Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session S10: Focus Session: Confined Nucleic Acids I |
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Sponsoring Units: DBIO Chair: Robert Riehn, North Carolina State University Room: 201 |
Thursday, March 6, 2014 8:00AM - 8:12AM |
S10.00001: Regimes of DNA confined in a nanochannel Liang Dai, Patrick Doyle Scaling regimes for polymers confined to tubular channels are well established when the channel cross-sectional dimension is either very small (Odjik regime) or large (classic de Gennes regime) relative to the polymer Kuhn length. In the literature, there is no clear consensus regarding the intermediate region and if subregimes even exist to connect these two classic bounding regimes. The confluence of emerging single DNA mapping technologies and a resurged interest in the fundamental properties of confined polymers has led to extensive research in this area using DNA as a model system. Due to the DNA molecule's properties and limitations of nanofabrication, most experiments are performed in this intermediate regime with channel dimensions of a few Kuhn lengths. Here we use simulations and theory to reconcile conflicting theories and show that there are indeed extended de Gennes, partial alignment and hairpin regimes located between the two classic regimes. Simulations results for both chain extension and free energy support the existence of these regimes. [Preview Abstract] |
Thursday, March 6, 2014 8:12AM - 8:24AM |
S10.00002: Modeling the Relaxation Time of DNA Confined in a Nanochannel Yanwei Wang, Douglas R. Tree, Kevin D. Dorfman Using a mapping between a dumbbell model and fine-grained Monte Carlo simulations, we have computed the relaxation time of $\lambda$-DNA in a high ionic strength buffer confined in a nanochannel (Tree {\it et al.}, {\it Biomicrofluidics} {\bf 2013}, {\it 7}, 054118). The relaxation time thus obtained agrees quantitatively with experimental data (Reisner {\it et al.}, {\it PRL} {\bf 2005}, {\it 94}, 196101) using only a single $O(1)$ fitting parameter to account for the uncertainty in model parameters. In addition to validating our mapping, this agreement supports our previous estimates of the friction coefficient of DNA confined in a nanochannel (Tree {\it et al.}, {\it PRL} {\bf 2012}, {\it 108}, 228105), which have been difficult to validate due to the lack of direct experimental data. Furthermore, our calculation shows that as the channel size passes below $\sim$100 nm (or roughly the Kuhn length of DNA) there is a dramatic drop in the relaxation time. Inasmuch as the chain friction rises with decreasing channel size, the reduction in the relaxation time can be solely attributed to the sharp decline in the fluctuations of the chain extension. Practically, the low variance in the observed DNA extension in such small channels has important implications for genome mapping. [Preview Abstract] |
Thursday, March 6, 2014 8:24AM - 8:36AM |
S10.00003: Topological events in single molecules of long genomic DNA confined in nanochannels Jeffrey Reifenberger, Kevin Dorfman, Han Cao ct- We present a rapid genome-wide analysis method based on new NanoChannel Array technology (Irys$^{\mathrm{TM}}$ System) that confines and linearizes extremely long DNA molecules (100 to 1,000 kilobases) for direct image analysis at tens to hundred of gigabases per run. Genomic DNA is stained with YOYO and labeled specifically at the `GCTCTTC' sequence with fluorescent dyes allowing each molecule to be uniquely patterned and mapped to its corresponding reference. This high-throughput platform automates the imaging of such barcoded patterns on genomic DNA to identify wide spread structural variations in a genome. Here we describe a method to rule out possible topologically altered molecules in linear confinement by identifying possible topological events through a T-test looking for spikes in the fluorescence of the YOYO stained DNA backbone. These events are confirmed through aligning the marked individual molecules to a standard reference and measuring a distance differential between labels surrounding the suspected topological event compared to the reference. Such events could be flagged to distinguish from true structural variations. [Preview Abstract] |
Thursday, March 6, 2014 8:36AM - 8:48AM |
S10.00004: Segregation and chain extension of overlapping semiflexible macromolecules in channel Peter Cifra, Dusan Racko Decrease of overall chain extension in channel by local backfolding together with an increased extension of sequences running parallel have been reported to complicate linearization experiments under moderate confinements. Less known related effect occurs in two overlapping chains in channel. Investigation of overlap and segregation of polymer coils in channel was extended here relative to previous studies from flexible to semiflexible chains. Results are based on simulation of confinement free energy of a chain and on direct simulation of coil segregation process. For confinement free energy we confirm the predicted opposite trend with increasing chain stiffness for the weak and strong confinement regimes. Results of two different approaches are consistent, in agreement with theoretical analysis and indicate a stronger segregation tendency of flexible chains relative to semiflexible chains, both in its extent and dynamics. Mutual excluded volume between confined chains leads to extension of overlapping chains along channel and this effect is stronger for flexible chains but weak for stiffer macromolecules such as DNA. Support from Slovak Res. and Develop. Agency (SRDA-0451-11) is acknowledged. D. Racko, P. Cifra, J. Chem. Phys. 138, 184904 (2013) [Preview Abstract] |
Thursday, March 6, 2014 8:48AM - 9:00AM |
