Significant alteration in DNA electrophoretic translocation velocity through soft nanopores by ion partitioning

Ganjizade, Ardalan; Ashrafizadeh, Seyed Nezameddin; Sadeghi, Arman

doi:10.1016/j.aca.2019.06.041

Cited by 16 publications

(15 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…29 Furthermore, it has been theoretically postulated that grafting polyelectrolyte chains on the inner walls of the pore can reduce translocation speed due to increased friction in combination with hydrodynamic effects and electrolyte ion partitioning. 31 In contrast, in the present experimental study, the source of reduction in translocation speed is created in the donor compartment of the device. Furthermore, depositing new layers on the surface of the membrane that has a nanopore is a much easier process than modifications of the inner surface of a nanopore.…”

Section: Introductionmentioning

confidence: 80%

“…The second obstacle is the temporal resolution because the passage speed of DNA in solid-state nanopores is very fast. , The speed of single-stranded DNA is greater than 1 nt/μs, and that of the double-stranded DNA is greater than 10 bp/μs. , Coupled with the bandwidth limitation of 250–500 kHz in various DNA translocation experiments, it is thus difficult to identify and distinguish adjacent bases. Over the past decade, various methods have been formulated to slow down the translocation rate of DNA in nanopores, such as increasing the viscosity of buffer solution, , introducing salt concentration gradient between the two sides of the nanopore, adding reverse pressure as resistance, modifying the inner surface of the nanopore, − manipulating the DNA, depositing a new layer on the surface of the nanopore, ,,− and pH variations. ,, Our method presented here to slow down the translocation of DNA in solid-state nanopores is distinctly different from these previous approaches. In our study, the source of the observed significant reduction of DNA translocation speed is created in the donor compartment by enabling multiple entropic traps that act on each DNA molecule.…”

Section: Introductionmentioning

confidence: 98%

“…Modification of surface charge density on the inner walls of the nanopore can also reduce the translocation speed due to electrostatic complexation between the DNA and the pore . Furthermore, it has been theoretically postulated that grafting polyelectrolyte chains on the inner walls of the pore can reduce translocation speed due to increased friction in combination with hydrodynamic effects and electrolyte ion partitioning . In contrast, in the present experimental study, the source of reduction in translocation speed is created in the donor compartment of the device.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Substantial Slowing of Electrophoretic Translocation of DNA through a Nanopore Using Coherent Multiple Entropic Traps

Chen

Muthukumar

2023

ACS Nano

View full text Add to dashboard Cite

One of the major challenges in the technology of sequencing DNA using single-molecule electrophoresis through a nanopore is to control the translocation of the macromolecule across the pore in order to allow sufficient time for accurate sequence reading at limited recording bandwidths. If the translocation speed is too fast, the signatures of the bases passing through the sensing region of the nanopore overlap in time, presenting difficulties in accurately identifying the bases in a sequential manner. Even though several strategies, such as enzyme ratcheting, have been implemented to reduce the translocation speed, the challenge to achieve a substantial reduction in the translocation speed continues to be of paramount significance. Toward achieving this goal, we have fabricated a nonenzymatic hybrid device that can reduce the translocation speed of long DNAs by more than 2 orders of magnitude, in comparison with the current status of the art. This device is made of a tetra-PEG hydrogel that is chemically anchored to the donor side of a solid-state nanopore. The idea behind this device is based on the recent discovery of the topologically frustrated dynamical state of confined polymers, whereby the front hydrogel matter of the hybrid device provides multiple entropic traps for a single DNA molecule holding it back against the electrophoretic driving force that pulls the DNA through the solid-state nanopore portion of the device. As a demonstration of slowing DNA translocation by a factor of about 500, we find the average translocation time realized in the present hybrid device for 3 kbp DNA as 23.4 ms, whereas the corresponding time for the bare solid-state nanopore under otherwise identical conditions is 0.047 ms. Our measurements on 1 kbp DNA and λ-DNA show that such a slowing down of DNA translocation with our hybrid device is general. An additional feature of our hybrid device is its incorporation of all features of the conventional gel electrophoresis to separate different DNA sizes in a clump of DNAs and to streamline them in an orderly and slow manner into the nanopore. Our results suggest the high potential of our hydrogel-nanopore hybrid device in further advancing the single-molecule electrophoresis technology to accurately sequence very large biological polymers.

