Dynamic translocation of ligand-complexed DNA through solid-state nanopores with optical tweezers

Sischka, Andy; Spiering, Andre; Khaksar, Maryam; Laxa, Miriam; König, Janine; Dietz, Karl‐Josef; Anselmetti, Dario

doi:10.1088/0953-8984/22/45/454121

Cited by 42 publications

(49 citation statements)

References 29 publications

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“…The somewhat counterintuitive result is that the larger the nanopore the smaller the electrophoretic force becomes. The optical tweezersnanopore combination was demonstrated by several other laboratories [87][88][89], extended to DNA-protein complexes [90] and single RNA molecules [91]. Recent results combining nanocapillaries with optical tweezers [26,27] extend the range of possible applications and will facilitate incorporation of other optical techniques, such as single molecule fluorescence detection.…”

Section: Mechanical Controlmentioning

confidence: 96%

Controlling molecular transport through nanopores

Keyser

2011

J. R. Soc. Interface.

173

191

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Nanopores are emerging as powerful tools for the detection and identification of macromolecules in aqueous solution. In this review, we discuss the recent development of active and passive controls over molecular transport through nanopores with emphasis on biosensing applications. We give an overview of the solutions developed to enhance the sensitivity and specificity of the resistive-pulse technique based on biological and solid-state nanopores.

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Section: Mechanical Controlmentioning

confidence: 96%

Controlling molecular transport through nanopores

Keyser

2011

J. R. Soc. Interface.

173

191

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“…A similar current drop was detected for a single DNA-2-CysPrx complex during its controlled translocation through nanopores in 20 mM KCl. 18 In our system, it is possible that the EOF contributes to the change of the …”

Section: Nano Lettersmentioning

confidence: 99%

“…The electrophoretic force acting on RecA-coated DNA inside nanocapillaries was smaller than on the bare DNA and differed from the results previously obtained in nanopores. 15,18,19 We proposed an explanation of these results based on the EOF-induced drag force. We modified a stochastic model from ref 19 by adapting it to the specific geometry of nanocapillaries to obtain the effective charge of DNA−protein complexes.…”

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confidence: 99%

“…27−29 Later it was used to estimate the charge of RNA 30 and detect nucleoprotein filaments 15 and DNA-bound ligands. 18,19 Glass nanocapillaries are a cheap and easy-to-produce alternative to nanopores in membranes used for various application including detection of DNA, 31,32 proteins, 33,34 and DNA−protein complexes. 23 They can be shrunken under SEM to diameters below 10 nm, 35 providing better signal-to-noise ratio (SNR) in the current signal compared to nanopores in silicon nitride or 2D materials, like graphene.…”

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confidence: 99%

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Relevance of the Drag Force during Controlled Translocation of a DNA–Protein Complex through a Glass Nanocapillary

2015

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Combination of glass nanocapillaries with optical tweezers allowed us to detect DNA−protein complexes in physiological conditions. In this system, a protein bound to DNA is characterized by a simultaneous change of the force and ionic current signals from the level observed for the bare DNA. Controlled displacement of the protein away from the nanocapillary opening revealed decay in the values of the force and ionic current. Negatively charged proteins EcoRI, RecA, and RNA polymerase formed complexes with DNA that experienced electrophoretic force lower than the bare DNA inside nanocapillaries. Force profiles obtained for DNA-RecA in our system were different than those in the system with nanopores in membranes and optical tweezers. We suggest that such behavior is due to the dominant impact of the drag force comparing to the electrostatic force acting on a DNA−protein complex inside nanocapillaries. We explained our results using a stochastic model taking into account the conical shape of glass nanocapillaries.

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“…8 Biological applications of this method include calculation of the charge of single RNA molecules 9 and DNA-protein complexes 10 and the detection of single proteins bound to DNA. 11,12 To produce a classical solid-state nanopore, first a Si 3 N 4 or SiO 2 membrane is fabricated using lithography techniques. Next, a pore of desired diameter is drilled by transmission electron microscopy (TEM) 13 or focused-ion beam (FIB).…”

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confidence: 99%

Measurement of the Position-Dependent Electrophoretic Force on DNA in a Glass Nanocapillary

et al. 2014

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ABSTRACT:The electrophoretic force on a single DNA molecule inside a glass nanocapillary depends on the opening size and varies with the distance along the symmetrical axis of the nanocapillary. Using optical tweezers and DNA-coated beads, we measured the stalling forces and mapped the position-dependent force profiles acting on DNA inside nanocapillaries of different sizes. We showed that the stalling force is higher in nanocapillaries of smaller diameters. The position-dependent force profiles strongly depend on the size of the nanocapillary opening, and for openings smaller than 20 nm, the profiles resemble the behavior observed in solid-state nanopores. To characterize the position-dependent force profiles in nanocapillaries of different sizes, we used a model that combines information from both analytical approximations and numerical calculations. KEYWORDS: Single molecule measurements, nanocapillary, solid-state nanopore, DNA translocation, optical tweezers, force measurements S olid-state nanopores are label-free sensing platforms for the detailed characterization of single molecules. They have found applications as detectors of DNA, 1 RNA, 2 proteins, 3 and DNA−protein complexes 4 and are currently promising candidates for next generation DNA sequencing. 5,6 Furthermore, when combined with optical tweezers, solid-state nanopores can answer fundamental questions by revealing single molecule mechanisms. This technique was first applied to measure the charge of DNA in solution. 7 Later, Van Dorp et al. used optical tweezers in combination with nanopores to estimate the impact of electroosmotic flow during translocation of DNA molecules through nanopores of different sizes. 8 Biological applications of this method include calculation of the charge of single RNA molecules 9 and DNA-protein complexes 10 and the detection of single proteins bound to DNA. 11,12 To produce a classical solid-state nanopore, first a Si 3 N 4 or SiO 2 membrane is fabricated using lithography techniques. Next, a pore of desired diameter is drilled by transmission electron microscopy (TEM) 13 or focused-ion beam (FIB). 14 A cheaper and faster alternative to nanopore fabrication is laser pulling of glass capillaries, a technique that does not require cleanroom facilities. This process results in nanocapillaries with openings as small as 50 nm. 15 Similar to solid-state nanopores, glass nanocapillaries can detect single molecules of DNA 15 and proteins. 16 They can also be combined with optical tweezers for ultrasensitive force measurement experiments. 17,18 In this combination, nanocapillaries have advantages over nanopores due to a simpler design of the microfluidic cell, more sensitive lateral displacement of the optically trapped bead during DNA capturing, and easier determination of the proximal location of the pore. Keyser et al. used this setup in a variety of applications including studying the mechanism of DNA relaxation, 19 investigating the behavior of charged polymers in crowded environments, 20 and measuring electroosmoti...

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Dynamic translocation of ligand-complexed DNA through solid-state nanopores with optical tweezers

Cited by 42 publications

References 29 publications

Controlling molecular transport through nanopores

Controlling molecular transport through nanopores

Relevance of the Drag Force during Controlled Translocation of a DNA–Protein Complex through a Glass Nanocapillary

Measurement of the Position-Dependent Electrophoretic Force on DNA in a Glass Nanocapillary

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