Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session A25: DNA-based Soft Matter: Design, Dynamics, and Active Mechanics IFocus Recordings Available
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Sponsoring Units: DSOFT DPOLY Chair: Rae Anderson, University San Diego Room: McCormick Place W-187A |
Monday, March 14, 2022 8:00AM - 8:36AM |
A25.00001: An active DNA liquid Invited Speaker: Omar A Saleh We seek to create self-assembled biomolecular liquid droplets that act as rough mimics of biological condensates, and to engineer mesoscopic structure and active functions into the droplets through molecular design. We form liquids from DNA nanostars, multi-armed DNA particles that condense through base-pairing interactions, forming liquids due to the nanostars’ internal flexibility and relatively weak bonding. These liquids show certain materials properties similar to biological condensates, while also displaying unique properties arising from their limited valence and semi-rigid, double-stranded arms. I will discuss methods we are pursuing to drive nanostar liquid droplets out of equilibrium through designed interactions with proteins and other nucleic acids. |
Monday, March 14, 2022 8:36AM - 8:48AM |
A25.00002: Flatness and Intrinsic Curvature of Linked-Ring Membranes James M Polson, Edgar J Garcia, Alexander R Klotz Recent experiments have elucidated the physical properties of kinetoplasts, which are chain-mail-like structures found in the mitochondria of trypanosome parasites formed from catenated DNA rings. Inspired by these studies, we use Monte Carlo simulations to examine the behavior of two-dimensional networks ("membranes'") of linked rings. For simplicity, we consider only identical rings that are circular and rigid and that form networks with a regular linking structure. We find that the scaling of the eigenvalues of the shape tensor with membrane size are consistent with the behavior of the flat phase observed in self-avoiding covalent membranes. Increasing ring thickness tends to swell the membrane. Remarkably, unlike covalent membranes, the linked-ring membranes tend to form concave structures with an intrinsic curvature of entropic origin associated with local excluded-volume interactions. The degree of concavity increases with increasing ring thickness and is also affected by the type of linking network. The relevance of the properties of linked-ring model membranes to those observed in kinetoplasts is discussed. |
Monday, March 14, 2022 8:48AM - 9:00AM |
A25.00003: Employing artificial neural networks to find reaction coordinates and pathways for self-assembly Jörn H Appeldorn, Arash Nikoubashman, Thomas Speck, Simon Lemcke Capturing the autonomous self-assembly of molecular building blocks in computer simulations is a persistent challenge, requiring to model complex interactions and to access long time scales. Advanced sampling methods allow to bridge these time scales but typically require constructing accurate low-dimensional representations of the transition pathways. In this work, we study the self-assembly of two single-stranded DNA (ssDNA) fragments into a ring-like structure, considering two cases with either symmetric or asymmetric ssDNA base sequences. We perform a time-lagged independent component analysis (TICA) for these systems, and demonstrate how autoencoder architectures based on unsupervised neural networks can be employed to reliably expose transition pathways and to provide a suitable low-dimensional representation. We find that the assembly occurs as a two-step process through distinct half-bound states, which are correctly identified by the TICA representation and the neural net. We use the representations to construct a Markov State Model for predicting the four molecular conformations and their transitions. Our work opens up new avenues for the computational modeling of multi-step and hierarchical self-assembly, which has proven challenging so far. |
Monday, March 14, 2022 9:00AM - 9:12AM |
A25.00004: DNA Hybridization Tunes Hierarchical Assembly of Supramolecular Copolymers Ronit Freeman In nature, the reversible supramolecular organization of biomolecules from the nanoscale to the macroscale creates functional structures that regulate key biological processes. Howvere, it remains challenging to tune hierachical assembly in synthetic analogs. Here, we report on DNA-decorated supramolecular brush nanofibers, where DNA base-pairing drives the hierarchical assembly of the peptide-DNA brush nanofibers. We tune hierarchy in the peptide-DNA material by designing peptide-DNA duplexes with varying stability and junction type. We also tune the reconfiguration of the material by controllably disrupting the amount of DNA hybridization between brush fibers using a chemical trigger. Finally, we demonstrate how this biomolecular reconfiguration can be used for the incremental release of a protein payload. This peptide-DNA platform provides a way to tune both hierarchical morphologies and stimuli responsiveness through material design. |
Monday, March 14, 2022 9:12AM - 9:24AM |
