DNA barcode by flossing through a cylindrical nanopore

Seth, Swarnadeep; Bhattacharya, Aniket

doi:10.1039/d1ra00349f

Cited by 4 publications

(6 citation statements)

References 37 publications

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“…8 a–f). Here, we observe that velocity increases/decreases as a function of the monomer index m for and translocation similar to a homopolymer 33 . Inclusion of the charge at protein tag locations does change the overall profile as expected but does not introduce significant nonuniformity in the velocity profile (Fig.…”

Section: Velocity Of the Tags From The Time Of Flight (Tof) Datamentioning

confidence: 59%

“…The simulation studies show that charged tags experience different forces compared to the dsDNA chain. This results in a nonuniform velocity profile along the chain which can be qualitatively understood using nonequilibrium tension propagation theory of Sakaue 25 and recently demonstrated in a single and dual nanopore setup 32 , 33 . In the following section we analyze how the mass and charge of the tags affect the velocity profile of the entire chain.…”

Section: Velocity Of the Tags From The Time Of Flight (Tof) Datamentioning

confidence: 69%

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Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device

Seth

Rand²,

Reisner

et al. 2022

Sci Rep

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We report Brownian dynamics simulation results with the specific goal to identify key parameters controlling the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. First, we validate the simulation scheme in silico by reproducing and explaining the physical origin of the asymmetric experimental dwell time distributions of the oligonucleotide flap markers on a 48 kbp long dsDNA at the left and the right pore. We study the effect of the electric field inside and beyond the pores, critical to discriminate the protein tags based on their effective charges and masses revealed through a generic power-law dependence of the average dwell time at each pore. The simulation protocols monitor piecewise dynamics at a sub-nanometer length scale and explain the disparate velocity using the concepts of nonequilibrium tension propagation theory. We further justify the model and the chosen simulation parameters by calculating the Péclet number which is in close agreement with the experiment. We demonstrate that our carefully chosen simulation strategies can serve as a powerful tool to discriminate different types of neutral and charged tags of different origins on a dsDNA construct in terms of their physical characteristics and can provide insights to increase both the efficiency and accuracy of an experimental dual-nanopore setup.

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Section: Velocity Of the Tags From The Time Of Flight (Tof) Datamentioning

confidence: 59%

Section: Velocity Of the Tags From The Time Of Flight (Tof) Datamentioning

confidence: 69%

Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device

Seth

Rand²,

Reisner

et al. 2022

Sci Rep

Self Cite

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“…Our direct velocity measurement requires no calibration and can be done directly for any tag detected at both pores. This advantage means that while regions can have variable scan speeds that create variable intertag times, direct knowledge of velocity can be exploited to produce more consistent distance estimates, as suggested in related studies …”

Section: Resultsmentioning

confidence: 99%

“…While this was not the case for λ-DNA with the 15-tag experiments, longer molecules may preferentially only be scanned near the end, and a failure to recapture the molecule may mean losing the opportunity to explore the entire tag set. Molecular dynamics simulations of molecule translocation and capture processes in two pore geometries may assist in further optimizing our scanning protocols to increase read-length, coverage and molecule capture efficiency. , …”

Section: Discussionmentioning

confidence: 99%

“…This advantage means that while regions can have variable scan speeds that create variable intertag times, direct knowledge of velocity can be exploited to produce more consistent distance estimates, as suggested in related studies. 35 Alignment of Single Scans to a Reference Map. A scan is a single pass of a region of a dsDNA molecule moving through the dual-pore sensors in either the L−R or the R−L direction.…”

Section: T H I S C O N T E N T Imentioning

confidence: 99%

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Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control

Rand¹,

Zimny²,

Nagel³

et al. 2022

ACS Nano

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We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed “DNA flossing” control logic generates multiple scans of each captured DNA. We extended this logic in two ways: first, to automate “zooming out” on each molecule to progressively increase the number of tags scanned during flossing, and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. Custom analysis methods were developed to produce consensus alignments from each multiscan event. The combined multiscanning and multicapture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1× across 2355 resolvable sites of the E. coli genome was achieved after 5.6 h of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed intertag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 intersite intervals shorter than 200 bp in the E. coli reference map. We present results on estimating distances in repetitive regions of the E. coli genome. With an appropriately designed array, higher throughput implementations could enable human-sized genome and epigenome mapping applications.

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