Enhanced nanochannel translocation and localization of genomic DNA molecules using three-dimensional nanofunnels

Zhou, Jinsheng; Wang, Yanqian; Ménard, Laurent; Panyukov, Sergey; Rubinstein, Michael; Ramsey, J. Michael

doi:10.1038/s41467-017-00951-4

Cited by 58 publications

(63 citation statements)

References 39 publications

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“…These experiments and simulations provided key insight into how polymer stretching is induced by single and multiple collisions and interaction events with stationary posts. The field of electrophoretic DNA manipulation continues to be vibrant today, as reviewed in an extensive article in 2010[26], with recent work showing that nanofabricated 'funnels' can be used to enhance the translocation and localization of genomic DNA in small devices[144].IV. DILUTE SOLUTION LINEAR POLYMER DYNAMICS: 2007 TO PRESENT Major advances in the field of single polymer dynamics have occurred over the last decade.…”

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confidence: 99%

Single polymer dynamics for molecular rheology

Schroeder

2018

Journal of Rheology

119

130

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Single polymer dynamics offers a powerful approach to study molecular-level interactions and dynamic microstructure in materials. Direct visualization of single chain dynamics has uncovered new ideas regarding the rheology and non-equilibrium dynamics of macromolecules, including the importance of molecular individualism, dynamic heterogeneity, and molecular sub-populations that govern macroscale behavior. In recent years, the field of single polymer dynamics has been extended to increasingly complex materials, including architecturally complex polymers such as combs, bottlebrushes, and ring polymers and entangled solutions of long chain polymers in flow. Single molecule visualization, complemented by modeling and simulation techniques such asBrownian dynamics and Monte Carlo methods, allow for unparalleled access to the molecular-scale dynamics of polymeric materials. In this review, recent progress in the field of single polymer dynamics is examined by highlighting major developments and new physics to emerge from these techniques. The molecular properties of DNA as a model polymer are examined, including the role of flexibility, excluded volume interactions, and hydrodynamic interactions in governing behavior. Recent developments in studying polymer dynamics in time-dependent flows, new chemistries and new molecular topologies, and the role of intermolecular interactions in concentrated solutions are considered. Moreover, cutting-edge methods in simulation techniques are further reviewed as an ideal complementary method to single polymer experiments. Future work aimed at extending the field of single polymer dynamics to new materials promises to uncover original and unexpected information regarding the flow dynamics of polymeric systems.

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confidence: 99%

Single polymer dynamics for molecular rheology

Schroeder

2018

Journal of Rheology

119

130

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“…Noise was also accumulated along a conduit channel. Anyhow, number of theoretical studies of DNA sequencing in nanochannel model continued to study and demonstrated its potential toward DNA sequencing [75][76][77]. Nano funnel structure integrated with nanochannel was also proposed to facilitate the DNA translocation as it can suppress the electric field effect onto the DNA [77].…”

Section: Transverse Electronic Currentmentioning

confidence: 99%

Speculation of Nano-gap Sensor for DNA sequencing technology: A Review on Synthetic Nanopores

Pungetmongkol

2018

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Nano-gap sensor is the next generation of single molecule analysis that consumes less resources, costs, times and spaces. The ultimate goal of this technology is rendering the ability to determine any living genetic code in several seconds using this portable device. In principle, DNA decryption was determined by tracking electrical signal change when DNA is passed through either natural or synthetic nanometer size gap. This review focuses on the synthetic nanopore, which is more robust, reliable and manageable with ease. Biological nanopore has been researched in parallel; however, the device reproducibility is a controversial issue. The history and development toward the future of this prospect technology will be elaborated attentively. The main limitation of nanopore sensor device is the controlling of DNA translocation dynamic through tiny pore. Many attempts had been tried and the synopsis will be contemplated in the review. Nonetheless, the present results of DNA sequencing have not been satisfied, the development of nanogap sensor is promising for genomic sequencing and molecular biology.

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“…Nanofluidics is a branch of fluid mechanics that deals with fluid flow and transport phenomena through nanoscale geometries and has lots of applications in medicine, biology, genetics, material science, and energy conversion technologies . Electrokinetic phenomena are wildly used in nanofluidic devices to perform many tasks such as generating flow field in nanochannels , transport of ions , and manipulating DNAs in the nanoconfinements . The electrokinetics will also affect cell membrane transport through natural or artificial nanopores created on cell membranes .…”

Section: Introductionmentioning

confidence: 99%

An improved hybrid continuum‐atomistic four‐way coupled model for electrokinetics in nanofluidics

2019

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In this study, an efficient hybrid continuum‐atomistic method is proposed to study electrokinetic transport of aqueous solutions in nanofluidics. The aqueous phase is considered as a continuous phase containing immersed ion particles. The behavior of the system is then simulated through utilization of an improved hybrid continuum‐atomistic four‐way coupled approach, including the MultiPhase Particle‐In‐Cell method for the short‐ranged interaction between the ion particles, the Brownian force for the collision between the aqueous phase molecules and the ion particles, and a wall force accounting for the short‐ranged interaction of ions and walls. The validation of the proposed model with the results of Molecular Dynamics simulations suggests that this model can be a promising approach for studying the electrokinetic phenomena in more complicated geometries where the Molecular Dynamics approach is computationally prohibitive. Finally, the effects of electrokinetic parameters, such as the height of the channel, the external electric field, and bulk ionic concentration, on the electroosmotic flow in a nanochannel are investigated and discussed.

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Enhanced nanochannel translocation and localization of genomic DNA molecules using three-dimensional nanofunnels

Cited by 58 publications

References 39 publications

Single polymer dynamics for molecular rheology

Single polymer dynamics for molecular rheology

Speculation of Nano-gap Sensor for DNA sequencing technology: A Review on Synthetic Nanopores

An improved hybrid continuum‐atomistic four‐way coupled model for electrokinetics in nanofluidics

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