1
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DeLuca M, Duke D, Ye T, Poirier M, Ke Y, Castro C, Arya G. Mechanism of DNA origami folding elucidated by mesoscopic simulations. Nat Commun 2024; 15:3015. [PMID: 38589344 PMCID: PMC11001925 DOI: 10.1038/s41467-024-46998-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA
| | - Daniel Duke
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA
| | - Tao Ye
- Department of Chemistry & Biochemistry, University of California, Merced, CA, 95343, USA
- Department of Materials and Biomaterials Science & Engineering, University of California, Merced, CA, 95343, USA
| | - Michael Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Carlos Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27705, USA.
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2
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Das A, Limmer DT. Nonequilibrium design strategies for functional colloidal assemblies. Proc Natl Acad Sci U S A 2023; 120:e2217242120. [PMID: 37748070 PMCID: PMC10556551 DOI: 10.1073/pnas.2217242120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 08/17/2023] [Indexed: 09/27/2023] Open
Abstract
We use a nonequilibrium variational principle to optimize the steady-state, shear-induced interconversion of self-assembled nanoclusters of DNA-coated colloids. Employing this principle within a stochastic optimization algorithm allows us to identify design strategies for functional materials. We find that far-from-equilibrium shear flow can significantly enhance the flux between specific colloidal states by decoupling trade-offs between stability and reactivity required by systems in equilibrium. For isolated nanoclusters, we find nonequilibrium strategies for amplifying transition rates by coupling a given reaction coordinate to the background shear flow. We also find that shear flow can be made to selectively break detailed balance and maximize probability currents by coupling orientational degrees of freedom to conformational transitions. For a microphase consisting of many nanoclusters, we study the flux of colloids hopping between clusters. We find that a shear flow can amplify the flux without a proportional compromise on the microphase structure. This approach provides a general means of uncovering design principles for nanoscale, autonomous, functional materials driven far from equilibrium.
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Affiliation(s)
- Avishek Das
- Department of Chemistry, University of California, Berkeley, CA94720
| | - David T. Limmer
- Department of Chemistry, University of California, Berkeley, CA94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
- Kavli Energy NanoSciences Institute, University of California, Berkeley, CA94720
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3
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Pathak SS, Kedarnath G, Panchakarla LS. Mechanistic Study of Amphiphilic-Assisted Self-Assembled Cadmium Sulfide Quantum Dots into 3D Superstructures. J Phys Chem Lett 2023; 14:8114-8120. [PMID: 37668342 DOI: 10.1021/acs.jpclett.3c02180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Self-assembling of nanoparticles into complex superstructures is very challenging, which usually depends on postorganizing techniques or pre-existing templates such as polypeptide chains or DNA or external stimulus. Such self-assembled processes typically lead to close-packed structures. Here, it has been demonstrated that under carefully template-free reaction conditions CdS quantum dots (QDs) could be synthesized and simultaneously self-assembled into complex superstructures without compromising individual QD properties. The superstructures of CdS QDs attained by the chemical-based method demonstrate Stokes-shifted photoluminescence (PL) from trap states. Remarkably, the PL decay of superstructures exhibits a single-exponential feature. This behavior is unusual for the synthesized superstructures, indicating that the trap states are restricted to a narrow range. The growth mechanism of these superstructures is explained through the formation of liquid crystal phases (LCPs) with the help of a small-angle X-ray scattering (SAXS) analysis.
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Affiliation(s)
- Sushil Swaroop Pathak
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Gotluru Kedarnath
- Chemistry Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Leela S Panchakarla
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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4
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Qureshi B, Juritz J, Poulton JM, Beersing-Vasquez A, Ouldridge TE. A universal method for analyzing copolymer growth. J Chem Phys 2023; 158:104906. [PMID: 36922142 DOI: 10.1063/5.0133489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Polymers consisting of more than one type of monomer, known as copolymers, are vital to both living and synthetic systems. Copolymerization has been studied theoretically in a number of contexts, often by considering a Markov process in which monomers are added or removed from the growing tip of a long copolymer. To date, the analysis of the most general models of this class has necessitated simulation. We present a general method for analyzing such processes without resorting to simulation. Our method can be applied to models with an arbitrary network of sub-steps prior to addition or removal of a monomer, including non-equilibrium kinetic proofreading cycles. Moreover, the approach allows for a dependency of addition and removal reactions on the neighboring site in the copolymer and thermodynamically self-consistent models in which all steps are assumed to be microscopically reversible. Using our approach, thermodynamic quantities such as chemical work; kinetic quantities such as time taken to grow; and statistical quantities such as the distribution of monomer types in the growing copolymer can be directly derived either analytically or numerically from the model definition.
