels whereas the frequency of the current level switching to be determined by the interactions between the molecules and the solid-state membrane. Finally, we prove the feasibility of using the nanopore docking principle for single molecule sensing using solid-state nanopores by detecting conformational changes of a tethered DNA molecule from a random coil to an i-motif states.

scholarly journals Fast Fabrication of Solid-State Nanopores for DNA Molecule Analysis

Nanomaterials ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2450
Author(s):  
Yin Zhang ◽  
Dexian Ma ◽  
Zengdao Gu ◽  
Lijian Zhan ◽  
Jingjie Sha
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Dna Analysis ◽  
Dielectric Breakdown ◽  
Ionic Current ◽  
Air Plasma ◽  
Dna Translocation ◽  
Accessible Method ◽  
Translocation Experiments ◽  
Single Molecule Analysis

Solid-state nanopores have been developed as a prominent tool for single molecule analysis in versatile applications. Although controlled dielectric breakdown (CDB) is the most accessible method for a single nanopore fabrication, it is still necessary to improve the fabrication efficiency and avoid the generation of multiple nanopores. In this work, we treated the SiNx membranes in the air–plasma before the CDB process, which shortened the time-to-pore-formation by orders of magnitude. λ-DNA translocation experiments validated the functionality of the pore and substantiated the presence of only a single pore on the membrane. Our fabricated pore could also be successfully used to detect short single-stranded DNA (ssDNA) fragments. Using to ionic current signals, ssDNA fragments with different lengths could be clearly distinguished. These results will provide a valuable reference for the nanopore fabrication and DNA analysis.

Single Molecule Solid State Light Emitting Electrochemical Cells with Lifetimes Superior to 3000 Hours

2008 ◽  
Author(s):  
Henk Bolink ◽  
Rubén D. Costa ◽  
Enrique Orti ◽  
Michele Sessolo ◽  
Stefan Graber ◽  
...  
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Electrochemical Cells ◽  
Light Emitting

Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule Interface

2019 ◽  
Author(s):  
Jiajun Wang ◽  
Meng-Yin Li ◽  
Jie Yang ◽  
Ya-Qian Wang ◽  
Xue-Yuan Wu ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Molecule ◽  
Genetic Diseases ◽  
High Sensitivity ◽  
Dna Lesions ◽  
Lesion Detection ◽  
The Novel ◽  
Structural Variations ◽  
Dna Lesion ◽  
Base Lesion

DNA lesion such as metholcytosine(<sup>m</sup>C), 8-OXO-guanine(<sup>O</sup>G), inosine(I) <i>etc</i> could cause the genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remain challenge due to the massive varieties and less distinguishable readouts for minor structural variations. Moreover, standard amplification and labelling hardly works in DNA lesions detection. Herein, we designed a single molecule interface from the mutant K238Q Aerolysin, whose confined sensing region shows the high compatible to capture and then directly convert each base lesion into distinguishable current readouts. Compared with previous single molecule sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced by 2-order. The novel K238Q could direct discriminate at least 3 types (<sup>m</sup>C, <sup>O</sup>G, I) lesions without lableing and quantify modification sites under mixed hetero-composition condition of oligonucleotide. Such nanopore could be further applied to diagnose genetic diseases at high sensitivity.

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