S10.00005: Linearization of DNA by a squeezing flow in a tunable nanoscale tube: a simulation study Minsub Han, Byoung Choul Kim, Toshiki Matsuoka, Shuichi Takayama Deoxyribose nucleic acid(DNA) is the biomaterial for storage of genetic information of all living organisms. The linearization of DNA is an initial step in one of the important methods to probe the vital information in biological and clinical settings. Squeezing the solution in flexible nanoscale channel proved to be a highly effective method for fully linearizing DNA (Toshiki et al. Nano Lett 2012). The detailed physical basis of the process is studied by using dissipative particle dynamics simulation, whose results corresponds to the lambda DNA in the nanoscale PDMS channel in the experiment. The squeezing process typically consists of a large degree of elongation by the advective flow, which is followed by recoiling back and adjusting to the narrower confinement. Strong gradient in advection and nanoscale confinement are thus the major thrust for the stretching in the process. The degree of the linearization also depends on the initial position relative to the center in the axial direction as well as the contour length. [Preview Abstract] |
Thursday, March 6, 2014 9:00AM - 9:12AM |
S10.00006: Measuring DNA Confinement and Excluded Volume Parameters: Scaling with confinement and ionic strength Alexander Klotz, Lyndon Duong, Laurence Coursol, Walter Reisner Using nanofluidic devices for genomic mapping requires an understanding of the underlying polymer physics of confined DNA. Despite many years of study, there are still aspects that are poorly understood, including the role that excluded volume and semiflexibility play under confinement. Here, a hybrid nanofluidic device consisting of a narrow slit embedded with a lattice of square pits was used to study confined DNA. At equilibrium, molecules tend to occupy one or more pits. The partitioning of molecular contour between the pits and the slit is dependent on maximizing entropy by removing contour from the highly confining slit while reducing excess free energy due to excluded volume interactions from increased concentration in the pit. Measurements of the average number of occupied pits as a function of pit dimension, slit height, and ionic strength serves as a probe of the underlying polymer physics. In particular, the free energy of slit-like confinement and the effective molecular width were measured across a range of slit heights and ionic strengths. It was found that effective width scales with ionic strength according to Stigter's charged rod theory, and that the Chen-Sullivan interpolation formula for the slit-like energy of confinement describes the data well for narrow slits. Unexpected scaling of the confinement free energy with ionic strength indicates that excluded volume effects are relevant for confined DNA. [Preview Abstract] |
Thursday, March 6, 2014 9:12AM - 9:48AM |
S10.00007: Dynamics of large DNA confined to nanoslits Invited Speaker: Patrick Doyle Microfabricated platforms present a model system to study the conformation and dynamics of DNA in reduced geometries. Slit and tube-like geometries have been widely studied. Slits confine DNA to a quasi-2D or so-called Hele-Shaw geometry. The role of slit confinement on polymer dynamics is not straightforward due to the lack of an intrinsic hydrodynamic screening length. In this talk I will discuss our recent work in understanding DNA conformation and dynamics in slits. We make use of both single molecule experiments and large-scale molecular simulations. This aforementioned work was performed in a good solvent. I will next explore the role of confinement on the coil-globule transition. We show that for modestly poor solvents, the collapse process has two stages and that the duration of both stages is significantly affected by confinement. Our results suggest that the primary effect is not hydrodynamic in nature, but more related to a modification of the free energy landscape. [Preview Abstract] |
Thursday, March 6, 2014 9:48AM - 10:00AM |
S10.00008: On the Odijk regime in nanoslits Wesley Reinhart, Douglas Tree, Kevin Dorfman The physics of polymer confinement has long been a topic of interest as a fundamental problem in soft matter physics. In biaxial confinement such as a tube or channel, there is a well-documented crossover from a regime dominated by flexible polymer blobs to a regime dominated by stiff deflection segments as the confinement length scale becomes much smaller than the persistence length. However, several fundamental questions remain concerning the exact nature of the strongly confined regime in uniaxial confinement in a slit, where the slit height is much smaller than the persistence length of the semiflexible polymer. We have investigated this problem by an off-lattice implementation of a chain-growth Monte Carlo algorithm, the pruned-enriched Rosenbluth method. Using our numerical results, we confirm that there is indeed a regime dominated by deflection segments in slits, and we provide a simple interpretation of the polymer size in this regime. Furthermore, we investigate previous claims in the literature regarding the effect of excluded volume on strongly confined polymers, where we find a connection between the slit geometry and a semiflexible polymer confined to a plane. [Preview Abstract] |
Thursday, March 6, 2014 10:00AM - 10:12AM |
