Passive and Electrically Actuated Solid-State Nanopores for Sensing and Manipulating DNA

Jiang, Zhijun; Mihovilovic, Mirna; Teich, Erin G.; Stein, Derek

doi:10.1007/978-1-61779-773-6_14

Cited by 4 publications

(3 citation statements)

References 20 publications

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“…Silicon chips with freestanding membranes suspended over 50-mm-wide square openings were microfabricated by standard procedures described in detail elsewhere 49 . We fabricated nanopore cage structures following the procedure described in the nanopore cage structure and experiments subsection of the Results.…”

Section: Methodsmentioning

confidence: 99%

Entropic cages for trapping DNA near a nanopore

2015

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Nanopores can probe the structure of biopolymers in solution; however, diffusion makes it difficult to study the same molecule for extended periods. Here we report devices that entropically trap single DNA molecules in a 6.2-femtolitre cage near a solid-state nanopore. We electrophoretically inject DNA molecules into the cage through the nanopore, pause for preset times and then drive the DNA back out through the nanopore. The saturating recapture time and high recapture probability after long pauses, their agreement with a convection-diffusion model and the observation of trapped DNA under fluorescence microscopy all confirm that the cage stably traps DNA. Meanwhile, the cages have 200 nm openings that make them permeable to small molecules, like the restriction endonuclease we use to sequence-specifically cut trapped DNA into fragments whose number and sizes are analysed upon exiting through the nanopore. Entropic cages thus serve as reactors for chemically modifying single DNA molecules.

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Section: Methodsmentioning

confidence: 99%

Entropic cages for trapping DNA near a nanopore

2015

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“…The 8 nm diameter solid-state nanopore we used (Fig. 1(a), detail) was fabricated in a 20 nm-thin low-stress silicon nitride membrane following procedures described elsewhere [9]. The nanopore bridged two fluid reservoirs containing degassed aqueous 1 M KCl, 10 mM Tris-HCl, 1 mM EDTA buffer (pH 7.7).…”

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confidence: 99%

Statistics of DNA Capture by a Solid-State Nanopore

2013

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A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm wide nanopore reveals a strong bias favoring the capture of molecules near their ends. A theoretical model shows that bias to be a consequence of configurational entropy, rather than a search by the polymer for an energetically favorable configuration. We also quantified the fluctuations and length-dependence of the speed of simultaneously translocating polymer segments from our study of folded DNA configurations.

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“…We also used the TEM to measure the diameter of the nanopore. The detailed fabrication procedure can be found in ref . Before use, we cleaned each nanopore by boiling in a piranha solution for 15 min.…”

Section: Methodsmentioning

confidence: 99%

Nanopore Measurements of Filamentous Viruses Reveal a Sub-nanometer-Scale Stagnant Fluid Layer

2017

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We report measurements and analyses of nanopore translocations by fd and M13, two related strains of filamentous virus that are identical except for their charge densities. The standard continuum theory of electrokinetics greatly overestimates the translocation speed and the conductance associated with counterions for both viruses. Furthermore, fd and M13 behave differently from one another, even translocating in opposite directions under certain conditions. This cannot be explained by Manning-condensed counterions or a number of other proposed models. Instead, we argue that these anomalous findings are consequences of the breakdown of the validity of continuum hydrodynamics at the scale of a few molecular layers. Next to a polyelectrolyte, there exists an extra-viscous, sub-nanometer-thin boundary layer that has a giant influence on the transport characteristics. We show that a stagnant boundary layer captures the essential hydrodynamics and extends the validity of the electrokinetic theory beyond the continuum limit. A stagnant layer with a thickness of about half a nanometer consistently improves predictions of the ionic current change induced by virus translocations and of the translocation velocity for both fd and M13 over a wide range of nanopore dimensions and salt concentrations.

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Passive and Electrically Actuated Solid-State Nanopores for Sensing and Manipulating DNA

Cited by 4 publications

References 20 publications

Entropic cages for trapping DNA near a nanopore

Entropic cages for trapping DNA near a nanopore

Statistics of DNA Capture by a Solid-State Nanopore

Nanopore Measurements of Filamentous Viruses Reveal a Sub-nanometer-Scale Stagnant Fluid Layer

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