Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session K07: DNA-based Soft Matter: Design, Dynamics, and Active Mechanics IFocus
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Sponsoring Units: DSOFT Chair: Rae Robertson-Anderson, University San Diego Room: Room 130 |
Tuesday, March 7, 2023 3:00PM - 3:36PM |
K07.00001: Deborah Fygenson Invited Speaker: Deborah K Fygenson
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Tuesday, March 7, 2023 3:36PM - 3:48PM |
K07.00002: Dynamic concatenation leads to anomalous transport of ring DNA in concentrated solutions Juexin Marfai, Philip D Neill, Ryan J McGorty, Rae M Robertson-Anderson Circular DNA polymers have been widely studied due to their biological relevance as well as the unique anomalous transport properties and viscoelasticity that concentrated solutions of ring DNA and their blends with linear DNA exhibit. We previously showed that in situ linearization and fragmentation of ring DNA via restriction enzymes leads to discrete thickening and thinning of DNA complex fluids and their composites with dextran. Here we use topoisomerase II to dynamically concatenate ring DNA, forming Olympic ring structures reminiscent of kinetoplasts. We visualize the fluorescent-labeled DNA rings comprising the concatemers and use particle tracking and differential dynamic microscopy to characterize the dynamics and time-varying size and shape of the actively linking and unlinking molecules. Beyond the insight our work provides to biological processes mediated by active restructuring of DNA, the complex fluids we engineer and study may have applications in the design of biocompatible active materials for cellular repair, toxin filtration and drug delivery. |
Tuesday, March 7, 2023 3:48PM - 4:00PM |
K07.00003: Non-equilibrium viscoelasticity driven by dynamic concatenation of ring DNA Philip D Neill, Juexin Marfai, Cindy Sumair, Ryan J McGorty, Rae M Robertson-Anderson Topoisomerases can cleave, twist, untwist and reconnect ring DNA to enable diverse biological processes including DNA replication and repair, as well as the formation of concatenated structures such as kinetoplasts. At the same time, dense solutions of topologically-varying DNA have been shown to exhibit unique viscoelastic properties that can be tuned by DNA concentration, size and topology. Here, we use dynamic light scattering and particle-tracking microrheology to characterize the non-equilibrium viscoelastic properties of dense solutions of ring DNA undergoing dynamic concatenation via the linking and unlinking action of Topoisomerase II. We show that the frequency-dependent viscoelastic properties of these active Olympic ring hydrogels can be precisely tuned by varying the size and concentration of the DNA rings as well as the rate at which Topoisomerase II links and unlinks the DNA. Future work will build on this bio-inspired platform by incorporating additional enzymes that fragment and ligate DNA for in situ alteration of DNA length. |
Tuesday, March 7, 2023 4:00PM - 4:12PM |
K07.00004: Time-varying stress response and deformation dynamics of topologically-active DNA solutions Karthik Peddireddy, Philip D Neill, Juexin Marfai, Ryan J McGorty, Rae M Robertson-Anderson Out-of-equilibrium materials that can autonomously alter their rheological and structural properties are at the forefront of active matter and materials engineering research. However, using the topological conversion of the material constituents as a route towards active restructuring and rheological state changes in materials remains underexplored. We recently demonstrated that in situ topological conversion of DNA via restriction enzymes can drive diverse time-varying rheological properties of entangled DNA solutions and composites that depend non-trivially on the lengthscale of the measurement. Yet how the stress response and material deformations propagate across these lengthscales, and how these dynamics depend on the rate of nonlinear straining remains elusive. Here, we use our recently established OpTiDDM (Optical Tweezers integrating Differential Dynamic Microscopy) methods to investigate the spatiotemporally varying rheology and deformation dynamics of topologically-active circular DNA solutions undergoing enzymatically driven linearization and fragmentation. We couple the nonlinear force response to the deformation dynamics and stress propagation field and show that these couplings depend non-trivially on the spatiotemporal scales of the measurements and the DNA concentration. |
Tuesday, March 7, 2023 4:12PM - 4:24PM |
K07.00005: Using DNA Nanostars to Program the Crystallization of DNA-Coated Colloids Adrian Koretsky, Thomas E Videbaek, W. Benjamin Rogers
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Tuesday, March 7, 2023 4:24PM - 4:36PM |