A25.00005: Kinetoplast DNA: topology and hydrodynamics of molecular chainmail Alexander R Klotz, Joshua Ragotskie, Dave Holling, Kyle Covington, Jin Jeon DNA topology is usually categorized into linear and circular molecules, with the latter having varying degrees of supercoiling. A much more complex DNA topology is found in the mitochondria of trypanosome parasites, which cause diseases such as Sleeping Sickness and Leishmaniasis. Their mitochondrial DNA consists of thousands of topologically connected loops, forming a two-dimensional but spatially curved network known as a kinetoplast, which can be thought of as "molecular chainmail." Much like linear DNA has served has a model polymer for several decades, kinetoplasts provide the opportunity to study the physics of exotic types of materials, including two dimensional materials and "Olympic gels," which are held together by topological rather than covalent bonds. In this talk, I will summarize what is known about the biology and topology of kinetoplast networks and overview recent work exploring the polymer physics of kinetoplasts in solution. Finally, I will highlight recent experiments attempting to measure the percolation threshold of kinetoplast networks through destructive testing, as well as efforts to explore the fluid mechanics of therse two-dimensional elastic objects. |
Monday, March 14, 2022 9:24AM - 9:36AM |
A25.00006: Topologically Active DNA with ATP-driven Ligation Maria Panoukidou, Simon Weir, Davide Michieletto DNA ligation is a vital biological process that consumes energy to repair double-strand DNA breaks by ATP-driven DNA end-joining reactions. While engineered ligase enzymes are now routinely used in cloning, their role as material actuators is elusive. Here, we design and investigate -via combined experimental and theoretical approaches- complex fluids made of DNA molecules that undergo ATP-driven ligation. Using a pulse field gel electrophoresis and (micro)rheology, we characterise the temporal evolution of the fluid’s elastic and viscous behaviours. Our findings are then rationalised by considering a modified Smoluchowski coagulation equation and coarse-grained living polymer simulations. Our work, inspired by the biology of DNA repair, offers a way to realise non-equilibrium “topologically active” complex fluids that can pave the way for responsive and adaptive materials. |
Monday, March 14, 2022 9:36AM - 9:48AM |
A25.00007: Diffusion of DNA-coated colloids on DNA coated surface Jeana Zheng, David J Pine DNA-coated colloids can self-assemble and crystalize into a wide variety of structures. In order |
Monday, March 14, 2022 9:48AM - 10:00AM |
A25.00008: Transcriptional regulation of DNA liquid phase separation Sam Wilken, Gabrielle R Abraham, Omar A Saleh The formation and control of membraneless compartments inside cells is integral to cell function. Multivalent DNA nanoscale particles, called nanostars, self-assemble via Watson-Crick base pairing into micron-sized membraneless liquid droplets. We have developed a nanostar system where the liquid-liquid phase separation is regulated in situ via transcription. Investigating the interplay between phase separation and transcriptional regulation will elucidate how real cells use phase separation to compartmentalize complex biomolecular reactions. |
Monday, March 14, 2022 10:00AM - 10:12AM |
A25.00009: Non-equilibrium microrheology of topologically-active DNA solutions Philip D Neill, Natalie Crist, Karthik Peddireddy, Davide Michieletto, Rae M Robertson-Anderson DNA, which naturally occurs in linear, ring, and supercoiled topologies, frequently undergoes enzyme-driven topological conversion and fragmentation in vivo, enabling it to perform a variety of functions within the cell. In vitro, highly concentrated DNA polymers form entanglements that yield viscoelastic properties dependent on the topologies and lengths of the DNA. Enzyme-driven alterations of DNA size and shape therefore offer a means of designing active materials with programmable viscoelastic properties. Here, we incorporate enzymes into dense DNA solutions to linearize and fragment circular DNA molecules. We use optical tweezers microrheology to measure the time-dependent linear and nonlinear viscoelastic properties over the course of enzymatic digestion. We show that these 'topologically-active' fluids initially thicken after which they undergo gradual and non-monotonic thinning with enhanced athermal fluctuations. In future work, we will examine different DNA lengths, topologies, and types of enzymes to create a class of non-equilibrium reconfigurable fluids with applications from drug delivery and wound-healing to infrastructure repair. |
Monday, March 14, 2022 10:12AM - 10:24AM |
A25.00010: Computational simulation of DNA origami with plasmonics nanoparticle. Pin-Yi Li, Christopher Maffeo, Aleksei Aksimentiev Self-assembled DNA systems provide low-cost, programmable control over matter at the nanoscale. One of the most promising frontiers involves coupling self-assembled DNA nanostructures, such as DNA origami, to plasmonic nanoparticles, which exhibit resonant response to excitation in the visible spectrum that may be useful for both molecular sensings and force transduction applications. To decrease the experimental cost, computational simulations are often desired. However, few simulations combining DNA origami and nanoparticles with plasmonic effects have been made. Here, we present a method to simulate the dynamics of DNA origami combined with gold nanoparticles. Our method works by iteratively evaluating the optical properties of nanoparticles using the finite element method and then coupling the result to atomic resolution Brownian dynamics (ARBD) simulations that capture the fluctuations of the DNA nanostructure using a particle-based coarse-grained MD description. Hence, the developed workflow can be used to model dynamic DNA origami nanostructures where light is used to power and direct nanoscale motion. |
Monday, March 14, 2022 10:24AM - 10:36AM |
A25.00011: Unzipping of a double-stranded block copolymer DNA by a periodic force Ramu K Yadav Using Monte Carlo simulations, |
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