1
|
Krauss SW, Weiss M. Controlling phase separations and reactions in trapped microfluidic droplets. Sci Rep 2024; 14:20998. [PMID: 39251851 PMCID: PMC11385582 DOI: 10.1038/s41598-024-71586-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024] Open
Abstract
Microfluidics and droplet-based assays are the basis for numerous high-throughput experiments, including bio-inspired microreactors and selection platforms for directed evolution. While elaborate techniques are available for the production of picoliter-sized droplets, there is an increasing demand for subsequent manipulation and control of the droplet interior. Here, we report on a straightforward method to rapidly adjust the size of single to several hundred double-emulsion droplets in a microfluidic sieve by varying the carrier fluid's salt concentration. We show that the concomitant concentration changes in the droplet interior can drive a reversible demixing transition in a biomimetic binary fluid. As another application, we show that growing and shrinking of trapped droplets can be utilized to achieve a reversible dissociation of double-stranded DNA into single strands, i.e. cycles of reversible DNA hybridization, similar to PCR cycles, can be achieved by reversibly changing the droplet size at constant temperature. Altogether, our approach shows how a simple and temporally tunable manipulation of the size and the chemistry in prefabricated droplets can be achieved by an external control parameter.
Collapse
Affiliation(s)
- Sebastian W Krauss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, 95447, Bayreuth, Germany.
| |
Collapse
|
2
|
Pokhrel P, Karna D, Jonchhe S, Mao H. Catalytic Relaxation of Kinetically Trapped Intermediates by DNA Chaperones. J Am Chem Soc 2024; 146:13046-13054. [PMID: 38710657 PMCID: PMC11135164 DOI: 10.1021/jacs.3c14350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Common in biomacromolecules, kinetically trapped misfolded intermediates are often detrimental to the structures, properties, or functions of proteins or nucleic acids. Nature employs chaperone proteins but not nucleic acids to escort intermediates to correct conformations. Herein, we constructed a Jablonski-like diagram of a mechanochemical cycle in which individual DNA hairpins were mechanically unfolded to high-energy states, misfolded into kinetically trapped states, and catalytically relaxed back to ground-state hairpins by a DNA chaperone. The capacity of catalytic relaxation was demonstrated in a 1D DNA hairpin array mimicking nanoassembled materials. At ≥1 μM, the diffusive (or self-walking) DNA chaperone converted the entire array of misfolded intermediates to correct conformation in less than 15 s, which is essential to rapidly prepare homogeneous nanoassemblies. Such an efficient self-walking amplification increases the signal-to-noise ratio, facilitating catalytic relaxation to recognize a 1 fM DNA chaperone in 10 min, a detection limit comparable to the best biosensing strategies.
Collapse
Affiliation(s)
- Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Sagun Jonchhe
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio 44242, United States
- Advanced Materials and Liquid Crystals Institute, Kent State University, Kent, Ohio 44242, United States
- School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| |
Collapse
|
3
|
Kang H, Yang Y, Wei B. Synthetic molecular switches driven by DNA-modifying enzymes. Nat Commun 2024; 15:3781. [PMID: 38710688 DOI: 10.1038/s41467-024-47742-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/10/2024] [Indexed: 05/08/2024] Open
Abstract
Taking inspiration from natural systems, in which molecular switches are ubiquitous in the biochemistry regulatory network, we aim to design and construct synthetic molecular switches driven by DNA-modifying enzymes, such as DNA polymerase and nicking endonuclease. The enzymatic treatments on our synthetic DNA constructs controllably switch ON or OFF the sticky end cohesion and in turn cascade to the structural association or disassociation. Here we showcase the concept in multiple DNA nanostructure systems with robust assembly/disassembly performance. The switch mechanisms are first illustrated in minimalist systems with a few DNA strands. Then the ON/OFF switches are realized in complex DNA lattice and origami systems with designated morphological changes responsive to the specific enzymatic treatments.
Collapse
Affiliation(s)
- Hong Kang
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yuexuan Yang
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China
| | - Bryan Wei
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Aksel T, Navarro EJ, Fong N, Douglas SM. Design principles for accurate folding of DNA origami. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585609. [PMID: 38562860 PMCID: PMC10983894 DOI: 10.1101/2024.03.18.585609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
We describe design principles for accurate folding of three-dimensional DNA origami. To evaluate design rules, we reduced the problem of DNA strand routing to the known problem of shortest-path finding in a weighted graph. To score candidate DNA strand routes we used a thermodynamic model that accounts for enthalpic and entropic contributions of initial binding, hybridization, and DNA loop closure. We encoded and analyzed new and previously reported design heuristics. Using design principles emerging from this analysis, we redesigned and fabricated multiple shapes and compared their folding accuracy using electrophoretic mobility analysis and electron microscopy imaging. We demonstrate accurate folding can be achieved by optimizing staple routes using our model, and provide a computational framework for applying our methodology to any design.
