Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session B26: Focus Session: Single Molecule Biophysics: DNA & RNA |
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Sponsoring Units: DBP DPOLY Chair: Ching-Hwa Kiang, Rice University Room: Baltimore Convention Center 323 |
Monday, March 13, 2006 11:15AM - 11:51AM |
B26.00001: Dynamics of molecular motors with finite processivity on heterogeneous tracks Invited Speaker: The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered.[1] Motivated by recent single-molecule experiments, we study a simple model for a motor moving along a disordered track using chemical energy while an external force opposes its motion. The motors also have finite processivity, i.e., they can leave the track with a position-dependent rate. We show that the response of the system to disorder in the hopping-off rate depends on the value of the external force. For most values of the external force, strong disorder causes the motors which survive for long times on the track to be localized at preferred positions. However, near the stall force, localization occurs for any amount of disorder. To obtain these results, we study the complex eigenvalue spectrum of the time evolution operator. Existence of localized states near the top of the band implies a stretched exponential contribution to the decay of the survival probability. A similar spectral analysis also provides a very efficient method for studying the dynamics of motors with infinite processivity. \newline \newline 1. Y. Kafri D. K. Lubensky and D. R. Nelson Phys. Rev. E 71, 041906 (2005). [Preview Abstract] |
Monday, March 13, 2006 11:51AM - 12:03PM |
B26.00002: DNA electrophoresis in Pluronic F127 Seungyong You, David Van Winkle Electrophoresis involves the separation of bio-molecules in a sieving medium by applying an electric field. DNA molecule fragments are separated in conventional gels and a several models have been successfully applied for understanding the separations. Recently, a pluronic gel was found to be an effective sieving medium for electrophoresis. However, the mobility of DNA in this gel cannot be described by the conventional theories. One reason is that Pluronic F127 is not a crosslinked gel, but a lattice of polymer micelles. The migration of single DNA molecules stained with various dye molecules was studied in slab gel electrophoresis by real-time fluorescence microscopy. Results for a variety of sizes will be presented. [Preview Abstract] |
Monday, March 13, 2006 12:03PM - 12:15PM |
B26.00003: Model for passage time of polymer trough a pore (weak external forces limit) Stanislav Kotsev, Anatoly Kolomeisky Polymer translocation through a pore is an important problem in biophysics. Recent experiments measure the dynamics of the process with a single-molecule precision. In these experiments a single-stranded RNA or DNA molecule is driven trough a narrow pore by an external electric field. In our work we concentrate on theoretical modeling of polymer translocation when external forces are weak. In this regime the entropic forces are dominating. Then for long polymers the passage time scales with the number of monomers as $N^{\alpha}$. However, the exact value of $\alpha$ is still a matter of discussion. We are proposing a simple phenomenological model which can be solved exactly. Our results are in a good agreement with off-lattice $3D$ Monte Carlo simulations. [Preview Abstract] |
Monday, March 13, 2006 12:15PM - 12:27PM |
B26.00004: Driven DNA translocation through thin and long nanopores Aniket Bhattacharya, William H. Morrison We utilize Brownian dynamics simulation to study polymer translocation through a nanopore driven by an electric field using a coarse-grained bead-spring model for the translocating DNA. We study mean translocation time $\langle \tau \rangle$ as a function of the chain length N, the width $w$ of the pore, and external bias F. Unlike many previous studies, we critically examine the scaling of $\langle \tau \rangle$ as a function of the ratio $N/w$ and F. For a thin pore, our preliminary results indicate that the mean translocation time $\langle \tau \rangle \sim N^{2\nu}$, where $\nu$ is the Flory exponent, although the slope shows a weak but non-negligible dependence on the external bias F for the chain lengths considered so far. Our simulation results are consistent with experiments done in solid-state nanopore$^{*,+}$.\\ $^{*}$Work done in collaboration with Heath Morrison, Prof. Kurt Binder and Prof. Andrey Milchev.\\ $^{+}$ A.~J. Storm, C. Storm, J. Chen, H. Zandbergen, J-F Joanny, C. Dekker, Nano Letters, {\bf 5}, 1193 (2005). [Preview Abstract] |
Monday, March 13, 2006 12:27PM - 12:39PM |
