Detection of DNA in a Nanopore Fabricated From Glass Tube

2013 ◽  
Author(s):  
Jingjie Sha ◽  
Yunfei Chen
Keyword(s):  
Single Molecule ◽  
Glass Tube ◽  
Electrical Current ◽  
Ionic Currents ◽  
Dna Molecules ◽  
Dna Translocation ◽  
Glass Capillary ◽  
Minimum Diameter ◽  
Osmotic Flow ◽  
Electro Osmotic Flow

Nanopores are increasingly utilized as tools for single molecule detection in biotechnology. Here, we report an improved fabrication process to make solid-state nanopores from glass tubes with the help of paraffin. Based on the physical footprint of the phase change of the paraffin, nanocavity is formed in the broken terminal after thermally compressing and pulling the glass capillary. Nanopores with the minimum diameter of 20 nm are fabricated. The key step is to control the thickness of paraffin layer attached in the inner wall, which could affect the diameter of the nanopore. We investigate 48Kb λ-DNA molecules translocate through the fabricated glass nanopore. Because DNA molecules with the negative charges could be driven by the electrical force to pass through the nanopore and could physically block the pore to produce measurable changes in ionic currents. A transient electrical current changing is used to detect the DNA molecules in the solution. In the experiments, many events of DNA translocation were observed under the positive potential. We demonstrate that DNA molecules could be detected by the nanopore fabricated from glass tube. However, we also find the events of DNA translocation under the negative potential, which is because of the electro-osmotic flow (EOF) effects. It is found that the electro-osmotic flow inside the nanopore plays an important role in the DNA translocation process, and thus depends on the size of the pore. We shows that the effective driving force on DNA in a nanopore is the co-effects of the force of the electric field and the drag force of the electro-osmotic flow.

scholarly journals Single bacterial resolvases first exploit, then constrain intrinsic dynamics of the Holliday junction to direct recombination

2021 ◽  
Author(s):  
Sujay Ray ◽  
Nibedita Pal ◽  
Nils G Walter
Keyword(s):  
Cluster Analysis ◽  
Homologous Recombination ◽  
Single Molecule ◽  
Holliday Junction ◽  
Energetic Cost ◽  
Genomic Integrity ◽  
Dna Molecules ◽  
Single Molecule Fluorescence ◽  
And Cluster Analysis ◽  
Fluorescence Observation

Abstract Homologous recombination forms and resolves an entangled DNA Holliday Junction (HJ) crucial for achieving genetic reshuffling and genome repair. To maintain genomic integrity, specialized resolvase enzymes cleave the entangled DNA into two discrete DNA molecules. However, it is unclear how two similar stacking isomers are distinguished, and how a cognate sequence is found and recognized to achieve accurate recombination. We here use single-molecule fluorescence observation and cluster analysis to examine how prototypic bacterial resolvase RuvC singles out two of the four HJ strands and achieves sequence-specific cleavage. We find that RuvC first exploits, then constrains the dynamics of intrinsic HJ isomer exchange at a sampled branch position to direct cleavage toward the catalytically competent HJ conformation and sequence, thus controlling recombination output at minimal energetic cost. Our model of rapid DNA scanning followed by ‘snap-locking’ of a cognate sequence is strikingly consistent with the conformational proofreading of other DNA-modifying enzymes.

scholarly journals Towards bio-inspired artificial muscle: a mechanism based on electro-osmotic flow simulated using dissipative particle dynamics

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ramin Zakeri
Keyword(s):  
Zeta Potential ◽  
Electric Field ◽  
Dissipative Particle Dynamics ◽  
Artificial Muscle ◽  
Particle Dynamics ◽  
Polymer Membrane ◽  
Channel Width ◽  
Micro Channel ◽  
Osmotic Flow ◽  
Electro Osmotic Flow

AbstractOne of the unresolved issues in physiology is how exactly myosin moves in a filament as the smallest responsible organ for contracting of a natural muscle. In this research, inspired by nature, a model is presented consisting of DPD (dissipative particle dynamics) particles driven by electro-osmotic flow (EOF) in micro channel that a thin movable impermeable polymer membrane has been attached across channel width, thus momentum of fluid can directly transfer to myosin stem. At the first, by validation of electro-osmotic flow in micro channel in different conditions with accuracy of less than 10 percentage error compared to analytical results, the DPD results have been developed to displacement of an impermeable polymer membrane in EOF. It has been shown that by the presence of electric field of 250 V/m and Zeta potential − 25 mV and the dimensionless ratio of the channel width to the thickness of the electric double layer or kH = 8, about 15% displacement in 8 s time will be obtained compared to channel width. The influential parameters on the displacement of the polymer membrane from DPD particles in EOF such as changes in electric field, ion concentration, zeta potential effect, polymer material and the amount of membrane elasticity have been investigated which in each cases, the radius of gyration and auto correlation velocity of different polymer membrane cases have been compared together. This simulation method in addition of probably helping understand natural myosin displacement mechanism, can be extended to design the contraction of an artificial muscle tissue close to nature.