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Affiliation(s)
- Benjamin Qureshi
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jordan Juritz
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jenny M Poulton
- Foundation for Fundamental Research on Matter (FOM), Institute for Atomic and Molecular Physics (AMOLF), 1098 XE Amsterdam, The Netherlands
| | | | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
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5
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Phan TM, Whitelam S, Schmit JD. Catalystlike role of impurities in speeding layer-by-layer growth. Phys Rev E 2019; 100:042114. [PMID: 31770938 PMCID: PMC8194389 DOI: 10.1103/physreve.100.042114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Indexed: 06/10/2023]
Abstract
Molecular self-assembly is usually done at low supersaturation, leading to low rates of growth, in order to allow time for binding mistakes to anneal. However, such conditions can lead to prohibitively long assembly times where growth proceeds by the slow nucleation of successive layers. Here we use a lattice model of molecular self-assembly to show that growth in this regime can be sped up by impurities, which lower the free-energy cost of layer nucleation. Under certain conditions impurities behave almost as a catalyst in that they are present at high concentration at the surface of the assembling structure, but at low concentration in the bulk of the assembled structure. Extrapolation of our numerics using simple analytic arguments suggests that this mechanism can reduce growth times by orders of magnitude in parameter regimes applicable to molecular systems.
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Affiliation(s)
- Tien M. Phan
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jeremy D. Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
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6
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Nicholson SB, Bone RA, Green JR. Typical Stochastic Paths in the Transient Assembly of Fibrous Materials. J Phys Chem B 2019; 123:4792-4802. [PMID: 31063371 DOI: 10.1021/acs.jpcb.9b02811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
When chemically fueled, molecular self-assembly can sustain dynamic aggregates of polymeric fibers-hydrogels-with tunable properties. If the fuel supply is finite, the hydrogel is transient, as competing reactions switch molecular subunits between active and inactive states, drive fiber growth and collapse, and dissipate energy. Because the process is away from equilibrium, the structure and mechanical properties can reflect the history of preparation. As a result, the formation of these active materials is not readily susceptible to a statistical treatment in which the configuration and properties of the molecular building blocks specify the resulting material structure. Here, we illustrate a stochastic-thermodynamic and information-theoretic framework for this purpose and apply it to these self-annihilating materials. Among the possible paths, the framework variationally identifies those that are typical-loosely, the minimum number with the majority of the probability. We derive these paths from computer simulations of experimentally-informed stochastic chemical kinetics and a physical kinetics model for the growth of an active hydrogel. The model reproduces features observed by confocal microscopy, including the fiber length, lifetime, and abundance as well as the observation of fast fiber growth and stochastic fiber collapse. The typical mesoscopic paths we extract are less than 0.23% of those possible, but they accurately reproduce material properties such as mean fiber length.
