828 research outputs found
Translocation of a Single Stranded DNA Through a Conformationally Changing Nanopore
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.Comment: 8 pages, 5 figures, Biophys. J., in pres
When translocation dynamics becomes anomalous
Recent single molecule experiments probing the passage process of a short
single-stranded DNA (ssDNA) through a membrane channel (translocation) allow to
measure the passage time distribution. Building on a recent modelling approach
(D. K. Lubensky and D. R. Nelson, Biophys. J. 77, 1824 (1999)), which has been
demonstrated to be valid for chains of up to nucleotides and
therefore well applies to the system we have in mind, we discuss the
consequences if the associated dynamics is not of Markov origin, but if strong
memory effects prevail during the translocation. Motivation is drawn from
recent results indicating that the distribution of translocation times is
broader than predicted by simple Markovian models based on Brownian motion.Comment: 5 pages, 2 figures, RevTeX4, submitted to Biophys.
Single Stranded DNA Translocation Through A Nanopore: A Master Equation Approach
We study voltage driven translocation of a single stranded (ss) DNA through a
membrane channel. Our model, based on a master equation (ME) approach,
investigates the probability density function (pdf) of the translocation times,
and shows that it can be either double or mono-peaked, depending on the system
parameters. We show that the most probable translocation time is proportional
to the polymer length, and inversely proportional to the first or second power
of the voltage, depending on the initial conditions. The model recovers
experimental observations on hetro-polymers when using their properties inside
the pore, such as stiffness and polymer-pore interaction.Comment: 7 pages submitted to PR
What can one learn from two-state single molecule trajectories?
A time trajectory of an observable that fluctuates between two values (say,
on and off), stemming from some unknown multi-substate kinetic scheme, is the
output of many single molecule experiments. Here we show that when all
successive waiting times along the trajectory are uncorrelated the on and the
off waiting time probability density functions (PDFs) contain all the
information. By relating the lack of correlation in the trajectory to the
topology of kinetic schemes, we can immediately specify those kinetic schemes
that are equally consistent with experiment, which means that it is impossible
to differentiate between them by any sophisticated analyses of the trajectory.
Correlated trajectories, however, contain additional information about the
underlying kinetic scheme, and we consider the strategy that one should use to
extract it. An example is given on correlations in the activity of individual
lipase molecules.Comment: Biophys. J., in press (2005
The effects of diffusion on an exonuclease/nanopore-based DNA sequencing engine
Over 15 years ago, the ability to electrically detect and characterize individual polynucleotides as they are driven through a single protein ion channel was suggested as a potential method for rapidly sequencing DNA, base-by-base, in a ticker tape-like fashion. More recently, a variation of this method was proposed in which a nanopore would instead detect single nucleotides cleaved sequentially by an exonuclease enzyme in close proximity to one pore entrance. We analyze the exonuclease/nanopore-based DNA sequencing engine using analytical theory and computer simulations that describe nucleotide transport. The available data and analytical results suggest that the proposed method will be limited to reading bases, imposed, in part, by the short lifetime each nucleotide spends in the vicinity of the detection element within the pore and the ability to accurately discriminate between the four mononucleotides
Molecular-scale structural and functional characterization of sparsely tethered bilayer lipid membranes
Surface-tethered biomimetic bilayer membranes (tethered bilayer lipid membranes (tBLMs)) were formed on gold surfaces from phospholipids and a synthetic 1-thiahexa(ethylene oxide) lipid, WC14. They were characterized using electrochemical impedance spectroscopy, neutron reflection (NR), and Fourier-transform infrared reflection-absorption spectroscopy (FT-IRRAS) to obtain functional and structural information. The authors found that electrically insulating membranes (conductance and capacitance as low as 1 microS cm(-2) and 0.6 microF cm(-2), respectively) with high surface coverage (>95% completion of the outer leaflet) can be formed from a range of lipids in a simple two-step process that consists of the formation of a self-assembled monolayer (SAM) and bilayer completion by "rapid solvent exchange." NR provided a molecularly resolved characterization of the interface architecture and, in particular, the constitution of the space between the tBLM and the solid support. In tBLMs based on SAMs of pure WC14, the hexa(ethylene oxide) tether region had low hydration even though FT-IRRAS showed that this region is structurally disordered. However, on mixed SAMs made from the coadsorption of WC14 with a short-chain "backfiller," beta-mercaptoethanol, the submembrane spaces between the tBLM and the substrates contained up to 60% exchangeable solvent by volume, as judged from NR and contrast variation of the solvent. Complete and stable "sparsely tethered" BLMs (stBLMs) can be readily prepared from SAMs chemisorbed from solutions with low WC14 proportions. Phospholipids with unsaturated or saturated, straight or branched chains all formed qualitatively similar stBLMs.This work was supported by the National Science Foundation
CBET-0555201 and 0457148. One of the authors
M.L. and the AND/R instrument were supported by the
National Institutes of Health under Grant No. 1 R01
RR14812 and by the Regents of the University of California
Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport
We study theoretically the feasibility of using transverse electronic
transport within a nanopore for rapid DNA sequencing. Specifically, we examine
the effects of the environment and detection probes on the distinguishability
of the DNA bases. We find that the intrinsic measurement bandwidth of the
electrodes helps the detection of single bases by averaging over the current
distributions of each base. We also find that although the overall magnitude of
the current may change dramatically with different detection conditions, the
intrinsic distinguishability of the bases is not significantly affected by pore
size and transverse field strength. The latter is the result of very effective
stabilization of the DNA by the transverse field induced by the probes, so long
as that field is much larger than the field that drives DNA through the pore.
In addition, the ions and water together effectively screen the charge on the
nucleotides, so that the electron states participating in the transport
properties of the latter ones resemble those of the uncharged species. Finally,
water in the environment has negligible direct influence on the transverse
electrical current.Comment: 14 pages, 5 figure
On the Lubensky-Nelson model of polymer translocation through nanopores
We revisit the one-dimensional stochastic model of Lubensky and Nelson
[Biophys. J 77, 1824 (1999)] for the electrically driven translocation of
polynucleotides through alpha-hemolysin pores. We show that the model correctly
describes two further important properties of the experimentally observed
translocation time distributions, namely their spread (width) and their
exponential decay. The resulting overall agreement between theoretical and
experimental translocation time distributions is thus very good
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