448 research outputs found
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
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
Fast DNA translocation through a solid-state nanopore
We report translocation experiments on double-strand DNA through a silicon
oxide nanopore. Samples containing DNA fragments with seven different lengths
between 2000 to 96000 basepairs have been electrophoretically driven through a
10 nm pore. We find a power-law scaling of the translocation time versus
length, with an exponent of 1.26 0.07. This behavior is qualitatively
different from the linear behavior observed in similar experiments performed
with protein pores. We address the observed nonlinear scaling in a theoretical
model that describes experiments where hydrodynamic drag on the section of the
polymer outside the pore is the dominant force counteracting the driving. We
show that this is the case in our experiments and derive a power-law scaling
with an exponent of 1.18, in excellent agreement with our data.Comment: 5 pages, 2 figures. Submitted to PR
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
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
Dragging a polymer chain into a nanotube and subsequent release
We present a scaling theory and Monte Carlo (MC) simulation results for a
flexible polymer chain slowly dragged by one end into a nanotube. We also
describe the situation when the completely confined chain is released and
gradually leaves the tube. MC simulations were performed for a self-avoiding
lattice model with a biased chain growth algorithm, the pruned-enriched
Rosenbluth method. The nanotube is a long channel opened at one end and its
diameter is much smaller than the size of the polymer coil in solution. We
analyze the following characteristics as functions of the chain end position
inside the tube: the free energy of confinement, the average end-to-end
distance, the average number of imprisoned monomers, and the average stretching
of the confined part of the chain for various values of and for the number
of monomers in the chain, . We show that when the chain end is dragged by a
certain critical distance into the tube, the polymer undergoes a
first-order phase transition whereby the remaining free tail is abruptly sucked
into the tube. This is accompanied by jumps in the average size, the number of
imprisoned segments, and in the average stretching parameter. The critical
distance scales as . The transition takes place when
approximately 3/4 of the chain units are dragged into the tube. The theory
presented is based on constructing the Landau free energy as a function of an
order parameter that provides a complete description of equilibrium and
metastable states. We argue that if the trapped chain is released with all
monomers allowed to fluctuate, the reverse process in which the chain leaves
the confinement occurs smoothly without any jumps. Finally, we apply the theory
to estimate the lifetime of confined DNA in metastable states in nanotubes.Comment: 13pages, 14figure
Duration learning for analysis of nanopore ionic current blockades
<p>Abstract</p> <p>Background</p> <p>Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties, with potential implications for DNA sequencing. The alpha-Hemolysin transmembrane channel interacts with a translocating molecule in a nontrivial way, frequently evidenced by a complex ionic flow blockade pattern. Typically, recorded current blockade signals have several levels of blockade, with various durations, all obeying a fixed statistical profile for a given molecule. Hidden Markov Model (HMM) based duration learning experiments on artificial two-level Gaussian blockade signals helped us to identify proper modeling framework. We then apply our framework to the real multi-level DNA hairpin blockade signal.</p> <p>Results</p> <p>The identified upper level blockade state is observed with durations that are geometrically distributed (consistent with an a physical decay process for remaining in any given state). We show that mixture of convolution chains of geometrically distributed states is better for presenting multimodal long-tailed duration phenomena. Based on learned HMM profiles we are able to classify 9 base-pair DNA hairpins with accuracy up to 99.5% on signals from same-day experiments.</p> <p>Conclusion</p> <p>We have demonstrated several implementations for <it>de novo </it>estimation of duration distribution probability density function with HMM framework and applied our model topology to the real data. The proposed design could be handy in molecular analysis based on nanopore current blockade signal.</p
Utilizing the information content in two-state trajectories
The signal from many single molecule experiments monitoring molecular
processes, such as enzyme turnover via fluorescence and opening and closing of
ion channel via the flux of ions, consists of a time series of stochastic on
and off (or open and closed) periods, termed a two-state trajectory. This
signal reflects the dynamics in the underlying multi-substate on-off kinetic
scheme (KS) of the process. The determination of the underlying KS is difficult
and sometimes even impossible due to the loss of information in the mapping of
the mutli dimensional KS onto two dimensions. Here we introduce a new procedure
that efficiently and optimally relates the signal to all equivalent underlying
KSs. This procedure partitions the space of KSs into canonical (unique) forms
that can handle any KS, and obtains the topology and other details of the
canonical form from the data without the need for fitting. Also established are
relationships between the data and the topology of the canonical form to the
on-off connectivity of a KS. The suggested canonical forms constitute a
powerful tool in discriminating between KSs. Based on our approach, the upper
bound on the information content in two state trajectories is determined.Comment: The file contains: main text (+4 figures), supporting information (+9
figures), poster (1 page
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