Collapse
Affiliation(s)
- Tural Aksel
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco
| | - Erik J. Navarro
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco
| | - Nicholas Fong
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco
| | - Shawn M. Douglas
- Department of Cellular and Molecular Pharmacology. University of California, San Francisco
| |
Collapse
|
6
|
Li L, Ding Y, Xie G, Luo S, Liu X, Wang L, Shi J, Wan Y, Fan C, Ouyang X. DNA Framework-Templated Fabrication of Ultrathin Electroactive Gold Nanosheets. Angew Chem Int Ed Engl 2024; 63:e202318646. [PMID: 38231189 DOI: 10.1002/anie.202318646] [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: 12/05/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/18/2024]
Abstract
Generally, two-dimensional gold nanomaterials have unique properties and functions that offer exciting application prospects. However, the crystal phases of these materials tend to be limited to the thermodynamically stable crystal structure. Herein, we report a DNA framework-templated approach for the ambient aqueous synthesis of freestanding and microscale amorphous gold nanosheets with ultrathin sub-nanometer thickness. We observe that extended single-stranded DNA on DNA nanosheets can induce site-specific metallization and enable precise modification of the metalized nanostructures at predefined positions. More importantly, the as-prepared gold nanosheets can serve as an electrocatalyst for glucose oxidase-catalyzed aerobic oxidation, exhibiting enhanced electrocatalytic activity (~3-fold) relative to discrete gold nanoclusters owing to a larger electrochemical active area and wider band gap. The proposed DNA framework-templated metallization strategy is expected to be applicable in a broad range of fields, from catalysis to new energy materials.
Collapse
Affiliation(s)
- Le Li
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| | - Yawen Ding
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| | - Gang Xie
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Lihua Wang
- Institute of Materials Biology, Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jiye Shi
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Ying Wan
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Xiangyuan Ouyang
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi, 710127, P. R. China
| |
Collapse
|
7
|
Chen Z, Cao L, Yun K, Lu J. Dynamic Study of Kinetically Trapped Byproducts during DNA Assembly: Case Study on a Pathway-Dependent Assembly. ACS Macro Lett 2024; 13:94-98. [PMID: 38176070 DOI: 10.1021/acsmacrolett.3c00680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Despite 40 years of development of DNA nanotechnology, the fundamental knowledge of the process of DNA strand assembly into targeted nanostructures remains unclear. Study of the dynamic process, especially the competing hybridizations in kinetic traps, provides insight into DNA assembly. In this study, a system of middle-domain first assembly (MDFA) was proposed to enable oligonucleotides to assemble into a 2D DNA monolayer in a pathway-dependent approach. This system was an ideal case to study the dynamic interactions between competing hybridizations during oligonucleotide assembly. Dynamic study revealed the coexistence of the kinetically trapped dead-end byproduct and target product at the early stage of annealing, followed by transformation of the byproduct into the target product by reverse disassembly, due to the equilibrium of the competing hybridizations increasingly favoring the target product pathway. This study offered a better understanding of the assembly pathway of DNA nanostructures for future design.
Collapse
Affiliation(s)
- Zhe Chen
- School of Forensic Medicine, Shanxi Medical University, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311100, China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
| | - Lingyan Cao
- Department of Prosthodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
| | - Jingxiong Lu
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311100, China
- Institute of Medi-X, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, China
| |
Collapse
|
8
|
Evans CG, O'Brien J, Winfree E, Murugan A. Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. Nature 2024; 625:500-507. [PMID: 38233621 PMCID: PMC10794147 DOI: 10.1038/s41586-023-06890-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/22/2023] [Indexed: 01/19/2024]
Abstract
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles1-3. Analogous high-dimensional, highly interconnected computational architectures also arise within information-processing molecular systems inside living cells, such as signal transduction cascades and genetic regulatory networks4-7. Might collective modes analogous to neural computation be found more broadly in other physical and chemical processes, even those that ostensibly play non-information-processing roles? Here we examine nucleation during self-assembly of multicomponent structures, showing that high-dimensional patterns of concentrations can be discriminated and classified in a manner similar to neural network computation. Specifically, we design a set of 917 DNA tiles that can self-assemble in three alternative ways such that competitive nucleation depends sensitively on the extent of colocalization of high-concentration tiles within the three structures. The system was trained in silico to classify a set of 18 grayscale 30 × 30 pixel images into three categories. Experimentally, fluorescence and atomic force microscopy measurements during and after a 150 hour anneal established that all trained images were correctly classified, whereas a test set of image variations probed the robustness of the results. Although slow compared to previous biochemical neural networks, our approach is compact, robust and scalable. Our findings suggest that ubiquitous physical phenomena, such as nucleation, may hold powerful information-processing capabilities when they occur within high-dimensional multicomponent systems.
