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 Z16: DNA-based Soft Matter: Design, Dynamics, and Active Mechanics II |
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Sponsoring Units: DSOFT Chair: Omar Saleh, University of California, Santa Barbara Room: Room 208 |
Friday, March 10, 2023 11:30AM - 11:42AM |
Z16.00001: Examining the Effect of DNA Flexibility in Complex Coacervates Anna N Nguyen, Omar A Saleh Complex coacervation, the phase separation driven by electrostatic associations of a polyanion and polycation, has been extensively studied by varying the charge structure of the macromolecules or by adjusting solution conditions. However, there is a lack of understanding of how internal flexibility of the constituents affects the process. To vary flexibility, we exploit the programmable nature of DNA specifically studying the coacervation of single-strands, double-strands, and hairpins complexing with poly-l-lysine. We measure the DNA versus salt concentration phase diagrams of these varying structures by fluorescently tagging the DNA and using confocal microscopy to quantify the concentration in the dense and dilute phase via fluorescence intensity. We discuss how DNA secondary structure impacts phase behavior, including the critical salt and DNA concentration in the dense phase. We expect our work will lead to a better understanding of how the individual molecular properties affect the formation and composition of biomolecular condensates. |
Friday, March 10, 2023 11:42AM - 11:54AM |
Z16.00002: The Growth Rate of DNA Condensate Droplets Increases with the Size of Participating Subunits Elisa Franco, Siddharth Agarwal, Dino Osmanovic, Melissa A Klocke The bottom-up synthesis of biomolecular condensates with simple constituents, like nucleic acids and peptides, is supporting the development of new amorphous materials. Understanding which parameters determine condensate growth kinetics is important for the synthesis of condensates with the capacity for active, dynamic behaviors. Here we use DNA nanotechnology to study artificial liquid condensates through programmable star-shaped subunits, focusing on the effects of changing subunit size. First, we show that condensation is achieved in a 6-fold range of subunit size. Second, we demonstrate that the rate of growth of condensate droplets scales with subunit size. Our investigation is supported by a general model that describes how coarsening and coalescence are expected to scale with subunit size under ideal assumptions. Beyond suggesting a route toward achieving control of condensation kinetics via design of subunit size in synthetic liquids, our work suggests that particle size may be a key parameter in biological phase separation. |
Friday, March 10, 2023 11:54AM - 12:06PM |
Z16.00003: Phase separation via simultaneous interactions: the cooperation of electrostatics and base pairing Gabrielle R Abraham, Anna N Nguyen, Sam Wilken, Omar A Saleh We investigate the interplay of two specific interactions, base pairing and electrostatics, in driving biomolecular phase separation. Particularly, we study condensation of a mixture containing poly-L-Lysine (PLL) and branched, self-hybridizing DNA particles. Electrostatic-driven phase separation arises from the attraction between PLL and DNA. Simultaneously, the DNA forms branched structures, nanostars (NSs), which are capable of base-pairing via self-complementary, single-stranded sequences at the end of each arm. We observe four distinct phases using fluorescent imaging of material structures at varying salt concentrations, charge ratios, and temperatures. This includes a complex coacervate-like transition from gel-like aggregates to liquid droplets with increasing salt; a high salt limit where the NSs form liquid drops that exclude PLL; and a regime where NS-only droplets coexist with NS/PLL coacervates. Overall, this work finds an extraordinary diversity of phase behaviors over a relatively narrow range of conditions, apparently due to a subtle balance between the electrostatic and base pairing interactions. |
Friday, March 10, 2023 12:06PM - 12:18PM |
Z16.00004: Emulsion imaging of a DNA nanostar condensate phase diagram reveals valence and electrostatic effects Nathaniel Conrad, Grace Chang, Deborah K Fygenson, Omar A Saleh Liquid-liquid phase separation (LLPS) in macromolecular solutions is relevant both to technology, and to the process of mesoscale structure formation in cells. The LLPS process is characterized by a temperature/concentration phase diagram, which must be quantified to predict the system's behavior. Experimentally, this can be difficult due to complications in handling the dense macromolecular phase. Here, we develop a method for accurately quantifying the phase diagram without direct handling: We confine the sample within micron-scale, water-in-oil emulsion droplets, then use precision fluorescent imaging to measure the volume fraction of the condensate within the droplet. We find this volume fraction grows linearly with macromolecule concentration; thus, by applying the lever rule, we can directly extract the dense and dilute phase concentrations. We use this approach to study a model LLPS system of self-assembled, fixed-valence DNA particles termed nanostars (NSs). We find that phase diagrams of NSs display, with certain exceptions, a larger co-existence regime upon increasing salt or NS valence, in line with expectations. Aspects of the measured phase behavior validate recent predictions that account for the role of NS valence in modulating the connectivity of the condensed phase. Generally, our results on NS phase diagrams give fundamental insight into limited-valence phase separation, while the method we have developed will likely be useful in the study of other LLPS systems. |
