Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session B25: DNA-based Soft Matter: Design, Dynamics, and Active Mechanics IIRecordings Available
|
Hide Abstracts |
Sponsoring Units: DSOFT DPOLY Chair: Deborah Fygenson, UCSB Room: McCormick Place W-187A |
Monday, March 14, 2022 11:30AM - 11:42AM |
B25.00001: A simple method to reprogram the binding specificity of DNA-coated colloids that crystallize Pepijn G Moerman, Thomas Videbaek, Huang Fang, William B Rogers, Rebecca Schulman DNA-coated particles are versatile building-blocks for self-assembly, but difficult, costly, and time-consuming to produce in a way that is compatible with equilibrium self-assembly. For each experiment or application that requires a different DNA sequence on the particle, the DNA grafting process needs to be repeated, standing in the way of the widespread use of DNA-coated colloids in research and commercial applications. Here, we introduce a method to convert generic DNA-coated colloids into building blocks with user-specified DNA sequences by appending new DNA domains onto the DNA grafted onto the colloid. The reaction we introduce is easy and fast, reaching $100\%$ conversion in 1h. We show that the assembly properties of particles produced via our conversion method are indistinguishable from those produced via click chemistry directly. Moreover, we show that one generic type of particle can be converted into a variety of assembly building blocks with differing specificity by appending different DNA sequences onto them. We expect that our approach will greatly improve access to DNA-coated particles that can crystallize and pave the way to their commercial application. |
Monday, March 14, 2022 11:42AM - 11:54AM |
B25.00002: Active DNA Hydrogels Yair Augusto Gutierrez Fosado, Giorgia Palombo, Davide Michieletto Active gels are exotic smart materials that consume energy to actuate and/or change their material properties. DNA nanostars hydrogels have now been extensively studied as prototypical examples of equilibrium gels, yet their enhancement using proteins or energy-consuming processes has been overlooked so far. In this talk, I will describe our combined experimental and computational work in designing and characterising generic active DNA hydrogels. More specifically, I will report on recent results that we obtained by encoding a different number of specific restriction sites on the arms of the DNA nanostars. Thanks to endonuclease specificity, we can carefully tune the rate and pathway through which DNA hydrogels dissolve and modulate their viscoelastic properties in time. I will present data using passive/active microrheology and confocal microscopy to characterise the temporal evolution of the hydrogels viscoelasticity and oxDNA-based computational models to rationalise our observations . These models are promising to be a key tool in the designing of the next generation of hydrogels. Our work paves the way for DNA-based scaffolds and drug-delivery systems with continuously time-varying rheology. |
Monday, March 14, 2022 11:54AM - 12:06PM |
B25.00003: 2D Auxetic DNA Origami: Mechanics, Deformation Behaviors and Design Recommendations Jong Hyun Choi, Ruixin Li Auxetic materials have unconventional mechanical properties which are believed to emerge from their periodic cellular structures rather than the chemical composition. Poisson’s ratio characterizes their properties distinct and different from those of regular materials. Auxetic structures have negative Poisson’s ratios, whereas regular materials show positive values. The auxetic behaviors offer significantly improved indentation resistance, greater shear modulus, and enhanced fracture toughness. In this work, we demonstrated architectured 2D auxetic metastructures using DNA origami, a bottom-up self-assembly method. We constructed several wireframe configurations, characterized their auxetic properties, and investigated relevant mechanics. Given their nanoscale dimensions, we achieved the auxetic deformations via 2-step DNA reactions. Coarse-grained molecular dynamics simulations were also performed to study mechanical deformation upon external loading, from which we extracted structural properties. We found that (1) structural behaviors by DNA reactions and mechanical loads are consistent and that (2) the auxetic behaviors are largely defined by structures, yet the DNA properties must be considered. Our elastic model suggests design guidelines for auxetic DNA metastructures. |
Monday, March 14, 2022 12:06PM - 12:18PM |
