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Register a new userDNA Barcodes using a Double Nanopore System
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Added by
Aniket Bhattacharya
Publication date
2021
fields
Physics
and research's language is
English
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The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chains backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.
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We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves the measurements to almost 100 % accuracy. The heavier protein tags along the DNA backbone introduce a large speed variation in the chain that can be understood using the idea of non-equilibrium tension propagation theory. However, from an initial rough characterization of velocities into fast (nucleotides) and slow (protein tags) domains, we introduce a physically motivated interpolation scheme that enables us to determine the barcode velocities rather accurately. Our theoretical analysis of the motion of the DNA through a cylindrical nanopore opens up the possibility of its experimental realization and carries over to multi-nanopore devices used for barcoding.
We simulate a tug-of-war (TOW) scenario for a model double-stranded DNA threading through a double nanopore (DNP) system. The DNA, simultaneously captured at both pores is subject to two equal and opposite forces $-vec{f}_L= vec{f}_R$ (TOW), where $vec{f}_L$ and $vec{f}_R$ are the forces applied to the left and the right pore respectively. Even though the net force on the DNA polymer $Delta vec{f}_{LR}=vec{f}_L+ vec{f}_R=0$, the mean first passage time (MFPT) $langle tau rangle$ depends on the magnitude of the TOW forces $ left | f_L right | = left |f_R right | = f_{LR}$. We qualitatively explain this dependence of $langle tau rangle$ on $f_{LR}$ from the known results for the single-pore translocation of a triblock copolymer. We demonstrate that the time of flight (TOF) of a monomer with index $m$ ($langle tau_{LR}(m) rangle$) from one pore to the other exhibits quasi-periodic structure commensurate with the distance between the pores $d_{LR}$. Finally, we study the case $Delta vec{f}_{LR}=vec{f}_L+ vec{f}_R e 0$, and qualitatively reproduce the experimental result of the dependence of the MFPT on $Deltavec{f}_{LR}$. For a moderate bias, the MFPT for the DNP system for a chain length $N$ follows the same scaling ansatz as that of for the single nanopore, $langle tau rangle = left( AN^{1+ u} + eta_{pore}N right) left(Delta f_{LR}right)^{-1}$, where $eta_{pore}$ is the pore friction, which enables us to estimate $langle tau rangle $ for a long chain. Our Brownian dynamics simulation studies provide fundamental insights and valuable information about the details of the translocation speed obtained from $langle tau_{LR}(m) rangle$, and accuracy of the translation of the data obtained in the time-domain to units of genomic distances.
The ability to measure or manipulate network connectivity is the main challenge in the field of connectomics. Recently, a set of approaches has been developed that takes advantage of next generation DNA sequencing to scan connections between neurons into a set of DNA barcodes. Individual DNA sequences called markers represent single neurons, while pairs of markers, called barcodes contain information about connections. Here we propose a strategy for copying or cloning connectivity contained in barcodes into a clean slate tabula rasa network. We show that a one marker one cell (OMOC) rule, which forces all markers with the same sequence to condense into the same neuron, leads to fast and reliable formation of desired connectivity in a new network. We show that OMOC rule yields convergence in a number of steps given by a power law function of the network size. We thus propose that copying network connectivity from one network to another is theoretically possible.
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical restrictions imposed on the cocaptured dsDNA segment in between the pores, the presence of tug-of-war forces at each pore results in a variation of the local chain stiffness for the segment of the chain in between the pores which increases the overall stiffness of the chain. We use BD simulation results to understand how the intrinsic chain stiffness and the TOW forces affect the escape dynamics by monitoring the local chain persistence length $ell_p$, the residence time of the individual monomers $W(m)$ in the nanopores, and the chain length dependence of the escape time $langle tau rangle$ and its distribution. Finally, we generalize the scaling theory for the unbiased single nanopore translocation for a fully flexible chain for the escape of a semi-flexible chain through a DNP in presence of TOW forces. We establish that the stiffness dependent part of the escape time is approximately independent of the translocation mechanism so that $langle tau rangle sim ell_p^{2/D+2}$, and therefore the generalized escape time for a semi-flexible chain can be written as $langle tau rangle = AN^alphaell_p^{2/D+2}$. We use BD simulation results to compare the predictions of the scaling theory. Our numerical studies supplemented by scaling analysis provide fundamental insights to design new experiments where a dsDNA moves slowly through a series of graphene nanopores.
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {em block length} $2n$ as well as on the {em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.
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