show abstract

Section: Introductionmentioning

confidence: 80%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Substantial Slowing of Electrophoretic Translocation of DNA through a Nanopore Using Coherent Multiple Entropic Traps

Chen

Muthukumar

2023

ACS Nano

View full text Add to dashboard Cite

show abstract

“…In a review study, Heller, et al Examined the principles and mechanisms of DNA separation by capillary electrophoresis [132]. Ganjizade, et al Modeled the DNA sequencing in polyelectrolytecoated nanopores [133]. Figure 11 shows a schematic of the capillary electrophoresis process for the separation and arrangement of molecules [134].…”

Section: Another Type Of Electrophoresis Is Capillary Electrophoresis...mentioning

confidence: 99%

Transition of chemical engineering from macro to micro/nano scales

Ashrafizadeh¹,

Seifollahi²

2022

Front Nanosci Nanotech

Self Cite

View full text Add to dashboard Cite

show abstract

“…Since each nucleotide of the DNA carries a specific charge, the passage of the DNA through nanopores within a threshold speed leads to a spectrum of ionic current that can be used for sequencing. , However, because of the underlying physical complexity stemming from the non-trivial electro-fluidic coupling, there often appears to be the possibility of an undesirable over-speeding of the DNA translocation, leading to disparities between the conceptual idealities and the practically obtained signals on the sequencing data. This may be attributed to the fact that the DNA may not reside long enough within the nanopore in practice to allow for recording the ionic current spectra with a high resolution . Such deficit establishes an imperative need of a reasonably accurate quantitative estimation of the DNA translocation speed a-priori, enabling the setting up of judicious operating parameters for achieving the desired sequencing task.…”

Section: Introductionmentioning

confidence: 99%

Slip-Coupled Electroosmosis and Electrophoresis Dictate DNA Translocation Speed in Solid-State Nanopores

Ahmadi,

Sadeghi,

Chakraborty

2023

Langmuir

Self Cite

View full text Add to dashboard Cite

Controlling the DNA translocation speed is critical in nanopore sequencing, but remains rather challenging in practice, as attributable to a complex coupling between nanoscale fluidics and electrically mediated migration of DNA in a dynamically evolving manner. One important factor influencing the translocation speed is the DNA−liquid slippage stemming from the hydrophobic nature of the oligonucleotide, an aspect that has been widely ignored in the reported literature. In an effort to circumvent this conceptual deficit, here we first develop an analytical model to bring out the slip-mediated coupling between the electroosmosis and DNA−electrophoresis in a solid-state nanopore at low surface charge limits, ignoring the end effects. Subsequently, we compare these results with the numerical simulation data on electrokinetically modulated DNA translocation in such a nanopore, albeit of finite length with due accommodation of the end effects, connecting two end reservoirs by deploying a fully coupled Poisson−Nernst−Plank−Stokes flow model. Both the numerical and analytical results indicate that the DNA translocation speed is a linearly increasing function of the slip length, with more than fourfold increase being observed for a slip length as minimal as 0.5 nm as compared to the no-slip scenario. Considering specific strategies on demand for arresting high translocation speeds for accurate DNA sequencing, the above results establish a theoretical proposition for the same, premised on an analytical expression of the DNA-hydrophobicity modulated enhancement in the translocation speed for designing a nanopore-based sequencing platform�a paradigm that remained to be underemphasized thus far.

show abstract

Significant alteration in DNA electrophoretic translocation velocity through soft nanopores by ion partitioning

Cited by 16 publications

References 26 publications

Substantial Slowing of Electrophoretic Translocation of DNA through a Nanopore Using Coherent Multiple Entropic Traps

Substantial Slowing of Electrophoretic Translocation of DNA through a Nanopore Using Coherent Multiple Entropic Traps

Transition of chemical engineering from macro to micro/nano scales

Slip-Coupled Electroosmosis and Electrophoresis Dictate DNA Translocation Speed in Solid-State Nanopores

Contact Info

Product

Resources

About