B25.00004: Exploring the effect of the number of arms and junction bases on DNA nanostar conformation using molecular dynamics simulations DUANYANG WANG, Deborah K Fygenson Immobile branched junctions in DNA, a.k.a. nanostars, are crosslinking nanostructures that, under the right conditions of concentration and temperature, condense to form a liquid or gel phase in water. Programmability of DNA base pairing offers unprecedented control over the number and strength of the weak bonds that drive condensation. To better understand how nanostar design affects the accessibility of those bonds, we used oxDNA2, a coarse-grained, molecular dynamics model of DNA, to simulate nanostars with different numbers of arms (3-6) and unpaired bases per arm in the junction (0-10). |
Monday, March 14, 2022 12:18PM - 12:30PM |
B25.00005: Mechanistic Model Study of Surface Based DNA Walkers Jong Hyun Choi, Yancheng Du, Jing Pan DNA walkers are engineered nanostructures that can migrate on prescriptive landscape based on various mechanisms including strand displacement and enzymatic reaction. Over the years, the focus on DNA walker studies have been on improving speed and processivity, where models analyzing walker behaviors are vital for improving the designs. Here, we introduce a comprehensive model for an enzyme-powered DNA walker that moves autonomously on 2D surfaces. Our analysis show that the walkers have multiple modes - ballistic, Lévy, self-avoiding, and diffusive. These different modes show distinct step time and velocity distributions. To understand the dynamics, we adopt a random walk model bridging the scaling of mean-squared displacement and statistical features of various movements. Coherence between the model and experimental results are demonstrated. Mechanistic studies were performed experimentally to investigate the effects of key parameters that govern walker behaviors. These include cargo types and sizes, strand lengths and sequences, design of walkers, and environmental conditions. The parameters influence the statistical features of motions and lead to walkers with various velocities and processivity. Finally, a set of design principles are proposed for future walker designs. |
Monday, March 14, 2022 12:30PM - 12:42PM |
B25.00006: Assembly kinetics of synthetic capsids made from DNA origami Wei-Shao Wei, Anthony Trubiano, Christian Sigl, Hendrik Dietz, Michael F Hagan, Seth Fraden The robust self-assembly of biological materials into large, but finite-size, superstructures is fundamental to life. One of the prototypical examples is a virus capsid, whose widely various geometries are built from either a single or a few species of repeating units. Inspired by this efficient paradigm, we previously developed a programmable engineering analog composed of user-prescribed DNA origami subunits. While the equilibrium structure of the synthetic capsid was determined, the dynamical transformation from a disorganized state of individual building blocks into an ordered state of a fully-closed capsid shell remains uncharacterized. To reveal the underlying mechanism, we firstly undertake a quantitative study of the on- and off- rates of the monomer-dimer transition as a function of interaction strength. Specifically, the inter-block lock-and-key docking with base-stacking plus variable hybridizations enables precise control of binding strength. We utilize static and dynamic light scattering to quantify the association affinity in situ and non-invasively monitor the assembly kinetics. With the knowledge thus gained, we aim to realize assembly of various artificial capsids with optimized yield and reaction time. |
Monday, March 14, 2022 12:42PM - 12:54PM |
B25.00007: Simulation study of the emergence of valency in colloidal crystals using DNA-functionalized particles Sangmin Lee, Sharon C Glotzer The concept of valence electrons is central to chemical bonding theory, which defines how atoms form anisotropic bonding geometries in molecules and crystalline solids. A recent study [Girard et al., Science, vol. 364, pp. 1174, 2019] showed that DNA-functionalized colloidal particles behave similarly when reduced in size and DNA grafting density. In this presentation, we introduce a simulation study of an approach to generating various low symmetry and complex colloidal crystals based upon programmable atom equivalents (PAE, nanoparticles functionalized with many DNA strands) and mobile electron equivalents (EE, small particles functionalized with a low number of DNA strands complementary to the PAEs). We developed a simplified particle model using the HOOMD-Blue MD simulation toolkit, where PAEs and EEs are represented by rigid spherical cores surrounded by soft DNA ligand shell. The finite number of DNA strands on EEs are modeled as spatially uniform anchoring points that can bind to isotropic DNA shells of PAEs. Under appropriate conditions, the spatial distribution of the EEs breaks the symmetry of isotropic PAEs, akin to the anisotropic distribution of valence electrons or coordination sites around a metal atom, leading to a set of well-defined coordination geometries and access to various low symmetry crystalline phases. |
Monday, March 14, 2022 12:54PM - 1:06PM |
