Direct observation of DNA knots using a solid-state nanopore

Plesa, Calin; Verschueren, Daniel; Pud, Sergii; Torre, Jaco van der; Ruitenberg, Justus W.; Witteveen, Menno J.; Jonsson, Magnus P.; Grosberg, Alexander Y.; Rabin, Yitzhak; Dekker, Cees

doi:10.1038/nnano.2016.153

Cited by 225 publications

(266 citation statements)

References 49 publications

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“…In knotted rings, due to the tightening of the intrinsic essential crossings, these loci typically involve several clasped or hooked double strands, as highlighted in the snapshots of Figure 5A. We observed that, similarly to what happens during the pore translocation of knotted filaments (59,60,64,65), the topological friction at these points is so high that the DNA strands are locally pinned while other parts of the chain can reconfigure.…”

Section: Resultsmentioning

confidence: 66%

“…We believe this would be a noteworthy problem to address in future studies, for instance using mesoscopic models incorporating the interaction of DNA and proteins, which would be essential for a realistic description of DNA organization and processing in vivo . In addition, we expect that long-lived multi-strand interlockings could be probed with single-molecule manipulation techniques such as pore translocation, which has been previously used on DNA rings with either knots or supercoiling (48,65,67–71). …”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking

Coronel

Suma

Micheletti

2018

Nucleic Acids Research

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Knots and supercoiling are both introduced in bacterial plasmids by catalytic processes involving DNA strand passages. While the effects on plasmid organization has been extensively studied for knotting and supercoiling taken separately, much less is known about their concurrent action. Here, we use molecular dynamics simulations and oxDNA, an accurate mesoscopic DNA model, to study the kinetic and metric changes introduced by complex (five-crossing) knots and supercoiling in 2 kbp-long DNA rings. We find several unexpected results. First, the conformational ensemble is dominated by two distinct states, differing in branchedness and knot size. Secondly, fluctuations between these states are as fast as the metric relaxation of unknotted rings. In spite of this, certain boundaries of knotted and plectonemically-wound regions can persist over much longer timescales. These pinned regions involve multiple strands that are interlocked by the cooperative action of topological and supercoiling constraints. Their long-lived character may be relevant for the simplifying action of topoisomerases.

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Section: Resultsmentioning

confidence: 66%

Section: Discussionmentioning

confidence: 99%

Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking

Coronel

Suma

Micheletti

2018

Nucleic Acids Research

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“…Since the pore diameter is larger than the diameter of DNA, multiple configurations of DNA can be measured and each one produces a unique ionic current signature (Figure 6B) [9]. Many events also show what is now understood to be DNA knots which are characterized by short spikes within an event [57]. For event detection, we used threshold based search algorithm which captures the maximum current drop values of the events.…”

Section: Resultsmentioning

confidence: 99%

“…The devices used to record λ-DNA had a SiN aperture size of ~500 nm, and was subsequently coated with ~100 nm of SiO 2 . An alternative approach is to make larger SiN apertures (i.e., 900–1000 nm) which were also used in previous work to detect λ-DNA [57]. …”

Section: Resultsmentioning

confidence: 99%

Substrate Dependent Ad-Atom Migration on Graphene and the Impact on Electron-Beam Sculpting Functional Nanopores

Freedman

Goyal

Ahn

et al. 2017

Sensors

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The use of atomically thin graphene for molecular sensing has attracted tremendous attention over the years and, in some instances, could displace the use of classical thin films. For nanopore sensing, graphene must be suspended over an aperture so that a single pore can be formed in the free-standing region. Nanopores are typically drilled using an electron beam (e-beam) which is tightly focused until a desired pore size is obtained. E-beam sculpting of graphene however is not just dependent on the ability to displace atoms but also the ability to hinder the migration of ad-atoms on the surface of graphene. Using relatively lower e-beam fluxes from a thermionic electron source, the C-atom knockout rate seems to be comparable to the rate of carbon ad-atom attraction and accumulation at the e-beam/graphene interface (i.e., Rknockout ≈ Raccumulation). Working at this unique regime has allowed the study of carbon ad-atom migration as well as the influence of various substrate materials on e-beam sculpting of graphene. We also show that this information was pivotal to fabricating functional graphene nanopores for studying DNA with increased spatial resolution which is attributed to atomically thin membranes.

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“…La détection du passage de ces molécules est réalisée par la mesure du courant ionique traversant le pore : un pore vide correspond à un courant élevé ; La présence d'une macromolécule, telle que l'ADN, réduit le flux d'ions au travers du pore, et permet de détecter le passage d'une molécule individuelle (Figure 1, encart haut). Cette méthode a, dès lors, été appliquée à la détection d'autres macromolécules (le polyéthylène glycol [PEG] [7] ou des protéines [8,9]), à la caractérisation de la distribution de masse d'un polymère [7], mais aussi à l'étude de la conformation de macromolécules (structures secondaires et tertiaires [8,10], noeuds [11], association spécifique de protéines [12]). Pour pouvoir identifier chacune des paires de base de la molécule transportée dans le nanopore, il a fallu résoudre de nombreuses difficultés techniques et améliorer fortement les performances du système.…”

Section: Séquençage De L'adn Par Nanopores Résultats Et Perspectivesunclassified

Séquençage de l’ADN par nanopores

Montel

2018

Med Sci (Paris)

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Après des années de développement, l’utilisation du nanopore comme sonde pour séquencer les molécules d’ADN est maintenant une possibilité viable et prometteuse. La détection d’une seule paire de bases lors du transport de l’ADN permet d’enregistrer de très longs fragments de polynucléotides, avec une parallélisation et des vitesses élevées. Dans cette revue, les méthodologies actuelles fondées sur la détection électrique et les nanopores biologiques seront présentées de même que les nouvelles méthodes utilisant des nanopores à l’état solide, ou la détection optique.

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Direct observation of DNA knots using a solid-state nanopore

Cited by 225 publications

References 49 publications

Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking

Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking

Substrate Dependent Ad-Atom Migration on Graphene and the Impact on Electron-Beam Sculpting Functional Nanopores

Séquençage de l’ADN par nanopores

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