Bulletin of the American Physical Society
APS March Meeting 2016
Volume 61, Number 2
Monday–Friday, March 14–18, 2016; Baltimore, Maryland
Session H41: Biopolymers in Confinement IIFocus
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Sponsoring Units: DBIO DPOLY Chair: Kevin Dorfman, University of Minnesota - Minneapolis Room: 344 |
Tuesday, March 15, 2016 2:30PM - 2:42PM |
H41.00001: Zero-Mode Waveguide detection of biomolecules transport through artificial nanopores and nuclear pore complexes Thomas Auger, Loic Auvray, Fabien Montel We have developed a novel single molecule optical observation method using a custom Zero-Mode Waveguide setup to study the translocation of biopolymers through artificial and biological nanopores. Our work focuses on two aspects. First we monitored the flow driven injection of DNA molecules through solid state nanopores and showed that DNA starts translocating over a flow threshold independent of the pore radius, the DNA concentration and length. We demonstrate that the translocation is controlled by an energy barrier as proposed by the de Gennes - Brochard suction model. The height of the energy barrier can be modulated by functionalizing the nanopores with PEG-Thiols. More recently we adapted our setup to the study of transport through the nuclear pore complex (NPC) using extracted nuclear membranes from Xenopus Laevis oocytes. We aim at probing the conformation of unstructured proteins -- the FG-Nucleoporins -- crowding the central channel of the NPC by monitoring the free diffusion of small Dextran molecules (3kDa). We have been able to estimate the radius of the central pore of the NPC. We want to study the effects of transporter molecules, which have a high affinity for the FG-Nups, on the central pore size and correlate it to the conformation of FG-Nups. [Preview Abstract] |
Tuesday, March 15, 2016 2:42PM - 2:54PM |
H41.00002: A Nanopore with an Internal Cavity to Selectively Translocate Polymers of a Specific Length Hendrick W. de Haan, Martin Magill In the majority of experimental and simulation studies of polymer translocation through a nanopore, the scaling of the translocation time, $\tau$, with polymer length, $N$, is well described by a single exponent: $\tau \sim N^\alpha$. Hence, an increase in $N$ always yields an increase in $\tau$. I will present a nanopore geometry in which there is a large central cavity between narrow nanopores at both the $cis$ entrance and the $trans$ exit. Results from simulations of this system reveal a complex dependence of $\tau$ on $N$. Most notably, the translocation time is now non-monotonic in polymer length such that $\tau$ is a minimum for polymers of an intermediate length with both longer and shorter polymers taking a longer time to cross across the membrane. A simple yet effective model for predicting this critical length as a function of the size of the cavity and the magnitude of the external field will be presented. The pore thus can be designed to be optimized for particular lengths – with some dynamic tuning being possible by varying the strength of the external field. These results suggest new applications for nanopore-based devices such as the ability to select DNA strands of a specific length from a sample containing both shorter and longer strands. [Preview Abstract] |
Tuesday, March 15, 2016 2:54PM - 3:06PM |
H41.00003: Effect of excluded volume on the force-extension of wormlike chains in slit confinement Xiaolan Li, Kevin Dorfman We will present a quantitative phase diagram for the stretching of a wormlike chain confined in a slit with excluded volume interactions. Using pruned-enriched Rosenbluth method (PERM) simulations, we demonstrate the existence of a ``confined Pincus'' regime in slit confinement. This regime is similar to the Pincus regime in free solution, where excluded volume effects are sensible. The lower bound for the confined Pincus regime in the force-contour length plane and the dependence of the extension with force and slit size are in agreement with scaling theory. The upper bound of the confined Pincus regime depends on the confinement strength; it ends in strong confinement when the Pincus blobs do not have excluded volume, while it ends in weak confinement when the Pincus blobs do not fit in the slit. We also show the existence of a free-solution Pincus regime in weak confinement that exists before ideal chain behavior sets in under strong forces. We will discuss the implication of our results on the analysis of experiments on the ``tug-of-war'' stretching of DNA partially confined to a slit. [Preview Abstract] |
Tuesday, March 15, 2016 3:06PM - 3:18PM |
H41.00004: Visualizing Chemical Interaction Dynamics of Confined DNA Molecules Gilead Henkin, Daniel Berard, Frank Stabile, Sabrina Leslie We present a novel nanofluidic approach to controllably introducing reagent molecules to interact with confined biopolymers and visualizing the reaction dynamics in real time. By dynamically deforming a flow cell using CLiC (Convex Lens-induced Confinement) microscopy, we are able to tune reaction chamber dimensions from micrometer to nanometer scales. We apply this gentle deformation to load and extend DNA polymers within embedded nanotopographies and visualize their interactions with other molecules in solution. Quantifying the change in configuration of polymers within embedded nanotopographies in response to binding/unbinding of reagent molecules provides new insights into their consequent change in physical properties. CLiC technology enables an ultra sensitive, massively parallel biochemical analysis platform which can acces a broader range of interaction parameters than existing devices. [Preview Abstract] |
Tuesday, March 15, 2016 3:18PM - 3:30PM |