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Affiliation(s)
- Schuyler B Nicholson
- Department of Chemistry , University of Massachusetts Boston , Boston , Massachusetts 02125 , United States
| | - Rebecca A Bone
- Department of Chemistry , University of Massachusetts Boston , Boston , Massachusetts 02125 , United States
| | - Jason R Green
- Department of Chemistry , University of Massachusetts Boston , Boston , Massachusetts 02125 , United States.,Department of Physics , University of Massachusetts Boston , Boston , Massachusetts 02125 , United States.,Center for Quantum and Nonequilibrium Systems , University of Massachusetts Boston , Boston , Massachusetts 02125 , United States
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7
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Ma X, Gu M, Zhang L, Lin J, Tian X. Sequence-Regulated Supracolloidal Copolymers via Copolymerization-Like Coassembly of Binary Mixtures of Patchy Nanoparticles. ACS NANO 2019; 13:1968-1976. [PMID: 30624891 DOI: 10.1021/acsnano.8b08431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synthetic copolymers of molecular systems serve as an inspiration for creation of one-dimensional copolymer-like superstructures via coassembly of anisometric nanoparticles. In contrast to the covalent and molecular copolymers, the details of formation mechanisms of copolymer-like superstructures, as well as the factors determining their length and the sequences of arranged nanoparticles, are still poorly understood. Herein, we propose a joint theoretical-computational framework to probe into the coassembly mechanism and kinetics of binary mixtures of patchy nanoparticles. By applying the coarse-grained molecular dynamics simulations, it is demonstrated that the coassembly of patchy nanoparticles markedly resembles many aspects of molecular step-growth copolymerization, and the sequences of nanoparticles inside the copolymer-like superstructures can be finely regulated by the relative activity and the initial ingredient of patchy nanoparticles as well as the coassembly strategy. A quantitatively copolymerization-like model is developed to account for the coassembly kinetics of patchy nanoparticles and the sequence distribution of arranged nanoparticles, all governed by the elaborate design of lower-level building units. The jointly theoretical and simulated studies offer mechanistic insights into the copolymerization-like kinetics and the sequence prediction for the coassembly of binary mixtures of patchy nanoparticles, paving the way toward the rational design of copolymer-like superstructures with various sequences and functionalities.
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Affiliation(s)
- Xiaodong Ma
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Mengxin Gu
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Liangshun Zhang
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Jiaping Lin
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Xiaohui Tian
- Shanghai Key Laboratory of Advanced Polymeric Materials, State Key Laboratory of Bioreactor Engineering, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering , East China University of Science and Technology , Shanghai 200237 , China
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8
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Nonequilibrium correlations in minimal dynamical models of polymer copying. Proc Natl Acad Sci U S A 2019; 116:1946-1951. [PMID: 30659156 DOI: 10.1073/pnas.1808775116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Living systems produce "persistent" copies of information-carrying polymers, in which template and copy sequences remain correlated after physically decoupling. We identify a general measure of the thermodynamic efficiency with which these nonequilibrium states are created and analyze the accuracy and efficiency of a family of dynamical models that produce persistent copies. For the weakest chemical driving, when polymer growth occurs in equilibrium, both the copy accuracy and, more surprisingly, the efficiency vanish. At higher driving strengths, accuracy and efficiency both increase, with efficiency showing one or more peaks at moderate driving. Correlations generated within the copy sequence, as well as between template and copy, store additional free energy in the copied polymer and limit the single-site accuracy for a given chemical work input. Our results provide insight into the design of natural self-replicating systems and can aid the design of synthetic replicators.
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9
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Dasbiswas K, Mandadapu KK, Vaikuntanathan S. Topological localization in out-of-equilibrium dissipative systems. Proc Natl Acad Sci U S A 2018; 115:E9031-E9040. [PMID: 30206153 PMCID: PMC6166820 DOI: 10.1073/pnas.1721096115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this paper, we report that notions of topological protection can be applied to stationary configurations that are driven far from equilibrium by active, dissipative processes. We consider two physically disparate systems: stochastic networks governed by microscopic single-particle dynamics, and collections of driven interacting particles described by coarse-grained hydrodynamic theory. We derive our results by mapping to well-known electronic models and exploiting the resulting correspondence between a bulk topological number and the spectrum of dissipative modes localized at the boundary. For the Markov networks, we report a general procedure to uncover the topological properties in terms of the transition rates. For the active fluid on a substrate, we introduce a topological interpretation of fluid dissipative modes at the edge. In both cases, the presence of dissipative couplings to the environment that break time-reversal symmetry are crucial to ensuring topological protection. These examples constitute proof of principle that notions of topological protection do indeed extend to dissipative processes operating out of equilibrium. Such topologically robust boundary modes have implications for both biological and synthetic systems.