Collapse
Affiliation(s)
- Constantine Glen Evans
- California Institute of Technology, Pasadena, CA, USA.
- Evans Foundation for Molecular Medicine, Pasadena, CA, USA.
- Maynooth University, Maynooth, Ireland.
| | | | - Erik Winfree
- California Institute of Technology, Pasadena, CA, USA.
| | | |
Collapse
|
9
|
Berg WR, Berengut JF, Bai C, Wimberger L, Lee LK, Rizzuto FJ. Light-Activated Assembly of DNA Origami into Dissipative Fibrils. Angew Chem Int Ed Engl 2023; 62:e202314458. [PMID: 37903739 DOI: 10.1002/anie.202314458] [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: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif-protonated, self-complementary poly(adenine) sequences-can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.
Collapse
Affiliation(s)
- Willi R Berg
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
- Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstraße 34-36, 14195, Berlin, Germany
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Changzhuang Bai
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Laura Wimberger
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Felix J Rizzuto
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| |
Collapse
|
10
|
Rossi-Gendron C, El Fakih F, Bourdon L, Nakazawa K, Finkel J, Triomphe N, Chocron L, Endo M, Sugiyama H, Bellot G, Morel M, Rudiuk S, Baigl D. Isothermal self-assembly of multicomponent and evolutive DNA nanostructures. NATURE NANOTECHNOLOGY 2023; 18:1311-1318. [PMID: 37524905 PMCID: PMC10656289 DOI: 10.1038/s41565-023-01468-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
Thermal annealing is usually needed to direct the assembly of multiple complementary DNA strands into desired entities. We show that, with a magnesium-free buffer containing NaCl, complex cocktails of DNA strands and proteins can self-assemble isothermally, at room or physiological temperature, into user-defined nanostructures, such as DNA origamis, single-stranded tile assemblies and nanogrids. In situ, time-resolved observation reveals that this self-assembly is thermodynamically controlled, proceeds through multiple folding pathways and leads to highly reconfigurable nanostructures. It allows a given system to self-select its most stable shape in a large pool of competitive DNA strands. Strikingly, upon the appearance of a new energy minimum, DNA origamis isothermally shift from one initially stable shape to a radically different one, by massive exchange of their constitutive staple strands. This method expands the repertoire of shapes and functions attainable by isothermal self-assembly and creates a basis for adaptive nanomachines and nanostructure discovery by evolution.
Collapse
Affiliation(s)
- Caroline Rossi-Gendron
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Farah El Fakih
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Laura Bourdon
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Koyomi Nakazawa
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Julie Finkel
- Centre de Biologie Structurale, Université Montpellier, CNRS, Inserm, Montpellier, France
| | - Nicolas Triomphe
- Centre de Biologie Structurale, Université Montpellier, CNRS, Inserm, Montpellier, France
- Université Grenoble Alpes, CEA, Leti,, Grenoble, France
| | - Léa Chocron
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Masayuki Endo
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Kyoto, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Ushinomaecho, Kyoto, Japan
| | - Gaëtan Bellot
- Centre de Biologie Structurale, Université Montpellier, CNRS, Inserm, Montpellier, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, France.
| |
Collapse
|
11
|
Ng C, Samanta A, Mandrup OA, Tsang E, Youssef S, Klausen LH, Dong M, Nijenhuis MAD, Gothelf KV. Folding Double-Stranded DNA into Designed Shapes with Triplex-Forming Oligonucleotides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302497. [PMID: 37311656 DOI: 10.1002/adma.202302497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/07/2023] [Indexed: 06/15/2023]
Abstract
The compaction and organization of genomic DNA is a central mechanism in eukaryotic cells, but engineered architectural control over double-stranded DNA (dsDNA) is notably challenging. Here, long dsDNA templates are folded into designed shapes via triplex-mediated self-assembly. Triplex-forming oligonucleotides (TFOs) bind purines in dsDNA via normal or reverse Hoogsteen interactions. In the triplex origami methodology, these non-canonical interactions are programmed to compact dsDNA (linear or plasmid) into well-defined objects, which demonstrate a variety of structural features: hollow and raster-filled, single- and multi-layered, with custom curvatures and geometries, and featuring lattice-free, square-, or honeycomb-pleated internal arrangements. Surprisingly, the length of integrated and free-standing dsDNA loops can be modulated with near-perfect efficiency; from hundreds down to only six bp (2 nm). The inherent rigidity of dsDNA promotes structural robustness and non-periodic structures of almost 25.000 nt are therefore formed with fewer unique starting materials, compared to other DNA-based self-assembly methods. Densely triplexed structures also resist degradation by DNase I. Triplex-mediated dsDNA folding is methodologically straightforward and orthogonal to Watson-Crick-based methods. Moreover, it enables unprecedented spatial control over dsDNA templates.