B26.00005: Conformational Analysis of Single DNA Molecules Undergoing Entropically Induced Motion in Nanochannels. John Mannion, Christian Reccius, Joshua Cross, Harold Craighead We have used the interface between a nanochannel and a microchannel as a tool for applying controlled forces on a DNA molecule. A molecule with a radius of gyration larger than a nanochannel width, that straddles such an interface, is subject to an essentially constant entropic force which can be balanced against other forces such as the electrophoretic force from an applied electric field. By controlling the applied field, we can position the molecule as desired and observe the conformation of the molecule as it stretches, relaxes and recoils from the nanochannel. We quantify and present models for the molecular motion in response to the entropic, electrophoretic and frictional forces acting on it. By determining the magnitude of the drag coefficients for DNA molecules in the nanostructure, we are able to estimate the confinement induced recoil force. Finally, we demonstrate that we can use a controlled applied field and the electrophoretic interfacial forces to unfold molecules, which can then be manipulated and positioned in their simple extended morphology. [Preview Abstract] |
Monday, March 13, 2006 12:39PM - 12:51PM |
B26.00006: The Physics of Nanoconfined DNA Walter Reisner, Keith Morton, Robert Riehn, Yang Mei Wang, Stephen Chou, Jonas Tegenfeldt, Robert Austin Top-down approaches to nanotechnology have the potential to revolutionize biology by making possible the construction of chip-based devices that can not only detect and separate single DNA molecules by size but also--it is hoped in the future--actually sequence at the single molecule level. While a number of top-down approaches have been proposed, all these approaches have in common the confinement of DNA to nanometer scales, typically 5-200nm. Nanoconfinement effects the equilibrium conformation of the DNA. Here we present measurements of the static and dynamic properties of single DNA molecules confined in nanochannels using fluorescence microscopy techniques. In particular, we investigate the dynamics of DNA in novel structures, including structures with defects (bulges and constrictions) and channels that funnel in depth and width. We also discuss observations of possible topological structures on the confined DNA (knots or loops observed on the extended molecules). [Preview Abstract] |
Monday, March 13, 2006 12:51PM - 1:03PM |
B26.00007: DNA entropic elasticity for short molecules Jinyu Li, Philip C. Nelson, M. D. Betterton Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer force-extension behavior to calibrate the experiments; typically the experiments use the worm-like chain (WLC) theory for double-stranded DNA and RNA. This theory agrees well with experiments for long molecules. Recent single-molecule experiments have used shorter molecules, with contour lengths in the range of 1-10 persistence lengths. Most WLC theory calculations to date have assumed infinite molecule lengths, and do not agree well with experiments on shorter chains. Key physical effects that become important when shorter molecules are used include (i) boundary conditions which constrain the allowed fluctuations at the ends of the molecule and (ii) rotational fluctuations of the bead to which the polymer is attached, which change the apparent extension of the molecule. We describe the finite worm-like chain (FWLC) theory, which takes into account these effects. We show the FWLC predictions diverge from the classic WLC solution for molecules with contour lengths a few times the persistence length. Thus the FWLC will allow more accurate experimental calibration for relatively short molecules, facilitating future discoveries in single-molecule force microscopy. [Preview Abstract] |
Monday, March 13, 2006 1:03PM - 1:15PM |
B26.00008: Single Molecule Visualization of DNA in Wicking Flows Chad DeLong, David Hoagland An understanding of polymers in flow through micro- and nano-structured materials is critical to the success of bioseparations (proteins, DNA, etc.). An open, nanofluidic system has been developed to drive flow through a packed bed of colloidal particles using capillary forces (wicking), allowing the study of polymer dynamics in the absence of the electric field is typically used to drive micro- and nano-fluidic flows. This is especially important when dealing with charged molecules whose confirmation can be affected by the electric field or those insoluble in water. Single molecule imaging is performed in this system on fluorescently labeled DNA using an optical microscope equipped with a fluorescent light source, image intensifier, and CCD camera. Chain elongation in the flow depends sharply on flow rate, with fully relaxed configurations observed below a critical flow rate. At high flow rates, flow induced degradation can be seen. Molecular entanglements with the separation matrix cause molecular weight separation because longer molecules elongate in the flow and become entangled, leading to a longer retention time. [Preview Abstract] |
Monday, March 13, 2006 1:15PM - 1:27PM |
B26.00009: Abundance of pseudoknots in the RNA world Daniel Aalberts, Evan Miller The pseudoknot fold is often seen in auto-catalytic RNA and in viruses. A recent polymer physics model and statistical-mechanical theory predicts relative probabilities of different pseudoknot folds consonant with a database of known folds. Now we extend that theory for a preliminary estimate of the abundance of pseudoknot folds in RNA sequences, finding approximately 1 per 40,000 nucleotides. This theoretical probability density compares favorably to what we infer from structure databases and has implications for genome organization, RNA folding algorithms, and the RNA World. [Preview Abstract] |