Friday, March 10, 2023 12:18PM - 12:30PM |
Z16.00005: Interplay between self-assembly and phase separation in a polymer-complex model Tianhao Li, Omkar Hegde, Marco Borja, Anjali Sharma, W. Benjamin Rogers, William M Jacobs Spatiotemporal organization of biological processes can be achieved both by assembling molecules into stoichiometric complexes and by demixing via liquid–liquid phase separation. Interestingly, in the case of biomolecules with low-complexity domains, self-assembly and phase separation can arise from the same set of multivalent interactions. In this work, we introduce a theoretical model inspired by a DNA nanostar system, where single-stranded DNA can either assemble into nanostars through hybridization or undergo liquid–liquid phase separation. We derive a mean-field free energy in terms of experimentally measurable parameters assuming two-state self-assembly kinetics. Our model exhibits rich phase behavior, which we study by calculating "master phase diagrams" for the complete parameter space. Parameterizing the model as a function of temperature or ionic strength yields a predicted phase diagram for a specific biomolecular system. Our model not only explains the re-entrant phase behavior observed in experiments on DNA nanostar systems, but also provides a theoretical framework for understanding the interplay between complex assembly and liquid–liquid phase separation in naturally occurring biomolecules with low-complexity domains. |
Friday, March 10, 2023 12:30PM - 12:42PM |
Z16.00006: Complexation of DNA Block Copolymers with Ionic Liquids Sheng Li, Young Hun Kim Block copolymers containing DNA and synthetic polymer segments are a special class of anionic-neutral copolymer materials that can potentially interact with cationic molecules to form polyelectrolyte complexes. Ionic liquids (ILs) are green solvents consisting of tunable cationic and anionic constituents, and their interaction with biomolecules, including DNA, has been reported. In this study, we synthesize DNA-b-poly(ethylene glycol) (DNA-b-PEG) block copolymers and investigate their complexation with a number of biocompatible ILs. DNA-b-PEG is prepared by coupling chemistry between amine-functionalized DNA and N-hydroxysuccinimide ester activated PEG. Thermal annealing is then employed to induce complex micelle formation. The binding strength of DNA-b-PEG and IL is determined by the hybridization state of the DNA, with double-stranded DNA (dsDNA) showing stronger binding to ILs than single-stranded DNA (ssDNA). The morphology and stability of the complex micelles are also examined, and they are influenced by the concentration of the IL and the alkyl chain length of the IL cation. |
Friday, March 10, 2023 12:42PM - 12:54PM |
Z16.00007: Molecular Excitonic Networks Organized by DNA Scaffolds Joseph S Melinger, Adam Meares, Kimihiro Susumu, Brian S Rolczynski, Young C Kim, Divita Mathur, Sebastian Diaz, Igor L Medintz Analogous to electronic circuits, molecular excitonic networks transport excitons through dye assemblies. Controlling this transport is critical to realizing artificial photosynthesis and alternative logic circuit platforms. DNA scaffolds are a powerful way to organize dye molecules on the nanoscale. Recently, we have shown that cyanine (Cy) dye aggregates on DNA exhibit strong electronic coupling, delocalized excitons, and long-lived vibronic coherences that could be exploited for quantum information and sensing applications. An unintended consequence is the creation of non-radiative relaxation pathways that can drastically shorten exciton lifetimes. Understanding the effect of aggregate geometry and environment on these pathways is critical to the development of useful molecular excitonic networks. |
Friday, March 10, 2023 12:54PM - 1:06PM |
Z16.00008: Curvature controlled self-limited assembly using DNA origami building blocks Rupam Saha, Thomas E Videbaek, Wei-Shao Wei, Daichi Hayakawa, Tijana Ivanovic, William B Rogers, Seth Fraden Our long-term goal is to design self-limited structures on length scales many times larger than the building blocks themselves. This project aims to construct large capsids with a high yield using a minimal number of building blocks. It is inspired by the ability of large viruses to form complete, functional capsids using very few components. Most of the smaller spherical viruses build icosahedral capsids to protect their genetic material, which can be explained by Caspar and Klug's theory of quasi-equivalence (1962). However, larger viruses like herpes simplex virus (T = 16) are built in layers. The inner layer is a type of vesicle comprising proteins around which the outer layer of protein subunits assembles into a highly symmetric icosahedral shape. Here, we describe an experimental strategy to mimic this design strategy using lipid vesicles as the inner layer and triangular building blocks (size ~ 50 nm) made of DNA origami for the outer layer. Our engineered triangular subunits are able to self-assemble on the vesicle surface with the help of cholesterol-modified DNA. Instead of using T = 16 quasi-equivalent interactions, as required by the Caspar-Klug paradigm, we use a spherical template to assemble a T = 16 structure using only 1 equivalent bonding interaction. Noteworthy, in principle, any triangulation number capsid can be assembled with just 1 equivalent interaction as long as the template size permits. We estimate this strategy has the potential to increase the yield of origami capsids by a million fold over current methods. |
Friday, March 10, 2023 1:06PM - 1:18PM |