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Affiliation(s)
- Kinjal Dasbiswas
- The James Franck Institute, The University of Chicago, Chicago, IL 60637
- Department of Physics, University of California, Merced, CA 95343
| | - Kranthi K Mandadapu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Suriyanarayanan Vaikuntanathan
- The James Franck Institute, The University of Chicago, Chicago, IL 60637;
- Department of Chemistry, The University of Chicago, Chicago, IL 60637
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10
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Whitelam S. Strong bonds and far-from-equilibrium conditions minimize errors in lattice-gas growth. J Chem Phys 2018; 149:104902. [DOI: 10.1063/1.5034789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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11
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Abstract
We present a theoretical model for the nucleation of amyloid fibrils. In our model we use helix-coil theory to describe the equilibrium between a soluble native state and an aggregation-prone unfolded state. We then extend the theory to include oligomers with β-sheet cores and calculate the free energy of these states using estimates for the energies of H-bonds, steric zipper interactions, and the conformational entropy cost of forming secondary structure. We find that states with fewer than ~10 β-strands are unstable relative to the dissociated state and three β-strands is the highest free energy state. We then use a modified version of Classical Nucleation Theory to compute the nucleation rate of fibrils from a supersaturated solution of monomers, dimers, and trimers. The nucleation rate has a non-monotonic dependence on denaturant concentration reflecting the competing effects of destabilizing the fibril and increasing the concentration of unfolded monomers. We estimate heterogeneous nucleation rates and discuss the application of our model to secondary nucleation.
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Affiliation(s)
- Lingyun Zhang
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS 66506, USA
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12
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Gooneie A, Sapkota J, Shirole A, Holzer C. Length controlled kinetics of self-assembly of bidisperse nanotubes/nanorods in polymers. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Ball P. Material Witness: A recipe for growth. NATURE MATERIALS 2016; 16:6. [PMID: 27994242 DOI: 10.1038/nmat4839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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14
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Abstract
We consider an important class of self-assembly problems, and using the formalism of stochastic thermodynamics, we derive a set of design principles for growing controlled assemblies far from equilibrium. The design principles constrain the set of configurations that can be obtained under nonequilibrium conditions. Our central result provides intuition for how equilibrium self-assembly landscapes are modified under finite nonequilibrium drive.
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15
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Self-organized architectures from assorted DNA-framed nanoparticles. Nat Chem 2016; 8:867-73. [PMID: 27554413 DOI: 10.1038/nchem.2540] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 04/28/2016] [Indexed: 12/25/2022]
Abstract
The science of self-assembly has undergone a radical shift from asking questions about why individual components self-organize into ordered structures, to manipulating the resultant order. However, the quest for far-reaching nanomanufacturing requires addressing an even more challenging question: how to form nanoparticle (NP) structures with designed architectures without explicitly prescribing particle positions. Here we report an assembly concept in which building instructions are embedded into NPs via DNA frames. The integration of NPs and DNA origami frames enables the fabrication of NPs with designed anisotropic and selective interactions. Using a pre-defined set of different DNA-framed NPs, we show it is possible to design diverse planar architectures, which include periodic structures and shaped meso-objects that spontaneously emerge on mixing of the different topological types of NP. Even objects of non-trivial shapes, such as a nanoscale model of Leonardo da Vinci's Vitruvian Man, can be self-assembled successfully.
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16
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Jacobs WM, Frenkel D. Self-Assembly of Structures with Addressable Complexity. J Am Chem Soc 2016; 138:2457-67. [DOI: 10.1021/jacs.5b11918] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- William M. Jacobs
- Department
of Chemistry and Chemical Biology, Harvard University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Daan Frenkel
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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17
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Abstract
For two-component assemblies, an inherent structure diagram (ISD) is the relationship between set inter-subunit energies and the types of kinetic traps (inherent structures) one may obtain from those energies. It has recently been shown that two-component ISDs are apportioned into regions or plateaux within which inherent structures display uniform features (e.g., stoichometries and morphologies). Interestingly, structures from one of the plateaux were also found to be robust outcomes of one type of non-equilibrium growth, which indicates the usefulness of the two-component ISD in predicting outcomes of some types of far-from-equilibrium growth. However, little is known as to how the ISD is apportioned into distinct plateaux. Also, while each plateau displays classes of structures that are morphologically distinct, little is known about the source of these distinct morphologies. This article outlines an analytic treatment of the two-component ISD and shows that the manner in which any ISD is apportioned arises from a single unitless order parameter. Additionally, the analytical framework allows for the characterization of local properties of the trapped structures within each ISD plateau. This work may prove to be useful in the design of novel classes of robust nonequilibrium assemblies.