S10.00009: Topological and metric properties of linear and circular DNA chains in nano-slits and nano-channels Enzo Orlandini, Cristian Micheletti Motivated by recent advancements in single DNA molecule experiments, based on nanofluidic devices, we investigate numerically the metric and topological properties of a modelof open and circular DNA chains confined inside nano-slits and nano-channles. The results reveal an interesting characterization of the metric crossover behaviour in terms of the abundance, type and length of occuring knots. In particular we find that the knotting probability is nonmonotonic for increasing confinement and can be largely enhanced or suppressed, compared to the bulk case, by simply varying the slit or channel trasversal dimension. The observed knot population consists of knots that are far simpler than for DNA chains in spherical (i.e. cavities or capsids) confinement. These results suggest that nanoslits and nanochannels can be properly designed to produce open DNA chains hosting simple knots or to sieve DNA rings according to their knotted state. Finally we discuss the implications that the presence of knots may have on the dynamical properties of confined DNA chains such as chain elongation, injection/ejection processes and entanglement relaxation. [Preview Abstract] |
Thursday, March 6, 2014 10:12AM - 10:24AM |
S10.00010: Convex Lens-Induced Nanoscale Templating Daniel Berard, Francois Michaud, Christopher McFaul, Sara Mahsid, Walter Reisner, Sabrina Leslie We demonstrate a new platform, ``Convex Lens-Induced Nanoscale Templating'' (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of actively transforming a macroscale flow-cell into a nanofluidic device without need for high-temperature direct bonding, leading to ease of sample loading and greater accessibility of the surface. Moreover, as DNA molecules present in the gap will be driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields necessitated by direct bonded nanofluidic devices for loading DNA in the confined structures. To demonstrate the versatility of CLINT, we confine DNA to nanogroove structures, demonstrating DNA nanochannel-based stretching. Using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub 30nm nanochannels, achieving high stretching (90\%) that is in good agreement with Odijk deflection theory. [Preview Abstract] |
Thursday, March 6, 2014 10:24AM - 10:36AM |
S10.00011: Fluctuations of DNA Mobility in Nanofluidic Entropic Traps Lingling Wu, Stephen Levy We studied the mobility of DNA molecules driven by an electric field through a nanofluidic device containing a periodic array of deep and shallow regions termed entropic traps. Since the depth of the shallow region is smaller than the DNA equilibrium size, DNA molecules are trapped for a characteristic time and must deform themselves to traverse the boundary between deep and shallow regions. Consistent with previous experimental results, we observed a nonlinear relationship between mobility and electric field strength and that longer DNA molecules have higher mobility. In repeated measurements under seemingly identical conditions we measured fluctuations in the mobility significantly larger than expected from statistical variation. The variation was most pronounced for lower electric field strengths where the trapping time is considerable relative to the drift time. To determine the origin of these fluctuations, we investigated the dependence of the mobility on several variables: DNA concentration, ionic strength, fluorescent dye staining ratio, ionic current, and electroosmotic flow. The mobility fluctuations were not strongly correlated with these variables within the ranges in which they were varied. [Preview Abstract] |
Thursday, March 6, 2014 10:36AM - 10:48AM |
S10.00012: Hindered DNA coordinated motion in nanochannels Yeng-Long Chen, Yu-Hui Lin, Dmytro Luzhbin We investigate the relaxation dynamics of long DNA molecules confined in micro- and nano-channels with Brownian dynamics simulations. Prior experiment by Reisner et al. found that the stretch fluctuation correlation time ($t_{relax}$) of DNA molecules in nanochannels increases as the channel height ($H$) decreases for $H$ greater than the DNA Kuhn length ($\sigma_k$), and $t_{relax}$ decreases as $H$ decreases for $H < \sigma_k$. Our simulations capture this behavior, and quantitatively agree with the experimental results within the error bars. The scaling-law dependence of $t_{relax}$ on $H$ in different regimes is verified. Rouse mode analysis of the chain relaxation mechanism further shows that segmental relaxation on length scale longer than $\sigma_k$ are hindered and the dynamics of segments shorter than $H$ dominate the chain relaxation processes. We also find that the inclusion of intra-chain hydrodynamic interactions affect segmental relaxation. The implications for DNA translocation through nanopores and nanochannels are discussed. [Preview Abstract] |
Thursday, March 6, 2014 10:48AM - 11:00AM |
S10.00013: Experimental Test of the Wormlike Chain Model for Confined DNA Damini Gupta, Julian Sheats, Abhiram Muralidhar, Jeremy J. Miller, Derek E. Huang, Kevin D. Dorfman, Walter Reisner We present experimental validation of a wormlike osculating-sphere model for double-stranded DNA. Single molecule fluorescence imaging of $\lambda $-DNA (48,500 base pairs) in rectangular nanochannel confinement was performed to measure the ensemble of molecule extensions in a low ionic strength buffer. The mean and variance of the extension furnish the parameters of the effective Hookean spring description of the chain extension. The geometric means of the channel widths range from 100 nm to 316 nm, thereby probing the transition between Odijk and de Gennes regimes in nanochannel sizes ranging from approximately 1.5 to 5 times the DNA persistence length. We found a steep drop in the variance of the extension as the channel size decreased in these channels. Our experimental results are in strong quantitative agreement with Pruned-Enriched Rosenbluth Method simulations using the wormlike osculating-sphere model in rectangular channels, where the only fitting parameter is the stained DNA contour length.~ [Preview Abstract] |
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