Z16.00009: Re-entrant condensation of DNA due to the competition between self-assembly and phase separation Omkar Hegde, Tianhao Li, Marco Borja, Anjali Sharma, William M Jacobs, W. Benjamin Rogers Biomolecular condensates formed by Liquid-Liquid Phase Separation (LLPS) carry out critical physiological functions of cells, such as controlling stress responses, maintaining homeostasis, biochemical reactions, transport, and signaling. Model systems made up of simple constituents, such as multivalent assemblies of DNA strands called "DNA nanostars (NSs)", can be used to probe the fundamental physics governing phase separation. In this talk, I will show that the phase behavior of DNA NSs is far richer than anticipated. At room temperature, DNA NSs phase separate due to attractive interactions between their sticky ends. The sticky-end interactions weaken with increasing temperature, leading to a transition to a single phase. Interestingly, upon further increasing the temperature, we find that the NSs again phase separate. We hypothesize that this re-entrant transition results from the disassembly of NSs and phase separation of the constituent DNA oligomers. To test this hypothesis, we construct the temperature-dependent phase diagram using droplet-based microfluidics and compare our measurements to predictions from a simple theoretical model. Quantitative agreement between our experiments and predictions suggests that the very same molecules can separate into condensates at both low and high temperatures and that the re-entrant transition between the two condensate regions is modulated by the competition between self-assembly and phase separation. |
Friday, March 10, 2023 1:18PM - 1:30PM |
Z16.00010: DNA Origami Arm Powered by a Local Heater Aditya Vikram Hardikar, Kun Wang, Heng Ni, Ruojie Sha, Paul M Chaikin DNA-based micromachines leverage forces generated by hybridization of DNA base pairs. This force, which is of the order of several piconewtons is sufficient to move micron-sized particles and achieve transport at the microscopic scale. We create a DNA origami-based machine that is a semi-flexible hinge made out of single-stranded DNA and a lever arm made with 6 helix bundles. Complimentary DNA single strands on either side of the hinge hybridize and hold the hinge in a closed position. The DNA strands dehybridize with increase in temperature resulting in opening of the hinge. A thin-film resistive heater that acts as its own thermometer is used as a local heating source in the vicinity of this DNA machine. We can cycle temperature between 20°C and 30°C above 100Hz close to the heater and measure the opening and closing response of the DNA hinge. |
Friday, March 10, 2023 1:30PM - 1:42PM |
Z16.00011: The Role of Oral Tests in the Advanced Lab ~ Impact of Covid Rudi Michalak Our Advanced Lab is a University Studies Program COM 3 class, in which communication skills in the field are honed. Class size at our small, public, Rocky Mountain university is about 12, usually all majors in physics and astronomy. Communication skills trained include professional report writing, equipment seminar presentations, oral prelabs (student preparedness for lab and safety), and oral exams (assess a student’s proficiency in lab and data analysis skills). We investigate the impact the covid closure and subsequent going online of classes has had on students (one class changed mode at midterm during Alpha wave), a later class was fully online during the peak of the Delta wave. Online classes were conducted via Zoom, and old data from previous students were handed out and were supported by lab equipment and lab performance videos. |
Friday, March 10, 2023 1:42PM - 1:54PM |
Z16.00012: Quadrupolarization as a Teaching Tool Brian Y Lee, Kevin Setter In the standard undergraduate Electricity and Magnetism curriculum, the topic of continuously-polarized matter is treated extensively. However, the related topic of continuously-quadrupolarized matter is not discussed, despite its potential relevance for quadrupolar fluids. Here, we extend the usual treatment of surface and bound charge to the quadrupolar case. Using only undergraduate-level techniques, we discuss how to convert quadrupolarization (quadrupole moment per unit volume) into an effective surface charge density, volume charge density, and normal surface polarization. This method allows one to efficiently solve for electrostatic potential due to quadrupolarization and serves as a pedagogical tool to 1) introduce students to normal surface dipole moment and the related boundary condition, 2) present a generally-applicable method to treat non-normally oriented surface polarization, 3) familiarize students with component notation, and 4) sharpen student's boundary value problem solving skills. We illustrate the method through four worked examples: 1) a uniformly quadrupolarized sphere, 2) a concentrically quadrupolarized sphere, 3) an infinite cylinder uniformly quadrupolarized parallel to axis, and 4) an infinite cylinder uniformly quadrupolarized perpendicular to axis. |
Friday, March 10, 2023 1:54PM - 2:06PM Author not Attending |
Z16.00013: Expanding in-class peer leadership format to large class sizes Mikkel H Jensen, Eliza Morris, Bita Rivas Introductory college courses in science, technology, engineering, and mathematics (STEM) often pose a significant hurdle to college students, and are disproportionately challenging for student from historically underserved groups and first-generation students. We have developed a student-centered active learning format that incorporates elements from Peer-Led Team Learning (PLTL) to engage students in active learning, teamwork, and peer leadership in to large classroom settings. This Integrated Peer Learning Program (IPLP) format has shown high learning gains and a substantial reduction in the failure rate for students, as well as a substantial reduction in achievement gap among historically underserved groups in STEM, when used in 80-student classrooms. |
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