K07.00006: Self-assembly of DNA origami nanoparticles into 2D tiling patterns Daichi Hayakawa, Thomas E Videbaek, W. Benjamin Rogers Self-assembly is a promising strategy for building functional nanoscale structures. Recent developments in molecular engineering, especially DNA nanotechnology, allow us to create complex nanoscale building blocks, opening up possibilities to create diverse patterns and geometries through self-assembly. However, as the assembly complexity increases, the number of unique sets of specific interactions quickly diverges, often hindering the exploration of the full breadth of accessible structures. In this talk, I will show how orthogonal local interactions lead to rich geometrical patterns, and that such patterns can be assembled in experiment using DNA origami nanoparticles. By enumerating all deterministic patterns accessible using up to four species of triangular building blocks that interact edge to edge, we find a zoo of 2D patterns, including fully addressable structures, linear tilings, and planar tilings. To characterize the assembly of these patterns in experiment, we design triangular subunits from DNA origami, which are each 50 nm in size, and encode specific interactions between their edges using sticky ends. We find that by tuning the interaction strength between edges, thousands of particles can crystallize into a single triangular sheet spanning microns in size. We also succeed in assembling noncanonical tiling patterns using multiple species of triangles, which enables us to control the relative location and orientation of triangles in a micron-scale object. |
Tuesday, March 7, 2023 4:36PM - 4:48PM |
K07.00007: Colloidal Droplet Chemistry with Mobile Interfaces Nicolas Judd, Angus McMullen, Sascha Hilgenfeldt, Jasna Brujic The self-assembly of DNA-functionalized colloids into complex architectures has wide ranging applications from the small-scale manufacture of novel materials to the mimicking of biological binding processes for controlled study. Here we derive a theoretical adhesion model for mobile surface linkers and test it using Brownian DNA-labeled oil droplets in water. The theory takes into account the molecular properties of DNA binders, the entropic penalties associated with binding, and the elasticity of emulsion interfaces, in order to predict the self-assembly of the resulting droplet clusters. The fact that binders can rearrange between droplet-droplet adhesion patches results in free energy minima that correspond to thermodynamically stable colloidal "molecules" of prescribed architecture. In chemistry, when a molecule reacts with another one, it changes its valence according to the rules of quantum mechanics. Analogously, a droplet can change its preferred valence upon binding with a droplet with a different concentration of DNA. This mechanism leads to programmable changes in the colloidal assemblies that are governed by the statistical mechanics of mobile DNA linkers. The theory covers the undeformed and the deformed droplet regime, as a function of surface tension, with applications spanning solid colloids with liquid interfaces, emulsions, all the way to liposomes and cellular membranes. |
Tuesday, March 7, 2023 4:48PM - 5:00PM |
K07.00008: A Temperature-dependent Dynamic Binding Protocol to study Folding of Colloidomers Gaurav Mitra Linear 'colloidomer' chains formed from droplets functionalized with mobile binders can fold into specific geometries, analogous to protein folding in biological phenomena. Recent experiments from the Brujic lab have demonstrated that incorporating secondary DNA interactions between droplets present in a colloidomer chain backbone can mediate the folding of these chains, via a suitable temperature protocol that takes into account two different melting temperatures (for the backbone and the secondary bonds) [McMullen et al. Nature (2022)]. In this work, we will present our coarse-grained (CG) model for colloidal particles with mobile linkers, which bind to each other via explicit formation and removal of bonded interactions. We have incorporated temperature-dependent binding/unbinding rates to mimic the cooperative melting behavior of the DNA used in experiment. This allows us to study folding pathways for our CG'ed colloidomer chains. We demonstrate that the relative yields of the foldamer geometries can be measured and also the kinetically accessible states can be determined from a folding energy landscape. Programming the order of secondary interactions can thus provide important design rules for generating foldamer structures which can be self-assembled further to form higher-dimensional supracolloidal materials. |
Tuesday, March 7, 2023 5:00PM - 5:12PM |
K07.00009: Controlling Phases of Isotropic DNA-grafted Nanoparticle Assembly through Tuning Pair Interactions Daniel McKeen Theoretically, complex isotropic pair potentials can yield complex periodic structures, but due to limited practical methods to engineer pair potentials, experimental realization remains challenging. DNA can direct self-assembly in a tailorable manner by leveraging complementary base pairing and repulsive polymeric effects, presenting a material well-suited to encoding designed pair potentials. We utilize a double-linker approach to DNA-grafted NP assembly; linkers have a non-complementary spacer and a hybridization sequence that is complementary to the linker of a paired particle. Complementary regimes drive attraction causing DNA shells to hybridize at an encoded distance (ratt) prescribed by shell length and location of the hybridization regime. Non-complementary regimes drive particle repulsion, the range of which (rrep) is prescribed by shell length alone. Computational simulations show that isotropic pair potentials are effectively approximated with the parameter: rrep/ratt. By fixing either linker length or hybridization regime location and altering the other, we achieve a range of rrep/ratt values, and we validate, via small-angle x-ray scattering, structural evolution from body-centered cubic to simple cubic crystals to weakly ordered cubic diamond-like networks. |
Tuesday, March 7, 2023 5:12PM - 5:24PM |