H41.00005: Relaxation dynamics of internal segments of DNA chains in nanochannels Aashish Jain, Abhiram Muralidhar, Kevin Dorfman We will present relaxation dynamics of internal segments of a DNA chain confined in nanochannel. The results have direct application in genome mapping technology, where long DNA molecules containing sequence-specific fluorescent probes are passed through an array of nanochannels to linearize them, and then the distances between these probes (the so-called “DNA barcode”) are measured. The relaxation dynamics of internal segments set the experimental error due to dynamic fluctuations. We developed a multi-scale simulation algorithm, combining a Pruned-Enriched Rosenbluth Method (PERM) simulation of a discrete wormlike chain model with hard spheres with Brownian dynamics (BD) simulations of a bead-spring chain. Realistic parameters such as the bead friction coefficient and spring force law parameters are obtained from PERM simulations and then mapped onto the bead-spring model. The BD simulations are carried out to obtain the extension autocorrelation functions of various segments, which furnish their relaxation times. Interestingly, we find that (i) corner segments relax faster than the center segments and (ii) relaxation times of corner segments do not depend on the contour length of DNA chain, whereas the relaxation times of center segments increase linearly with DNA chain size. [Preview Abstract] |
Tuesday, March 15, 2016 3:30PM - 3:42PM |
H41.00006: Controlling the Motion of Knotted Polymers through Nanopores Vivek Narsimhan, C. Benjamin Renner, Patrick Doyle Nanopore sequencing is a technique where DNA moves through a pore and base-pair information is read along the chain as an electric signal. One hurdle facing this technique is that DNA passes too quickly through the pore, rendering the signal to be too noisy. In this talk, we discuss one strategy to control the speed by which polymers move through pores. By tying a knot on a polymer chain, we find that we can jam the polymer at the pore's entrance and halt translocation completely. This idea by itself may not seem useful, but by cycling the field on and off at the relaxation time scale of the knot, we can control the swelling dynamics of the knot at the pore's entrance, and hence ratchet the polymer through the pore. This talk focuses on two parts. First, we will discuss the dynamics of a knot jamming at the pore entrance and determine what sets the critical tension to halt translocation. We will determine how knot topology affects these results and discuss what regimes lead to large fluctuations in the translocation speed. We will then discuss the dynamics of a knot under a time-dependent, periodic force. Lastly, we develop a model to describe the knot's swelling dynamics during relaxation, and use this to explain some of the trends observed in our simulations. [Preview Abstract] |
Tuesday, March 15, 2016 3:42PM - 4:18PM |
H41.00007: Confined polymers in the extended de Gennes regime Invited Speaker: Bernhard Mehlig In the "extended de Gennes regime" the problem of describing the conformations of a semiflexible polymer confined to a channel can be mapped onto the weakly self-avoiding random-walk model. For large contour lengths the asymptotically exact solution of this model predicts how the conformational fluctuations of the confined polymer depend upon the channel dimensions and upon the physical properties of the polymer, its effective width and persistence length. The extended de Gennes regime (where the polymer is neither weakly nor strongly confined) has recently been studied intensively experimentally and by means of computer simulations of worm-like chain models. In this talk I explain the mapping, summarise the predictions derived from the exact solution, and compare the predictions to results of computer simulations [Dorfman {\em et al.}] and experiments [Westerlund {\em et al.}] of DNA molecules confined to nanochannels. I conclude by summarising open questions. This talk is mainly based on joint work with E. Werner [Phys. Rev. E {\bf 90} (2014) 062602]. [Preview Abstract] |
Tuesday, March 15, 2016 4:18PM - 4:30PM |
H41.00008: From stripe to slab confinement for DNA linearization in nanochannels Peter Cifra, Zuzana Benkova, Pavol Namer We investigate suggested advantageous analysis in the linearization experiments with macromolecules confined in a stripe-like channel using Monte Carlo simulations. The enhanced chain extension in a stripe that is due to significant excluded volume interactions between monomers in two dimensions weakens on transition to experimentally feasible slit-like channel. Based on the chain extension-confinement strength dependence and the structure factor behavior for the chain in stripe we infer the excluded volume regime typical for two-dimensional systems. On transition to the slab geometry, the advantageous chain extension decreases and the Gaussian regime is observed for not very long semiflexible chains. The evidence for pseudo-ideality in confined chains is based on indicators such as the extension curves, variation of the extension with the persistence length or the structure factor. The slab behavior is observed when the stripe (originally of monomer thickness) reaches the thickness larger than cca 10nm in the third dimension. This maximum height of the slab to retain the advantage of the stripe is very low and this have implication for DNA linearization experiments. The presented analysis, however, has a broader relevance for confined polymers. [Preview Abstract] |
Tuesday, March 15, 2016 4:30PM - 4:42PM |
