pH Tuning of DNA Translocation Time through Organically Functionalized Nanopores

Anderson, Brett N.; Muthukumar, Murugappan; Meller, A.

doi:10.1021/nn3051677

Cited by 122 publications

(153 citation statements)

References 21 publications

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“…For example, modifications to solid-state nanopores have included adjusting the nanopore diameter to increase friction [58][59][60], modulating the nanopore surface charge with laser light [61], functionalizing the nanopore with hydrogen-bonding molecules [62] or coating it with a lipid bilayer [63], and altering the properties of a pH-responsive organic nanopore coating [64]. Additional methods have been proposed, including local heating of a gold layer surrounding the nanopore to stretch the DNA [65,66] and ratcheting of nucleotide strands through introduction of a third electrode [67,68].…”

Section: The Nanoporementioning

confidence: 99%

Interfacing solid‐state nanopores with gel media to slow DNA translocations

et al. 2015

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We demonstrate the ability to slow DNA translocations through solid‐state nanopores by interfacing the trans side of the membrane with gel media. In this work, we focus on two reptation regimes: when the DNA molecule is flexible on the length scale of a gel pore, and when the DNA behaves as persistent segments in tight gel pores. The first regime is investigated using agarose gels, which produce a very wide distribution of translocation times for 5 kbp dsDNA fragments, spanning over three orders of magnitude. The second regime is attained with polyacrylamide gels, which can maintain a tight spread and produce a shift in the distribution of the translocation times by an order of magnitude for 100 bp dsDNA fragments, if intermolecular crowding on the trans side is avoided. While previous approaches have proven successful at slowing DNA passage, they have generally been detrimental to the S/N, capture rate, or experimental simplicity. These results establish that by controlling the regime of DNA movement exiting a nanopore interfaced with a gel medium, it is possible to address the issue of rapid biomolecule translocations through nanopores—presently one of the largest hurdles facing nanopore‐based analysis—without affecting the signal quality or capture efficiency.

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Section: The Nanoporementioning

confidence: 99%

Interfacing solid‐state nanopores with gel media to slow DNA translocations

et al. 2015

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“…26 Furthermore, it is well known in the literature that the characteristics of polymer translocation through nanopores are dramatically influenced by pore-polymer interactions. 12,[27][28][29][30][31][32][33][34][35] Using simulations in two dimensions, Ikonen et al have shown that the attractive pore-polymer interactions significantly induce resonant activation. 36 Stochastic resonance has been realized 37,38 in several practical situations such as electronic circuits, bistable ring-lasers, sensory processes of crayfish, and voltage-dependent ion channels.…”

Section: Introductionmentioning

confidence: 99%

Stochastic resonance during a polymer translocation process

Mondal

Muthukumar

2016

The Journal of Chemical Physics

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We have studied the occurrence of stochastic resonance when a flexible polymer chain undergoes a single-file translocation through a nano-pore separating two spherical cavities, under a time-periodic external driving force. The translocation of the chain is controlled by a free energy barrier determined by chain length, pore length, pore-polymer interaction, and confinement inside the donor and receiver cavities. The external driving force is characterized by a frequency and amplitude. By combining the Fokker-Planck formalism for polymer translocation and a two-state model for stochastic resonance, we have derived analytical formulas for criteria for emergence of stochastic resonance during polymer translocation. We show that no stochastic resonance is possible if the free energy barrier for polymer translocation is purely entropic in nature. The polymer chain exhibits stochastic resonance only in the presence of an energy threshold in terms of polymer-pore interactions. Once stochastic resonance is feasible, the chain entropy controls the optimal synchronization conditions significantly. C 2016 AIP Publishing LLC. [http://dx

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“…Proteins such as RecA from Escherichia coli form filaments around the DNA that slows DNA transport and prevents its folding (26,34,35), although this approach inherently masks chemical information contained within the DNA, such as the presence of DNA chemical modifications (7,36) or small bound drug/reporter molecules (37)(38)(39)(40). Explorations of the effects of parameters such as the electrolyte viscosity (41,42), salt type (43,44), membrane material (45,46), applied pressure (47,48), and chemical composition inside (49)(50)(51)(52) and outside (53) the pore have yielded only moderate DNA retardation factors.…”

Section: Introductionmentioning

confidence: 99%

Smooth DNA Transport through a Narrowed Pore Geometry

Carson

Wilson

Aksimentiev

et al. 2014

Biophysical Journal

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Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35-20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics.

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pH Tuning of DNA Translocation Time through Organically Functionalized Nanopores

Cited by 122 publications

References 21 publications

Interfacing solid‐state nanopores with gel media to slow DNA translocations

Interfacing solid‐state nanopores with gel media to slow DNA translocations

Stochastic resonance during a polymer translocation process

Smooth DNA Transport through a Narrowed Pore Geometry

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