Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session Q18: Single-Molecule Characterization of Polymers and Soft Matter II: Nanoconfinement and Complex TopologiesRecordings Available
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Sponsoring Units: DPOLY Chair: Alex Klotz, California State University, Long Beach Room: McCormick Place W-184D |
Wednesday, March 16, 2022 3:00PM - 3:12PM |
Q18.00001: Statistics of Gaussian Polymer Chains in Quadratic Applied Fields John P Mikhail, Gregory C Rutledge This work derives statistics for a continuous Gaussian chain exposed to multidimensional, quadratic applied fields. Results include closed-form expressions for the partition function, moment generating function of the spatial distribution, total and potential energies, and radius of gyration of the chain. The sensitivity of the statistics to different initial distributions, chain lengths, and field strengths is discussed. The result is shown to be consistent with Monte Carlo simulations of discrete Gaussian chains for a wide logarithmic range of the aforementioned input parameters. The general nature of both the potential and the chain model allows for a variety of applications, including polymer confinement in a tube or channel, response of a polymeric material to traveling waves, etc. |
Wednesday, March 16, 2022 3:12PM - 3:24PM |
Q18.00002: Simulation studies of nonequilibrium dynamics of charged motifs in a dual nanopore device Arthur Rand, Walter W Reisner, Robert Sladek, William Dunbar, Aniket Bhattacharya Accurate detection of DNA motifs has essential applications in taxonomical research, conserving biodiversity, characterizing unknown species, identifying disease vectors, authenticating herbal products, and unambiguously labeling food specimens. We use Brownian dynamics simulation to study the detailed translocation process of a coarse-grain DNA scanning through a double nanopore setup using an extended electric field. We use a 48kbp long dsDNA with seven motifs (spherical/elongated) with different partial change content. Our study explains the origin of the asymmetric distribution of the dwell time observed experimentally in lambda-phage DNA with seven motifs (X. Liu et al., Small 2020). We demonstrate that the electric field inside and beyond the pores is critical to discriminate protein tags based on their effective charges and can be a viable method directly applicable to experiments. Our mesoscopic simulation provides a complete description of the time-of-flight velocity variation along the chain arising from the non-equilibrium tension propagation in presence of the extended electric field. |
Wednesday, March 16, 2022 3:24PM - 3:36PM |
Q18.00003: Nonlinear Electrophoretic Velocity of DNA in Slitlike Confinement Michael Lamontagne, Stephen Levy We have applied zero-time-averaged alternating electric fields to DNA molecules in cross-shaped nanofluidic slits. We observed a net drift of DNA molecules, the magnitude of which depends on the square of the electric field amplitude. From the rate of accumulation of DNA at the center of the device, we derive an estimate for the second order electrophoretic mobility, μ2. We observe that μ2 depends on such parameters as the frequency of the alternating fields, the slit height, and DNA contour length. The observation of a nonzero μ2 suggests that frequency dependent electrophoretic DNA separation by length is achievable with high amplitude alternating electric fields in the absence of a sieving matrix. |
Wednesday, March 16, 2022 3:36PM - 3:48PM |
Q18.00004: Interactions between two knots in nanochannel-confined DNA molecules Zixue Ma, Kevin D Dorfman Long polymers such as DNA can form composite knots in the polymer chains. The interaction between two knots in DNA molecules remains an open question: Do the knots stay separated or do they attract one another? We will present experimental data on knot-knot interactions in single DNA molecules under nanochannel confinement. We observed that widely separated knots predominantly undergo independent random walks but, when in close proximity, knots attract each other but only remain in close contact for several seconds. The corresponding free energy landscape shows that the separated knot state is more stable than the intertwined knot state, in which the knots have a separation distance of approximately zero. Our experimental observation contradicts observations of knot-knot interactions under tension in flow, where the knots experience an attraction and then can stay in proximity for a much longer time. |
Wednesday, March 16, 2022 3:48PM - 4:00PM |