H41.00009: Knotted DNA in Nanofluidic Confinement Alexander Klotz, Patrick Doyle The behavior of topologically simple semiflexible polymers such as DNA has become well-understood in the last several years. Recently, several computational analyses have predicted that certain topological features of a polymer, such as the average size of pseudo-knots and the probability of knot formation, are enhanced by confinement. Here, we extend recent work on the stretching of knotted DNA and examine diffusion, relaxation, and chain statistics of topologically complex linear DNA molecules. Topological phenomena are studied both in the bulk and under nanofluidic confinement to examine the interplay between knotting and confinement in semiflexible polymers, as well as to provide a controlled experimental interrogation of the knotted region of the polymer. [Preview Abstract] |
Tuesday, March 15, 2016 4:42PM - 4:54PM |
H41.00010: DNA Partitioning in Confining Nanofluidic Slits Madeline Greenier, Stephen Levy We measure the partitioning of double stranded DNA molecules in moderately and strongly confining nanofluidic slit-like structures. Using fluorescent microscopy, the free energy penalty of confinement is inferred by comparing the concentration of DNA molecules in adjoining slits of different depths. These depths range in size from several persistence lengths to the DNA molecule's radius of gyration. The partition coefficient is determined as a function of the slit depth, DNA contour length, and DNA topology. We compare our results to theory and Monte Carlo simulations that predict the loss of free energy for ideal and semiflexible excluded volume polymers confined between parallel plates. [Preview Abstract] |
Tuesday, March 15, 2016 4:54PM - 5:06PM |
H41.00011: To Knot or Not-That is the Question: A Nanofluidic Knot Factory based on Compression of Single DNA Molecules against Slit Barriers in Nanochannels Susan Amin, Ahmed Khorshid, Lili Zeng, Philip Zimny, Walter Reisner Knots can form during DNA packaging in chromosome and obstruct mapping of DNA in nanochannels. Studies have focused on theoretical and numerical studies of knots, but an efficient and fully controlled means of knotting has not yet been explored. Here, we introduce a knot factory on chip based on pneumatic compression of single T4 DNA against a slit barrier in a nanochannel. The DNA are compressed to a well-defined fraction of their initial equilibrium extension. The pressure is then released and the DNA molecules relax back to their equilibrium extension; knots are present along the relaxed DNA, visualized as sharply localized regions of high intensity. Via repeated compression and relaxation, we can measure the probabilities of forming single and multiple knot states and the distribution of knot sizes as a function of fractional compression and waiting time in the compressed state. We show that the total probability of knot formation increases with greater compression and waiting time.These findings are well described via a knot formation free energy derived from scaling arguments, suggesting that the enhanced knotting probability at high compression arises from avoiding the free energy cost due to self-exclusion interactions that would arise from contour stored in the knot. [Preview Abstract] |
Tuesday, March 15, 2016 5:06PM - 5:18PM |
H41.00012: Polymer translocation from a confining tube: the effect of a finite tube length David Sean, Gary W Slater Coarsed-grained Langevin Dynamics simulations of driven polymer translocation are used to study situations where the polymer is initialized inside a confining cylindrical cavity. The latter limits the number of conformations at the onset of translocation, which (in the highly driven limit) should lead to a net reduction in the variance of the mean translocation time. We vary both the confinement volume and the cavity aspect ratio to minimize the coefficient of variation of the translocation time. We also use a tension-propagation model and find that its predictions are in good agreement with our simulation results: both yield a minimum in the coefficient of variation for a tube having an aspect ratio corresponding to a diameter which is roughly twice the tube length. Moreover, fluctuations in the translocation coordinate $s(t)$ do not generally follow a power law with time $\langle \Delta s ^2\rangle \sim t^\beta$; for some of the geometries we actually observed non-monotonic fluctuations. We attribute this result to conformations containing hairpins, which are an outcome of having a polymer initially confined in a tube with a finite volume. [Preview Abstract] |
Tuesday, March 15, 2016 5:18PM - 5:30PM |
H41.00013: Experimental Evidence of Weak Excluded Volume Effects for Nanochannel Confined DNA Damini Gupta, Jeremy J. Miller, Abhiram Muralidhar, Sara Mahshid, Walter Reisner, Kevin D. Dorfman In the classical de Gennes picture of weak polymer nanochannel confinement, the polymer contour is envisioned as divided into a series of isometric blobs. Strong excluded volume interactions are present both within a blob and between blobs. In contrast, for semiflexible polymers like DNA, excluded volume interactions are of borderline strength within a blob but appreciable between blobs, giving rise to a chain description consisting of a string of anisometric blobs. We present experimental validation of this subtle effect of excluded volume for DNA nanochannel confinement by performing measurements of variance in chain extension of T4 DNA molecules as a function of effective nanochannel size (305-453 nm).\footnote{Gupta et al., ACS MacroLett. 4, 759 (2015)} Additionally, we show an approach to systematically reduce the effect of molecular weight dispersity of DNA samples, a typical experimental artifact, by combining confinement spectroscopy with simulations. [Preview Abstract] |
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