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

Bulushev, Roman D.; Marion, Sanjin; Radenović, Aleksandra

doi:10.1021/acs.nanolett.5b03264

Cited by 23 publications

(46 citation statements)

References 68 publications

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“…Water molecules that are dynamically oriented by the interfacial DC field can be probed with the XXX polarization combination, as in Figure 2. Another place where the electrostatic field reaches similarly high values is inside the < 1 µm radius opening of the micro-capillary (50).…”

Section: S3mentioning

confidence: 97%

Optical imaging of surface chemistry and dynamics in confinement

Macias-Romero

Nahálka

Okur

et al. 2017

Science

106

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Surface chemistry and dynamics are optically imaged label-free and non-invasively in a 3D confined geometry and on sub-second time scales AbstractThe interfacial structure and dynamics of water in a microscopically confined geometry is imaged in three dimensions and on millisecond time scales. We developed a 3D wide-field second harmonic microscope that employs structured illumination. We image pH induced chemical changes on the curved and confined inner and outer surfaces of a cylindrical glass micro-capillary immersed in aqueous solution. The image contrast reports on the orientational order of interfacial water, induced by chargedipole interactions between water molecules and surface charges. The images constitute surface potential maps. Spatially resolved surface pK a,s values are determined for the silica deprotonation reaction.Values range from 2.3

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Section: S3mentioning

confidence: 97%

Optical imaging of surface chemistry and dynamics in confinement

Macias-Romero

Nahálka

Okur

et al. 2017

Science

106

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“…Thus nanopore is a powerful sensor for investigation of fundamental physical, chemical or biological issues, such as molecule gating and cation‐induced current changing, at single‐molecule resolution compared to other traditional technologies. To date, nanopores have been exploited for expanded applications, including detection of nanoparticles, biopolymers, proteins, DNA‐origami, DNA‐protein complexes, and so on. One of the most potential applications of nanopore technology is nucleic acid sequencing, which is characterized as low cost and high throughput.…”

Section: Introductionmentioning

confidence: 99%

Discrimination of Protein Amino Acid or Its Protonated State at Single‐Residue Resolution by Graphene Nanopores

Zhang

et al. 2019

Small

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cellular processes at a single-molecule level by taking advantage of the electrochemical nanoconfinement of a nanopore. Thus nanopore is a powerful sensor for investigation of fundamental physical, chemical or biological issues, such as molecule gating [5] and cation-induced current changing, [6] at single-molecule resolution [8] compared to other traditional technologies. To date, nanopores have been exploited for expanded applications, including detection of nanoparticles, [9][10][11] biopolymers, [1,12] proteins, [13][14][15] DNA-origami, [16] DNA-protein complexes, [17][18][19][20] and so on. One of the most potential applications of nanopore technology is nucleic acid sequencing, which is characterized as low cost and high throughput. Most recently, a lot of works have shown that each type of DNA nucleotide can induce correlated modulation of ionic current as they translocate through a nanopore. [12,[21][22][23] With the help of enzyme [24] or polymerase, [25] some biological nanopores [26,27] have shown the ability to determine the nucleotide sequence of a singlestranded DNA at single-base resolution.Different from DNA molecules, proteins consist of more than 20 amino acids (AAs) and are irregularly and slightly charged. Besides, proteins usually keep in folded state in natural environment. Thus, investigation of proteins is much more challenging than DNA. Unraveling the mechanisms of protein folding and unfolding and even realizing protein sequencing are essential for cellular behaviors and diseases. [28] Measurement of tunneling current [29,30] was reported to recognize single amino acids, however to make the tunneling device be a protein sequencing tool it should be coupled with a means that can thread the peptide chain through the gap in a controllable way, which could be possibly realized if the tunneling device is coupled to a nanopore. In the past two decades, most interests in nanopores have focused on DNA sequencing. Only in recent years, nanopore technology has been extended to protein sequencing as nanopores could sequence full-length proteins with high temporal and spatial resolution while traditional sequencing methods such as mass spectrometry [31] and Edman degradation [32] only rely on digestion of proteins into short peptides. Many experiments have shown that protein molecules can be electrophoretically driven through nanopores. [33,34] Some experiments showed that proteins can be unfolded using nanopores by adjusting pH values of the solution, [35] The function of a protein is determined by the composition of amino acids and is essential to proteomics. However, protein sequencing remains challenging due to the protein's irregular charge state and its high-order structure. Here, a proof of principle study on the capability of protein sequencing by graphene nanopores integrated with atomic force microscopy is performed using molecular dynamics simulations. It is found that nanopores can discriminate a protein sequence and even its protonation state at single-residue resolution. Both the pull...

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“…In the pore-driven case an electric field, due to a voltage bias between the two sides of the membrane, acts on the monomers inside the pore. On the other hand, in the end-pulled case the polymer is pulled through a nanopore by either an optical or a magnetic tweezer [42][43][44][45][46][47]. End-pulled translocation has been suggested to be a good method to slow down and control the translocation process which is crucial for proper identification of the nucleotides in DNA sequencing [16,49,50].…”

mentioning

confidence: 99%

Dynamics of end-pulled polymer translocation through a nanopore

Sarabadani¹,

Ghosh²,

Chaudhury³

et al. 2017

EPL

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We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory to include friction arising from the trans side subchain. The theory reveals a complicated scenario of multiple scaling regimes depending on the configurations of the cis and the trans side subchains. In the limit of high driving forces f such that the trans subchain is strongly stretched, the theory is in excellent agreement with molecular dynamics simulations and allows an exact analytic solution for the scaling of the translocation time τ as a function of the chain length N0 and f . In this regime the asymptotic scaling exponents for τ ∼ N α 0 f β are α = 2, and β = −1. The theory reveals significant correction-to-scaling terms arising from the cis side subchain and pore friction, which lead to a very slow approach to α = 2 from below as a function of increasing N0.

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

Cited by 23 publications

References 68 publications

Optical imaging of surface chemistry and dynamics in confinement

Optical imaging of surface chemistry and dynamics in confinement

Discrimination of Protein Amino Acid or Its Protonated State at Single‐Residue Resolution by Graphene Nanopores

Dynamics of end-pulled polymer translocation through a nanopore

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