Q18.00005: Phase Transition of Catenated DNA Networks in Poly(ethylene glycol) Solutions Indresh Yadav, Dana Al Sulaiman, Beatrice Soh, Patrick Doyle Conformational phase transitions of macromolecules are an important class of problems in fundamental polymer physics. While the conformational phase transitions of linear DNA have been extensively studied, this feature of topologically complex DNA remains unexplored. We studied the polymer-and-salt-induced (psi) phase transition of kinetoplasts, using single-molecule fluorescence microscopy. A single kinetoplast molecule from Crithidia fasciculata is a giant planar network of thousands (~ 5000) of catenated circular DNAs. We observe that kinetoplasts can undergo a reversible phase transition from the flat to the collapsed phase in the presence of NaCl as a function of the concentration of crowding agent poly(ethylene glycol). The nature of this phase transition is tunable through varying ionic strength. For linear DNA, the co-existence of coil and globule phases was attributed to a first order phase transition, associated with a double well potential in the transition regime. In contrast, kinetoplasts navigate from the flat to the collapsed phase by passing through an intermediate regime, characterized by the co-existence of a thermodynamically stable multi-population with varying shapes and sizes. Long temporal stability of the multi-population in the transition regime suggests a rugged energy landscape. |
Wednesday, March 16, 2022 4:00PM - 4:12PM |
Q18.00006: Translocations of topologically linked rings from kinetoplast DNA through a solid-state nanopore Sierra Breyer, Alexander R Klotz A nanopore sensor measures the ionic current through a solid-state pore over time. DNA molecules translocating through a nanopore results in the displacement of the current, which depends on the size, topology, and conformation of each molecule. Topologically complex DNA structures such as knots have been observed in nanopores, but topologically linked catenanes have only been studied computationally. Kinteoplasts are complex DNA structures formed from several thousand topologically interlocked circles, found in the mitochondria of trypanosome parasites. The kinetoplast can be broken down into smaller complex shapes through an enzyme reaction, allowing simpler catenanes to be isolated from the network. We use a solid-state nanopore device to observe complex topologies, such as Hopf links, isolated from kinetoplasts from Crithidia fasciculata. Here, we present preliminary observations of the translocation signal and dwell time associated with catenated molecular topologies, and the implications for understanding topological friction in polymers and for determining kinetoplast topology. |
Wednesday, March 16, 2022 4:12PM - 4:24PM |
Q18.00007: DNA Nunchucks: Nanoinstrumentation for Dynamic, Single-Molecular Characterization of DNABending Xinyue Cai, Deborah K Fygenson The dynamic bending of a double-stranded DNA (dsDNA) sequence is an essential aspect of its structure and biological function that is rarely characterized because direct measurement, even at the single-molecule level, can be difficult and time consuming. The DNA nunchuck is an origami-based instrument that makes the single-molecule bend fluctuations of short dsDNA sequences visible using fluorescence microscopy. Nunchuck data reveal that even "generic" dsDNA, containing no special bend-inducing sequences, regularly explore meta-stable bent states. For dsDNA containing a bend-inducing sequence, such as the 6-thymine DNA "bulge", nunchucks reveal the complete landscape of bent states, and a significantly higher frequency of transitions between bent and straight states compared to well-paired dsDNA. Bent state duration distribution shows that nunchucks have the temporal resolution to detect bend states that persist for only a few seconds. |
Wednesday, March 16, 2022 4:24PM - 4:36PM |
Q18.00008: Expanding the Molecular Alphabet of DNA Data Storage Systems with Single-molecule Nanopore Readout Kasra Tabatabaei, Charles M Schroeder, Olgica Milenkovic, Chao Pan, Aleksei Aksimentiev, Jingqian Liu, Bach Pham, Min Chen, Shubham Chandak, Alvaro G Hernandez, Spencer A Shorkey DNA is a promising next-generation data storage medium, however, the recording latency and synthesis cost of DNA oligos using the four natural nucleotides remain high. In this talk, we describe a new DNA storage system that uses an extended 11-letter molecular alphabet combining natural and chemically modified nucleotides. Experimental results involving a library of 77 oligo sequences show that one can readily discriminate different combinations of monomers using single-molecule detection with MspA nanopores. We further demonstrate full nanopore sequencing of hybrid synthetic DNA oligos using commercial Oxford Nanopores by developing a custom neural network architecture to classify raw current signals, yielding an average accuracy exceeding 60%, which is 39 times higher than random guessing. Molecular dynamics simulations show that most chemically modified nucleotides do not induce dramatic disruption of the DNA double helix, which suggests that the extended alphabet is compatible with PCR-based random access data retrieval. Broadly, these methodologies provide a forward path for new implementations of molecular recorders. |