B25.00008: Probing nanoscale interactions between DNA-coated colloids using total internal reflection microscopy Fan Cui, Sophie Marbach, Jeana Zheng, Miranda Holmes-Cerfon, David J Pine DNA-coated colloids are our most versatile tool for the targeted self-assembly of colloidal materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic understanding of DNA-mediated colloidal interactions. Here we use total internal reflection microscopy (TIRM) to measure the interaction potential between DNA-coated colloids with nanometer resolution and the macroscopic melting behavior. The range and strength of the interaction are measured and linked to key material design parameters, including DNA sequence, polymer length, grafting density, and complementary fraction. We build a first-principles model that quantitatively reproduces our experimental data without fitting parameters over a wide range of DNA ligand designs. Our work identifies a subtle competition between DNA binding and steric repulsion and accurately predicts adhesion and melting at a molecular level. |
Monday, March 14, 2022 1:06PM - 1:18PM |
B25.00009: "Flexible hinge" dynamics in mismatched DNA revealed by fluorescence lifetime and correlation spectroscopy Viktoriya Zvoda, Timour B Ten, Manas K Sarangi, Serguei V Kuznetsov, Anjum Ansari Enhanced fluctuations at DNA lesion sites are implicated in damage-sensing by DNA-repair proteins. We investigated the dynamics of DNA oligomers containing 3-bp mismatched sites specifically recognized in vitro by NER protein Rad4. A previous study mapped DNA conformational distributions using fluorescence lifetime (FLT) with cytosine-analog FRET pair sensitive to DNA unwinding (Chakraborty et al., 2018, NAR, 46, 1240). These studies revealed B-DNA conformations for low-specificity/nonspecific substrates but significant unwinding for high-specificity substrates, even in the absence of Rad4. The timescales of these unwinding fluctuations, however, remained elusive. Here, we labeled DNA with FRET dyes suitable for fluorescence correlation spectroscopy (FCS). FLT with these probes detected higher FRET in specific, mismatched DNA versus matched DNA, indicating bending deformations in the mismatched DNA. FCS uncovered ~100-300 µs dynamics on mismatched DNA with no dynamics detected for matched DNA, thus providing direct evidence of equilibrium unwinding/bending fluctuations in mismatched DNA on timescales that overlap with the <500 µs 1D stepping times of repair proteins diffusing on DNA. Such “flexible hinge” dynamics could arrest a diffusing protein to facilitate recognition. |
Monday, March 14, 2022 1:18PM - 1:30PM |
B25.00010: Measurements of DNA Binding Kinetics with High-Performance Electronics Arvind Balijepalli, Jacob M Majikes, Seulki Cho, James A Liddle Measurements of DNA hybridization kinetics were performed using field-effect transistors (FET). The measurements utlized AC electric fields that induced either small capacitance changes at the transistor gate or changes to the local electric field due to the induced oscillatory motion of the DNA strand. In each case, an anchor strand of DNA was conjugated to a gold surface that was remotely connected to the FET gate. Complementary strands were introduced, and the time-series of DNA hybridization was then measured to estimate the association and dissociation rates of binding. The results demonstrate a rapid and label-free approach to measuring DNA hybridization kinetics. Because the approach relies on scalable CMOS devices it can be adapted for massively parallel measurements for numerous applications in biotechnology and biophysics. |
Monday, March 14, 2022 1:30PM - 1:42PM |
B25.00011: Characterizing the Impact of Abasic Sites on Sequence-Dependent DNA Duplex Dehybridization with Temperature-Jump IR Spectroscopy and Coarse-Grained Molecular Simulation Brennan Ashwood, Mike S Jones, Andrew L Ferguson, Andrei Tokmakoff The biological responsibilities and recent nanotechnology applications of DNA often rely on dynamic interactions between oligonucleotides. The binding affinity and kinetics of (de)hybridization are most commonly tuned by nucleobase sequence due to the development of robust models of two-state duplex (D)-to-single-strand (S) thermodynamics. Nucleobase sequence also impacts the configurational breadth of the duplex ensemble and dynamics of (de)hybridization, yet the details of these effects remain poorly understood. We are studying how the cooperativity and time-dependent properties of the DNA D-to-S transition depend on nucleobase sequence using temperature-jump (T-jump) IR spectroscopy and MD simulations. We are currently investigating how removing specific nucleobases (abasic site) alters (de)hybridization behavior in oligonucleotides of varying sequence. Incorporation of an abasic site reshapes the free energy landscape of the DNA duplex, but does so in a position- and sequence-dependent manner. T-jump experiments and MD simulations reveal how DNA (de)hybridization dynamics change on timescales from ns to ms in response to abasic site incorporation. Overall, our results provide insight into the contribution of single specific nucleobases to the global process of duplex (de)hybridization. |