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Affiliation(s)
- Ranjan V Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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18
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Sue ACH, Mannige RV, Deng H, Cao D, Wang C, Gándara F, Stoddart JF, Whitelam S, Yaghi OM. Heterogeneity of functional groups in a metal-organic framework displays magic number ratios. Proc Natl Acad Sci U S A 2015; 112:5591-6. [PMID: 25901326 PMCID: PMC4426423 DOI: 10.1073/pnas.1416417112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multiple organic functionalities can now be apportioned into nanoscale domains within a metal-coordinated framework, posing the following question: how do we control the resulting combination of "heterogeneity and order"? Here, we report the creation of a metal-organic framework, MOF-2000, whose two component types are incorporated in a 2:1 ratio, even when the ratio of component types in the starting solution is varied by an order of magnitude. Statistical mechanical modeling suggests that this robust 2:1 ratio has a nonequilibrium origin, resulting from kinetic trapping of component types during framework growth. Our simulations show how other "magic number" ratios of components can be obtained by modulating the topology of a framework and the noncovalent interactions between component types, a finding that may aid the rational design of functional multicomponent materials.
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Affiliation(s)
- Andrew C-H Sue
- Department of Chemistry, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Department of Chemistry, Northwestern University, Evanston, IL 60201
| | - Ranjan V Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and
| | - Hexiang Deng
- Department of Chemistry, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Dennis Cao
- Department of Chemistry, Northwestern University, Evanston, IL 60201
| | - Cheng Wang
- Department of Chemistry, Northwestern University, Evanston, IL 60201
| | - Felipe Gándara
- Department of Chemistry, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - J Fraser Stoddart
- Department of Chemistry, Northwestern University, Evanston, IL 60201;
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and
| | - Omar M Yaghi
- Department of Chemistry, University of California, Berkeley, and Lawrence Berkeley National Laboratory, Berkeley, CA 94720; Kavli Energy NanoScience Institute, Berkeley, CA 94720
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19
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Undesired usage and the robust self-assembly of heterogeneous structures. Nat Commun 2015; 6:6203. [DOI: 10.1038/ncomms7203] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 01/05/2015] [Indexed: 01/04/2023] Open
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20
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Zenk J, Schulman R. An assembly funnel makes biomolecular complex assembly efficient. PLoS One 2014; 9:e111233. [PMID: 25360818 PMCID: PMC4215988 DOI: 10.1371/journal.pone.0111233] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/30/2014] [Indexed: 11/18/2022] Open
Abstract
Like protein folding and crystallization, the self-assembly of complexes is a fundamental form of biomolecular organization. While the number of methods for creating synthetic complexes is growing rapidly, most require empirical tuning of assembly conditions and/or produce low yields. We use coarse-grained simulations of the assembly kinetics of complexes to identify generic limitations on yields that arise because of the many simultaneous interactions allowed between the components and intermediates of a complex. Efficient assembly occurs when nucleation is fast and growth pathways are few, i.e. when there is an assembly "funnel". For typical complexes, an assembly funnel occurs in a narrow window of conditions whose location is highly complex specific. However, by redesigning the components this window can be drastically broadened, so that complexes can form quickly across many conditions. The generality of this approach suggests assembly funnel design as a foundational strategy for robust biomolecular complex synthesis.
