DNA sequencing by nanopores: advances and challenges

Agah, Shaghayegh; Zheng, Ming; Pasquali, Matteo; Kolomeisky, Anatoly B.

doi:10.1088/0022-3727/49/41/413001

Cited by 44 publications

(34 citation statements)

References 107 publications

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“…Inspired by small, poreforming biological channels on one hand and their micrometer-scale analogue, the famous Coulter counter on the other, the field was initially strongly motivated by developing a fast and label-free DNA sequencing technology. 1,2,3,4 After approximately 30 years from its inception, this impressive feat has now been achieved, based on carefully designed biological pores (-hemolysin). However, the field has a lot more to offer and new platforms, as well as new applications are now coming into focus.…”

Section: Introductionmentioning

confidence: 99%

Progress in single-biomolecule analysis with solid-state nanopores

Albrecht

2017

Current Opinion in Electrochemistry

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Solid-state nanopores and nanopipettes are a new class of stochastic, single-molecule sensors that have now reached a certain degree of maturity. While DNA sequencing has been a major driving force in the field of nanopore sensing since the early 1990s, a feat that has now been achieved with modified biological pores, new potential applications emerge, in particular for solid-state devices. These capitalize on some of the advantages of solid-state pores over their biological counterparts as well as recent technological advances and progress in our fundamental understanding of the translocation process. Here, we will discuss and highlight some of these developments with particular focus on single-molecule analysis of and structures based on double-stranded DNA.

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Section: Introductionmentioning

confidence: 99%

Progress in single-biomolecule analysis with solid-state nanopores

Albrecht

2017

Current Opinion in Electrochemistry

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“…DNA knotting | pore translocation | molecular dynamics simulations H ow filamentous molecules behave when driven through a narrow pore is one of the classic, yet still open questions in polymer physics. The problem has important applications for single-molecule manipulation techniques, including the sequencing of single-stranded DNA filaments (1)(2)(3)(4)(5)(6)(7)(8), and is relevant for fundamental research as well, particularly for biological systems where the processing of DNA (9,10), RNA (11), and protein chains (12) often depends on their active translocation through narrow pores.…”

mentioning

confidence: 99%

Pore translocation of knotted DNA rings

Suma

Micheletti

2017

Proc. Natl. Acad. Sci. U.S.A.

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We use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp-long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers.

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“…In principle, the same current trace could also be used to detect the base sequence in a DNA or RNA molecule. [4][5][6] In practice, this has proved to be challenging for several reasons. pore geometry shown in Figure 1 could be useful for controlling the rate of polyelectrolyte translocation.…”

Section: Introductionmentioning

confidence: 99%

Polyelectrolyte Translocation through a Corrugated Nanopore

Nagarajan

Chen

2020

Macro Theory & Simulations

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The problem of slowing down the rate of DNA translocation through a nanopore so as to facilitate detection of the genetic information remains a major challenge. In this study, the effectiveness of employing corrugated nanopores to reduce the polymer translocation velocity is investigated using dissipative particle dynamics (DPD) simulations. The average translocation time, <τ>, increases with the pore length and extent of variation of the pore cross‐sectional area. A systematic comparison of <τ> between flat and corrugated nanopores with walls that are either neutral or attractive for the polymer is performed. The value of <τ> for a corrugated nanopore with an attractive wall is 158% greater than that for a flat pore with a neutral wall. The extent of increase in <τ> obtained by manipulating either the geometry of the pore or the nature of its interaction with the polymer alone is significantly smaller. This is because the combined effect of monomer‐pore interactions and the spatial variation of the electric field strength significantly slows down the entry and escape of the chain from the pore.

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DNA sequencing by nanopores: advances and challenges

Cited by 44 publications

References 107 publications

Progress in single-biomolecule analysis with solid-state nanopores

Progress in single-biomolecule analysis with solid-state nanopores

Pore translocation of knotted DNA rings

Polyelectrolyte Translocation through a Corrugated Nanopore

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