Monday, March 13, 2006 1:27PM - 1:39PM |
B26.00010: DNA sequencing via transverse electronic transport Johan Lagerqvist, Michael Zwolak, Massimiliano Di Ventra Recently, it was theoretically shown that transverse current measurements could be used to distinguish the different bases of single stranded DNA. [1] If electrodes are embedded in a device, e.g., a nanopore, which allows translocation of ss-DNA, the strand can be sequenced by continuous measurement of the current in the direction perpendicular to the DNA backbone. [1] However, variations of the electronic signatures of each base in a real device due to structural fluctuations, counter-ions, water and other sources of noise will be important obstacles to overcome in order to make this theoretical proposal a reality. In order to explore these effects we have coupled molecular dynamics simulations with transport calculations to obtain the real time transverse current of ss-DNA translocating into a nanopore. We find that distributions of currents for each base are indeed different even in the presence of all the sources of noise discussed above. These results support even more the original proposal [1] that fast DNA sequencing could be done using transverse current measurements. Work supported by the National Humane Genome Research Institute. \newline \newline [1] M. Zwolak and M. Di Ventra, ``Electronic Signature of DNA Nucleotides via Transverse Transport'', Nano Lett. 5, 421 (2005). [Preview Abstract] |
Monday, March 13, 2006 1:39PM - 1:51PM |
B26.00011: Polymer effects in forced passage of DNA and macromolecules through nanopores Francisco Solis The forced passage of DNA, RNA and other linear molecules through nanopores has been proposed as a method to investigate the properties of these molecules and, in particular, as a sequencing method. This talk will discuss the polymer effects that arise when a macromolecule is pulled with constant velocity and with adjustable force through a pore. For homogeneous, strongly stretched molecules, the passage rate is proportional but slower than the pulling velocity. In addition, if the molecule contains a set of inhomogeneities that act as well defined obstacles, each of these will exhibit a waiting time for passage, and a relaxation period to return to the steady passage rate. These waiting and relaxation times increase with the length of the segment of already processed molecule. [Preview Abstract] |
Monday, March 13, 2006 1:51PM - 2:03PM |
B26.00012: Mapping the phase diagram of DNA force-induced melting in the presence of DNA intercalators Ioana Vladescu, Micah McCauley, Megan Nunez, Ioulia Rouzina, Mark Williams The interactions between single DNA molecules and different non-covalent binding agents - the classical intercalator ethidium and compounds from the family of ruthenium complexes - are investigated using an optical tweezers instrument and their effects on the structure and mechanical stability of DNA molecules are quantitatively analyzed using a model of force-induced melting. When a single DNA molecule is stretched beyond its normal contour length, a melting phase transition is observed. Drug binding increases the dsDNA contour length, decreases the DNA elongation upon melting, and increases the DNA melting force. At concentrations of intercalator above critical, no force induced melting of dsDNA is possible. The DNA stretching curves map out a phase diagram for DNA melting in the presence of intercalator, and define its critical point in the force-extension-drug concentration space. Our results allow for the complete thermodynamic characterization of the interaction of these intercalators with DNA. [Preview Abstract] |
Monday, March 13, 2006 2:03PM - 2:15PM |
B26.00013: DNA and RNA unzipping using nanopore force spectroscopy Amit Meller, Jerome Mathe, Meni Wanunu, Barak Akabayov, Irit Sagi DNA and RNA molecules can be electrophoreticaly threaded through nanoscale pores, such as the $\sim $1.5 nm alpha-Hemolysin. Information about their translocation dynamics is obtained by probing the ionic current flowing through the pore during their passage. We experimentally study the translocation process of unstructured and structured DNA molecules through a single nanopore. We find that the translocation process depends on DNA properties, such as its sequence and its direction of entry. With intense electrical field structured DNA and RNA can be unzipped in a controlled way, and the unzipping kinetics can be directly quantified. We study the unzipping kinetics of DNA and RNA molecules under a wide range of voltage gradients. We find that the unzipping kinetics is characterized by two limiting regimes: the strong field limit in which the system is unzipped in an irreversible process, and the weak field regime, in which it is in quasi equilibrium. Interestingly the unzipping kinetics of RNA molecules is very different from their DNA analogues. A theoretical model that accounts for our experimental results will be discussed. [Preview Abstract] |
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