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Affiliation(s)
- John Zenk
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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21
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Hedges LO, Mannige RV, Whitelam S. Growth of equilibrium structures built from a large number of distinct component types. SOFT MATTER 2014; 10:6404-6416. [PMID: 25005537 DOI: 10.1039/c4sm01021c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We use simple analytic arguments and lattice-based computer simulations to study the growth of structures made from a large number of distinct component types. Components possess 'designed' interactions, chosen to stabilize an equilibrium target structure in which each component type has a defined spatial position, as well as 'undesigned' interactions that allow components to bind in a compositionally-disordered way. We find that high-fidelity growth of the equilibrium target structure can happen in the presence of substantial attractive undesigned interactions, as long as the energy scale of the set of designed interactions is chosen appropriately. This observation may help explain why equilibrium DNA 'brick' structures self-assemble even if undesigned interactions are not suppressed [Ke et al. Science, 338, 1177, (2012)]. We also find that high-fidelity growth of the target structure is most probable when designed interactions are drawn from a distribution that is as narrow as possible. We use this result to suggest how to choose complementary DNA sequences in order to maximize the fidelity of multicomponent self-assembly mediated by DNA. We also comment on the prospect of growing macroscopic structures in this manner.
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Affiliation(s)
- Lester O Hedges
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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Gaspard P, Andrieux D. Kinetics and thermodynamics of first-order Markov chain copolymerization. J Chem Phys 2014; 141:044908. [DOI: 10.1063/1.4890821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Ruiz L, Keten S. Thermodynamics versus Kinetics Dichotomy in the Linear Self-Assembly of Mixed Nanoblocks. J Phys Chem Lett 2014; 5:2021-2026. [PMID: 26273889 DOI: 10.1021/jz500776g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report classical and replica exchange molecular dynamics simulations that establish the mechanisms underpinning the growth kinetics of a binary mix of nanorings that form striped nanotubes via self-assembly. A step-growth coalescence model captures the growth process of the nanotubes, which suggests that high aspect ratio nanostructures can grow by obeying the universal laws of self-similar coarsening, contrary to systems that grow through nucleation and elongation. Notably, striped patterns do not depend on specific growth mechanisms, but are governed by tempering conditions that control the likelihood of depropagation and fragmentation.
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Whitelam S, Hedges LO, Schmit JD. Self-assembly at a nonequilibrium critical point. PHYSICAL REVIEW LETTERS 2014; 112:155504. [PMID: 24785052 DOI: 10.1103/physrevlett.112.155504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Indexed: 06/03/2023]
Abstract
We use analytic theory and computer simulation to study patterns formed during the growth of two-component assemblies in two and three dimensions. We show that these patterns undergo a nonequilibrium phase transition, at a particular growth rate, between mixed and demixed arrangements of component types. This finding suggests that principles of nonequilibrium statistical mechanics can be used to predict the outcome of multicomponent self-assembly, and suggests an experimental route to the self-assembly of multicomponent structures of a qualitatively defined nature.
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Affiliation(s)
- Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Lester O Hedges
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
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Abstract
The growth of amyloid fibrils requires a disordered or partially unfolded protein to bind to the fibril and adapt the same conformation and alignment established by the fibril template. Since the H-bonds stabilizing the fibril are interchangeable, it is inevitable that H-bonds form between incorrect pairs of amino acids which are either incorporated into the fibril as defects or must be broken before the correct alignment can be found. This process is modeled by mapping the formation and breakage of H-bonds to a one-dimensional random walk. The resulting microscopic model of fibril growth is governed by two timescales: the diffusion time of the monomeric proteins, and the time required for incorrectly bound proteins to unbind from the fibril. The theory predicts that the Arrhenius behavior observed in experiments is due to off-pathway states rather than an on-pathway transition state. The predicted growth rates are in qualitative agreement with experiments on insulin fibril growth rates as a function of protein concentration, denaturant concentration, and temperature. These results suggest a templating mechanism where steric clashes due to a single mis-aligned molecule prevent the binding of additional molecules.
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Affiliation(s)
- Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA.
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Multistep kinetic self-assembly of DNA-coated colloids. Nat Commun 2013; 4:2007. [DOI: 10.1038/ncomms3007] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/12/2013] [Indexed: 01/25/2023] Open
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