Wednesday, March 16, 2022 4:36PM - 4:48PM |
Q18.00009: Nanopore genomic mapping using single-strand binding protein Alexander R Klotz, Nathan Howald Nanopore sequencing measures the electrical signal associated with the translocation of long strands of DNA through a nanoscale pore. Base-level sequencing is possible with biological pores, but long times and high parallelization are required compared to solid-state nanopores. Rapid genomic mapping technologies have been developed that image the AT content of DNA molecules confined in nanochannels. Here, we develop an assay to combine the speed of nanochannel mapping with the portability of solid-state nanopores for rapid point-of-care genomics. We heat DNA to the sequence-dependent denaturation point of it's AT bonds and introduce a single-strand binding protein (SSB) that will bind the open AT bond sites. This binding protein provides a large blockade signal as it translocates through the nanopore, allowing us to map the DNA and create a barcode of AT density along the molecule. Here, we present preliminary results from standard reference genomes and discuss the physics of DNA-SSB complexes. |
Wednesday, March 16, 2022 4:48PM - 5:00PM |
Q18.00010: Genome Mapping using a Dual Nanopore Device Walter W Reisner, Xavier Capaldi, Arthur Rand, Philip Zimny, Roland Nagel, Chaitra Telang, Justin Mollison, Aaron Bruns, Emily Leff, An Vuong, Swarnadeep Seth, Aniket Bhattacharya, William Dunbar We have developed a dual nanopore device that features feedback-driven dynamic control over single translocating dsDNA. In this device, active control logic “catches molecules in the act” of translocating between two closely separated pores. The molecules are halted in a “tug-of-war” configuration whereby a molecule experiences competing electrophoretic forces generated by the two pores. The control logic is then used to dynamically adjust the opposing forces to scan the DNA molecule back and forth (“DNA flossing”). We will discuss recent new results from our dual-pore system and accompanying simulations, including improvements such as zoom scanning and recapture protocols that enable acquisition of a tremendous degree of statistics from a captured single labeled DNA. We will next discuss bioinformatic approaches that enable alignment of single-molecule dual-pore scans and construction of consensus alignments with application to intermediate size genomes, such as E. Coli. |
Wednesday, March 16, 2022 5:00PM - 5:12PM |
Q18.00011: Orientational fluctuations and bimodality in semiflexible nunchucks Panayotis Benetatos, Mohammadhosein Razbin Semiflexible nunchucks are block copolymers consisting of two rather stiff arms linked together with a softer polymer segment. Recently, nunchucks consisting of DNA nanorods linked with a segment of dsDNA have been used as a tool to measure the bending stiffness of dsDNA (Fygenson et al., Nano Lett. 2020). The same geometry also appears in dsDNA with a hinge defect (e.g., a long lived bubble) or in end linked F-actin filaments. In this talk, we present a theoretical analysis of the conformational fluctuations of this system. In particular, we focus on the bimodality in the transverse fluctuations of the free end of a grafted nunchuck. We also consider a nunchuck under tension and show the emergence of bimodality in the elastic response as a function of the hinge position. |
Wednesday, March 16, 2022 5:12PM - 5:24PM |
Q18.00012: Organized States Arising from Compression of Single Semi-Flexible Polymer Chains in Nanochannels Lili Zeng, Walter W Reisner We use molecular dynamics (MD) simulation to probe the non-equilibrium physics of single nanochannel-confined semi-flexible polymers in a homogeneous flow field. The flow field compresses the polymer against the end of the nanochannel, simulating an experiment of a nanochannel confined chain compressed against a slit barrier. For sufficiently stiff chains inside a cylindrical channel, we observe that the flow-based compression gives rise to a packing of the chain against the channel end that possesses a striking organization, consisting of interweaving of hairpin folds and circular coils along the channel walls. At low flow, we find that the organization is dominated by repeated folds. At higher flow, we observe that circular coils arise along with the folds, with folding and coiling domains becoming interwoven at the highest flow speeds. Notably, such chain organization starts appearing even when the chain persistence length is only on order of the channel width. We show that the global polymer organization, consisting of a number of defined folds and coils, arises from the minimization of the total chain free energy. |
