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Register a new userNoise Activated DNA Translocation for Faster Screening
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Added by
Partho Sarathi Gooh Pattader
Publication date
2021
fields
Physics
and research's language is
English
Authors
Aniruddha Deb
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Nonlinear solid friction between the gel matrix and DNA molecules inhibits the motion of DNA during electrophoresis. We report enhanced mobility of the DNA using external noise to alleviate the effect of solid friction. In presence of noise, the mobility of 1 kbp DNA increases ~ 86% compared to the conventional gel electrophoresis, whereas the increment is more than ~113 % for 6 kbp DNA. At low power of the noise, super Arrhenius kinetics suggest the collective behavior of the activated motion of DNA molecules. Stochastic simulation following modified Langevin equation with the asymmetric pore size distribution of the agarose gel successfully predicts the mobility of DNA molecules and estimates the huge frictional force at the DNA-gel matrix interface.
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We investigate the translocation of a single stranded DNA through a pore which fluctuates between two conformations, using coupled master equations. The probability density function of the first passage times (FPT) of the translocation process is calculated, displaying a triple, double or mono peaked behavior, depending on the interconversion rates between the conformations, the applied electric field, and the initial conditions. The cumulative probability function of the FPT, in a field-free environment, is shown to have two regimes, characterized by fast and slow timescales. An analytical expression for the mean first passage time of the translocation process is derived, and provides, in addition to the interconversion rates, an extensive characterization of the translocation process. Relationships to experimental observations are discussed.
Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of double-stranded DNA translocations through conical quartz nanopores with mean opening diameter 15 nm. We observe an entropic barrier limited, length dependent translocation frequency at 4M LiCl salt concentration and a drift-dominated, length independent translocation frequency at 1M KCl salt concentration. These observations are described by a unifying convection-diffusion equation which includes the contribution of an entropic barrier for polymer entry.
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.
We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases $A$ and $C$, having different base-pore interactions, {textit e.g.}, a strong (weak) attractive force between the pore and the base $A$ ($C$) inside the pore. From a series of studies on hetero-DNAs with repeat units $A_mC_n$, we find that the translocation time decreases exponentially as a function of the volume fraction $f_C$ of the base $C$. %($epsilon_{pC} < epsilon_{pA}$). For longer $A$ sequences with $f_C le 0.5$, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length $N$ with repeat units $A_mC_n$, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of $m$, $n$ and $N$ respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection technic.
Electron transfer (ET) in biological molecules such as peptides and proteins consists of electrons moving between well defined localized states (donors to acceptors) through a tunneling process. Here we present an analytical model for ET by tunneling in DNA, in the presence of Spin-Orbit (SO) interaction, to produce a strong spin asymmetry with the intrinsic atomic SO strength in meV range. We obtain a Hamiltonian consistent with charge transport through $pi$ orbitals on the DNA bases and derive the behavior of ET as a function of the injection state momentum, the spin-orbit coupling and barrier length and strength. A highly consistent scenario arises where two concomitant mechanisms for spin selection arises; spin interference and differential spin amplitude decay. High spin filtering can take place at the cost of reduced amplitude transmission assuming realistic values for the spin-orbit coupling. The spin filtering scenario is completed by addressing the spin dependent torque under the barrier, with a consistent conserved definition for the spin current.
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