K07.00010: Hierarchical assembly is more efficient than egalitarian assembly in synthetic capsids Wei-Shao Wei, Anthony S Trubiano, Christian Sigl, Stefan Paquay, Hendrik Dietz, Michael F Hagan, Seth Fraden The robust self-assembly of biological materials into large, but finite-size, superstructures is fundamental to life. However, competitive engineering approaches lag far behind. Here, we employ DNA origami patchy colloids designed to assemble into large capsids comprising 60 identical subunits. The individual building blocks have addressable interactions specified using a bioinspired lock-and-key mechanism with a tunable binding strength controlled to kBT precision and with bond directionality determined to 2-3 degrees. Static light scattering is used as a non-invasive approach to quantify the inter-block association affinity in situ and to characterize the block-block association/disassociation rates. We consider assembly pathways that occur when all interparticle interactions are identical (egalitarian), and pathways in which subassemblies, e.g., dimers or pentamers, are preferred (hierarchical). Observations and modeling reveal that hierarchical assembly pathways in which the blocks first assemble into pentamers before further assembling into completed capsids are more efficient than egalitarian pathways with no preferred intermediate structure. This finding raises the question of whether hierarchical assembly is a general engineering principle for optimizing self-assembly of new materials that capture the remarkable functionalities found in living organisms. |
Tuesday, March 7, 2023 5:24PM - 5:36PM |
K07.00011: Investigation of ion-dependent conformational changes of DNA G-quadruplex: Molecular dynamics simulation Juhwa Lee, Chang Yun Son Single-stranded nucleic acids have high flexibility and can be folded in various ways. Recently, the importance of DNA G-quadruplex (G4) has been emphasized in gene regulation and telomere maintenance in vivo. G4 can form various conformations in one sequence depending on different conditions, such as changes in cations, pH, and crowding, and there are over 700,000 regions exist that could be G4 in the human genome. In particular, cations located in the core of G4 and having a great influence on stability are the most investigated factor for the conformation of G4. Despite the crucial role of cations, the detailed mechanism of ion-dependent conformational change of G4 is not reported yet. Here, we performed all-atom molecular dynamics (MD) simulation to check the stability of the G4 structure affected by the core-forming cations, using two representative crystallographically resolved G4 structures with the same sequence but different cations. Calculating the free energy difference of interconversion of Na+ and K+ using the alchemical transformation method, we identify the molecular features that play a key role in the stability of G4 structure and give critical assessments on the existing force fields for simulating non-helical DNA structure with strong electrostatic interactions. |
Tuesday, March 7, 2023 5:36PM - 5:48PM |
K07.00012: Polyelectrolyte Complex Micelle Formation by PEGylated DNA and Polylysine Kwanghee Lee, Sheng Li Nucleic acids are considered to be a special class of negatively charged polymers. They can interact with positively charged polymers to form polyelectrolyte complexes. A major limitation of the system is that the complexes formed may be unstable, particularly at charge ratios near the isoelectric point. The replacement of charged homopolymers with charged-neutral block copolymers can improve the stability of the complexes, leading to the observation of polyelectrolyte complex micelles (PCMs). In this study, we investigate the complexation behavior and morphology of PCMs formed by polylysine (PLys) as the cationic homopolymer and DNA-b-polyethylene glycol (DNA-b-PEG) as the anionic-neutral block copolymer. The PCMs consist of a pseudo-neutral PLys/DNA core and a neutral-hydrophilic PEG corona, and they remain stable over a wide range of charge ratios, including at the isoelectric condition. The binding strength of PLys to DNA-b-PEG is determined as a function of the charge ratio. The PCM morphology is also investigated as a function of PEG and PLys chain lengths. |
Tuesday, March 7, 2023 5:48PM - 6:00PM |
K07.00013: Assembly of DNA-Functionalized Nanoparticles in Concentrated Electrolytes Roger J Reinertsen, Sumit Kewalramani, Felipe Jimenez, Monica Olvera De La Cruz, Michael J Bedzyk In concentrated electrolytes, ion-ion correlations and solvent effects modulate electrostatic interactions, potentially producing counterintuitive behaviors. In this study, we study the manner in which high salt concentrations in solution influence the assembly of gold nanoparticles functionalized with non-base-pairing DNA. Our small-angle X-ray scattering (SAXS) measurements reveal that various divalent cations induce the reversible crystallization of these nanoparticles into various structures, dependent on cation type and concentration. Additionally, interparticle separations within the assemblies are found to vary throughout the full accessible ranges of salt concentrations, even increasing at the highest concentrations, where classical theory predicts electrostatic forces to be of negligible range. Observations from wide-angle X-ray scattering measurements and molecular dynamics simulations will be analyzed in order to elaborate upon the underlying mechanisms governing these behaviors. Additionally, effects associated with solvent composition, ion valency, and temperature will be discussed. This work demonstrates the continuous evolution of interactions between charged objects well above biological salt concentrations. |
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