Wednesday, March 16, 2022 5:24PM - 5:36PM |
Q18.00013: Polymer Ejecting from a Cavity through a Nanochannel into a Semi-Infinite Space Pai-Yi Hsiao The outstanding problem of a polymer ejecting spontaneously from a confining cavity into an outer semi-space through a nanochannel is investigated. A two-stage model, which divides the process into the confined and the non-confined stages, is developed. By using the Onsager's variational principle, ejection velocity is derived in the two stages. The decrease of the number of the monomers in the cavity can be calculated by solving the kinetics equations. The scaling properties of the ejection velocity and the ejection time are carefully studied. The theory is then verified by performing molecular dynamics simulations. We vary systematically the chain length and the cavity size, and explore the scaling behaviors over the entire parameter spaces. An astonishing stalling behavior is observed at the beginning of a process. We are able to identify the behavior as a pre-stage related to the transportation of the heading monomers through the channel. By varying the channel length, we show that the pre-stage is analogous to a nucleation process and can be treated as a Kramers escape problem. After the pre-stage, the ejection process goes smoothly and can be properly described by the two-stage model. Physical pictures behind different ejection conditions are stated. This study provides deep insight into the complicated phenomena of biopolymer ejection occurred in nature and in applications. |
Wednesday, March 16, 2022 5:36PM - 5:48PM |
Q18.00014: Entropic localization of multiple plasmids in a nanofluidic compartment Zezhou Liu, Xavier Capaldi, Lili Zeng, Yuning Zhang, Rodrigo Reyes-Lamothe, Walter W Reisner Bacteria typically have multiple copies of plasmids distributed in the compact intracellular environment. In vivo studies show that plasmids are not distributed randomly, instead they form clusters at the nucleoid circumference. Here, using a nanofluidic system that enables confinement variation based on pneumatic actuation of a thin membrane lid, we confine multiple plasmids along with a larger DNA molecule inside nano-compartments of varying anisotropy. The plasmids and larger DNA are differentially stained so they can be differentiated within the confined volume. We find that polymer-polymer excluded volume interactions combined with interaction with the compartment boundary lead to a spontaneous organization mimicking the biological system, with plasmids preferring the compartment periphery and poles. Increasing the compartment anisotropy leads to a stronger polar preference. In addition, we explore the effect of adding small molecules (dextran) to simulate the effect of molecular crowding. |
Wednesday, March 16, 2022 5:48PM - 6:00PM |
Q18.00015: Current fluctuations in nanopores reveal the polymer-wall adsorption potential Stuart F Knowles, Alice L Thorneywork Modification of surface properties by polymer adsorption is a widely used technique to tune interactions in molecular experiments such as nanopore sensing. Here, we explore passive adsorption of neutral polymers to the surface of glass nanopores by studying the fluctuations in the ionic current. We find a characteristic change in the spectral density of current fluctuations upon the introduction of polyethylene glycol (PEG) to the pore, however, this noise increase depends sensitively on both salt concentration and polymer length. By systematically varying these two parameters and combining our experimental results with Monte Carlo simulations we confirm the source of the noise as transient polymer adsorption. Furthermore, we use this analysis to infer details of the adsorption potential, yielding significant insight into surface interactions within the pore. This paves the way to in-situ characterisation of functionalised nanopores, and highlights the detailed and fundamental insight that noise analysis provides into molecular adsorption phenomena. |
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