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.

scholarly journals Nanopore device-based fingerprinting of RNA oligos and microRNAs enhanced with an Osmium tag

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Madiha Sultan ◽  
Anastassia Kanavarioti
Keyword(s):  
Solid State ◽  
Nucleotide Sequence ◽  
Nucleic Acids ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Selective Labeling ◽  
Base Calling ◽  
Alpha Hemolysin ◽  
Oxford Nanopore ◽  
Single Molecule Analysis

Abstract Protein and solid-state nanopores are used for DNA/RNA sequencing as well as for single molecule analysis. We proposed that selective labeling/tagging may improve base-to-base resolution of nucleic acids via nanopores. We have explored one specific tag, the Osmium tetroxide 2,2′-bipyridine (OsBp), which conjugates to pyrimidines and leaves purines intact. Earlier reports using OsBp-tagged oligodeoxyribonucleotides demonstrated proof-of-principle during unassisted voltage-driven translocation via either alpha-Hemolysin or a solid-state nanopore. Here we extend this work to RNA oligos and a third nanopore by employing the MinION, a commercially available device from Oxford Nanopore Technologies (ONT). Conductance measurements demonstrate that the MinION visibly discriminates oligoriboadenylates with sequence A15PyA15, where Py is an OsBp-tagged pyrimidine. Such resolution rivals traditional chromatography, suggesting that nanopore devices could be exploited for the characterization of RNA oligos and microRNAs enhanced by selective labeling. The data also reveal marked discrimination between a single pyrimidine and two consecutive pyrimidines in OsBp-tagged AnPyAn and AnPyPyAn. This observation leads to the conjecture that the MinION/OsBp platform senses a 2-nucleotide sequence, in contrast to the reported 5-nucleotide sequence with native nucleic acids. Such improvement in sensing, enabled by the presence of OsBp, may enhance base-calling accuracy in enzyme-assisted DNA/RNA sequencing.

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 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.

Nanopore Sensors for Ultra-Fast DNA Analysis

2006 ◽  
Author(s):  
Min Jun Kim ◽  
Meni Wanunu ◽  
Gautam Soni ◽  
Amit Meller
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Dna Analysis ◽  
Ionic Current ◽  
Dna Translocation ◽  
Silicon Nitride Membrane ◽  
Optical Readout ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Current Blockage

We have developed novel approaches for ultra-fast DNA analysis by measuring of an ionic current blockage and parallel optical readout of DNA translocation through single nanopores and nanopore arrays. Parallelism is achieved by the fabrication of high density solid-state arrays of single nanometer resolution pores and simultaneous optical readout of DNA translocation. Optical readout in arrays circumvents the direct electrical addressing of each pore. We will present new nanofabrication techniques to create nanoscale pores in 50 nm thick silicon nitride membrane using transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) and discuss our progress towards ultra-fast DNA sequencing.

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.

scholarly journals Slowing down DNA translocation through solid-state nanopores by edge-field leakage

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ceming Wang ◽  
Sebastian Sensale ◽  
Zehao Pan ◽  
Satyajyoti Senapati ◽  
Hsueh-Chia Chang
Keyword(s):  
Solid State ◽  
Electric Field ◽  
Single Molecule ◽  
Exponential Dependence ◽  
Dna Translocation ◽  
Slowing Down ◽  
Edge Field ◽  
Surface Field ◽  
Voltage Dependent ◽  
Molecular Rigidity

AbstractSolid-state nanopores allow high-throughput single-molecule detection but identifying and even registering all translocating small molecules remain key challenges due to their high translocation speeds. We show here the same electric field that drives the molecules into the pore can be redirected to selectively pin and delay their transport. A thin high-permittivity dielectric coating on bullet-shaped polymer nanopores permits electric field leakage at the pore tip to produce a voltage-dependent surface field on the entry side that can reversibly edge-pin molecules. This mechanism renders molecular entry an activated process with sensitive exponential dependence on the bias voltage and molecular rigidity. This sensitivity allows us to selectively prolong the translocation time of short single-stranded DNA molecules by up to 5 orders of magnitude, to as long as minutes, allowing discrimination against their double-stranded duplexes with 97% confidence.

Single-Molecule Analysis with Solid-State Nanopores

2019 ◽  
Vol 12 (1) ◽  
pp. 371-387 ◽  
Author(s):  
Tim Albrecht
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Analytical Technique ◽  
Single Molecule Biophysics ◽  
Biomedical Sensing ◽  
Analytical Applications ◽  
Recent Developments ◽  
Single Molecule Analysis

Solid-state nanopores and nanopipettes are an exciting class of single-molecule sensors that has grown enormously over the last two decades. They offer a platform for testing fundamental concepts of stochasticity and transport at the nanoscale, for studying single-molecule biophysics and, increasingly, also for new analytical applications and in biomedical sensing. This review covers some fundamental aspects underpinning sensor operation and transport and, at the same time, it aims to put these into context as an analytical technique. It highlights new and recent developments and discusses some of the challenges lying ahead.

Single-molecule DNA Translocation Through Si3N4- and Graphene Solid-state Nanopores

2012 ◽  
pp. 99-105
Author(s):  
A. Spiering ◽  
S. Knust ◽  
S. Getfert ◽  
A. Beyer ◽  
K. Rott ◽  
...  
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Dna Translocation
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