Modeling electro-osmotic flow and thermal transport of Caputo fractional Burgers fluid through a micro-channel

2021 ◽  
pp. 095440892110259
Author(s):  
Mohammed Abdulhameed ◽  
Garba Tahiru Adamu ◽  
Gulibur Yakubu Dauda
Keyword(s):  
Electric Field ◽  
Laplace Transform ◽  
Inverse Laplace Transform ◽  
Micro Channel ◽  
Osmotic Flow ◽  
Sine Transform ◽  
Fourier Sine ◽  
Fourier Sine Transform ◽  
Burgers Fluid ◽  
Electro Osmotic Flow

In this paper, we construct transient electro-osmotic flow of Burgers’ fluid with Caputo fractional derivative in a micro-channel, where the Poisson–Boltzmann equation described the potential electric field applied along the length of the microchannel. The analytical solution for the component of the velocity profile was obtained, first by applying the Laplace transform combined with the classical method of partial differential equations and, second by applying Laplace transform combined with the finite Fourier sine transform. The exact solution for the component of the temperature was obtained by applying Laplace transform and finite Fourier sine transform. Further, due to the complexity of the derived models of the governing equations for both velocity and temperature, the inverse Laplace transform was obtained with the aid of numerical inversion formula based on Stehfest's algorithms with the help of MATHCAD software. The graphical representations showing the effects of the time, retardation time, electro-kinetic width, and fractional parameters on the velocity of the fluid flow and the effects of time and fractional parameters on the temperature distribution in the micro-channel were presented and analyzed. The results show that the applied electric field, electro-osmotic force, electro-kinetic width, and relaxation time play a vital role on the velocity distribution in the micro-channel. The fractional parameters can be used to regulate both the velocity and temperature in the micro-channel. The study could be used in the design of various biomedical lab-on-chip devices, which could be useful for biomedical diagnosis and analysis.

Concentration Gradient Effect on the Capturing Ratio of Nanopore for DNA

2015 ◽  
Vol 656-657 ◽  
pp. 554-560
Author(s):  
Jing Jie Sha ◽  
Wei Si ◽  
Yin Zhang ◽  
Yun Fei Chen
Keyword(s):  
Concentration Gradient ◽  
Electrical Potential ◽  
Ionic Currents ◽  
Fixed Time ◽  
Controlled Delivery ◽  
Glass Capillary ◽  
Ion Conductance ◽  
Duration Time ◽  
In Trans ◽  
Pass Through

As the single molecules detection tool, nanopore is applied in more and more fields, such as medicine controlled delivery, ion conductance microscopes, nanosensors and DNA sequencing. When molecules pass through a nanopore, they will physically block the pore and produce measurable changes in ionic currents under an external electrical potential. Based on analyzing the resultant electrical signals, it is possible to detect various bio-molecules.Generally, the capturing ratio of nanopre for molecules is dependent on the intensity of electrical potential, to which the duration time of event is inversely proportional. It is difficult to analyze the too short duration time. Therefore, we investigate the study on concentration gradient of ionic solution effect on the capturing ratio of nanopore for DNA, which is in order to get the higher capturing ratio with the invariant duration time.In the experiments, we add different concentration solution in trans and cis parts of naopore separately to form the concentration gradient. We use three different types nanopore (α-hemolysin nanopore, Si3N4 membrane nanopore, glass capillary nanopore) to compare and get the similar results. The events of DNA translocating through nanopore are observed more compressed during the fixed time under the higher concentration gradient and there is no change to the duration time of DNA passing through the nanopore. It is demonstrated that concentration gradient could increase the capturing ratio of nanopore for DNA.

scholarly journals AC-driven electro-osmotic flow in charged nanopores

2018 ◽  
Vol 123 (5) ◽  
pp. 58006 ◽  
Author(s):  
J. Catalano ◽  
P. M. Biesheuvel
Keyword(s):  
Osmotic Flow ◽  
Electro Osmotic Flow
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