Monday, March 14, 2022 1:42PM - 1:54PM |
B25.00012: Effect of monovalent and divalent ionic environments on the in-lattice nanoparticle-grafted single-stranded DNA. Anuj Chhabra, Sunita Srivastava, Oleg Gang Polyelectrolyte polymers (PEs) are sensitive to change in environment around them such as pH, temperature, presence of different type of salt, type of solvent etc., which affect the chain morphology and its conformation in the solution. Although much work is done on the free PEs morphology in the presence of the different salts and concentrations but not much work has been done when the movement of the chains are constricted when they are attached on the spherical surface. Our work investigates, using in-situ small-angle x-ray scattering (SAXS), the morphology of PEs (single-stranded DNA) chains grafted onto a surface of spherical gold nanoparticles assembled in a lattice in the presence of monovalent and divalent salts. Our experiments reveal that when DNA chains are present in the divalent salt the chain length decreases at faster rate when compared to the monovalent salts. Power law and modified Daoud Cotton has been used to get insight about the behaviour of the DNA chains in different ionic environments. It has been found that for monovalent salts electrostatic interaction is leading to the decrease of the DNA chain length whereas for divalent salts both electrostatic interactions and the ion-bridging contributes leading to faster decrease of the DNA chain length. |
Monday, March 14, 2022 1:54PM - 2:06PM |
B25.00013: Computational modelling and single-molecule rotor bead study of DNA plectoneme pinning in the presence of base-pair mismatches Parth Rakesh Desai, Adam Fineberg, Yeonee Seol, Haksung Jung, Siddhartha Das, Keir C Neuman In vivo, mismatched or damaged bases introduce defects into the DNA, these must be efficiently repaired. A common motif in defect recognition is the imposition of a sharp bend in the DNA. DNA supercoiling could potentially facilitate defect recognition by pinning defects at the ends of the plectonemes where DNA is sharply bent. We use MD simulations and single-molecule rotor bead assay to study the effect of mismatches on DNA supercoiling. Magnetic tweezers studies have shown that in 1M NaCl a single mismatch can localize a plectoneme at a mismatch. In physiological salt condition theoretical studies predict plectoneme localization becomes probabilistic. However, approaches were limited to positively supercoiled DNA. We developed a mismatch model in the OxDNA framework and study the effect of mismatches on positively and negatively supercoiled DNA. The simulations reproduce the experimental and theoretical results for positive supercoiling. The probability of plectoneme pinning is greatly enhanced by negative supercoiling. We validate the simulation predictions experimentally with a single-molecule rotor bead assay that extends previous measurements into the probabilistic localization regime for both positive and negative supercoiling in physiological salt conditions. |
Monday, March 14, 2022 2:06PM - 2:18PM |
B25.00014: Colloidal Valence as Thermodynamic Equilibrium States predicted by Molecular and Surface Properties Sascha Hilgenfeldt, Angus McMullen, Jasna Brujic Building complex structures in two or three dimensions by directed self-assembly holds great promise for the efficient synthesis of materials with novel mechanical or optical properties. Self-assembly of colloidal objects also serves as a prototypical system for protein folding or the chemistry of macromolecules. For all these applications, control of the valence of individual objects is crucial. Using colloidal droplets decorated with mobile DNA binders, we show experimentally and theoretically that the mechanical properties of the droplet surfaces and the binder molecules predetermine the droplet-droplet binding characteristics, and in particular determine valence manifested as the spontaneous formation of a predictable number of bond patches between droplets. These valence states are thermodynamic equilibria, and thus offer a robust way of achieving complex self-assembly. Moreover, we show how the molecular properties of the binder (length or stiffness of e.g. dsDNA or ssDNA) govern the size and binder population of bond patches between droplets. Droplet deformation is part of this description, but, contrary to common thinking, is not necessary to establish such patches. We identify guidelines for choices of binder molecules and droplets leading to efficient valence control. |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700