Collapse
Affiliation(s)
- Cindy Ng
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Anirban Samanta
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Ole Aalund Mandrup
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Emily Tsang
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Sarah Youssef
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Lasse Hyldgaard Klausen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Mingdong Dong
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Minke A D Nijenhuis
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Kurt V Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| |
Collapse
|
12
|
Gambietz S, Stenke LJ, Saccà B. Sequence-dependent folding of monolayered DNA origami domains. NANOSCALE 2023; 15:13120-13132. [PMID: 37503690 DOI: 10.1039/d3nr02537c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Current models of DNA origami folding can explain the yield of the assembly process and the isomerization of the structure upon the application of mechanical forces. Nevertheless, the role of the sequence in this conformational transformation is still unclear. In this work, we address this question by performing a systematic thermodynamic study of three origami domains that have an identical design but different sequence contents. By comparing the thermal stability of the domains in various settings and measuring the extent of isomerization at equilibrium (both at the global and single-molecule levels), we extract the contribution to folding given by the sequence and propose thermal criton maps of the isomers to rationalize our findings. Our data contribute to a deeper understanding of DNA origami assembly by considering both the topological- and thermal-dependent properties of the sites of initial folding. While the former are responsible for the mechanical aspects of the process, the latter justify the observed sequence-dependent conformational preferences, which appear evident in simple origami structures but remain typically undisclosed in large and more intricate architectures.
Collapse
Affiliation(s)
- Sabrina Gambietz
- Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg Essen (CENIDE), University Duisburg-Essen, 45141 Essen, Germany.
| | - Lena J Stenke
- Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg Essen (CENIDE), University Duisburg-Essen, 45141 Essen, Germany.
| | - Barbara Saccà
- Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg Essen (CENIDE), University Duisburg-Essen, 45141 Essen, Germany.
| |
Collapse
|
13
|
Pothineni BK, Grundmeier G, Keller A. Cation-dependent assembly of hexagonal DNA origami lattices on SiO 2 surfaces. NANOSCALE 2023; 15:12894-12906. [PMID: 37462427 DOI: 10.1039/d3nr02926c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO2 surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca2+ is found to be superior to Mg2+ in promoting the assembly of ordered lattices, while the presence of Mg2+ rather results in DNA origami aggregation and multilayer formation at the comparably high Na+ concentrations of 200 to 600 mM. Furthermore, Na+ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na+ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO2 surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.
Collapse
Affiliation(s)
- Bhanu Kiran Pothineni
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| |
Collapse
|
14
|
Shirt-Ediss B, Connolly J, Elezgaray J, Torelli E, Navarro SA, Bacardit J, Krasnogor N. Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists. Comput Struct Biotechnol J 2023; 21:3615-3626. [PMID: 37520280 PMCID: PMC10371787 DOI: 10.1016/j.csbj.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023] Open
Abstract
Designs for scaffolded DNA origami nanostructures are commonly and minimally published as the list of DNA staple and scaffold sequences required. In nearly all cases, high-level editable design files (e.g. caDNAno) which generated the low-level sequences are not made available. This de facto 'raw sequence' exchange format allows published origami designs to be re-attempted in the laboratory by other groups, but effectively stops designs from being significantly modified or re-purposed for new future applications. To make the raw sequence exchange format more accessible to further design and engineering, in this work we propose the first algorithmic solution to the inverse problem of converting staple/scaffold sequences back to a 'guide schematic' resembling the original origami schematic. The guide schematic can be used to aid the manual re-input of an origami into a CAD tool like caDNAno, hence recovering a high-level editable design file. Creation of a guide schematic can also be used to double check that a list of staple strand sequences does not have errors and indeed does assemble into a desired origami nanostructure prior to costly laboratory experimentation. We tested our reverse algorithm on 36 diverse origami designs from the literature and found that 29 origamis (81 %) had a good quality guide schematic recovered from raw sequences. Our software is made available at https://revnano.readthedocs.io.
Collapse
Affiliation(s)
- Ben Shirt-Ediss
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Jordan Connolly
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Juan Elezgaray
- Centre de Recherche Paul Pascal, CNRS, UMR503, Pessac 33600, France
| | - Emanuela Torelli
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Silvia Adriana Navarro
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Jaume Bacardit
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex Biosystems Research Group, School of Computing, Newcastle University, Newcastle-upon-Tyne NE4 5TG, UK
| |
Collapse
|
15
|
Falk MJ, Wu J, Matthews A, Sachdeva V, Pashine N, Gardel ML, Nagel SR, Murugan A. Learning to learn by using nonequilibrium training protocols for adaptable materials. Proc Natl Acad Sci U S A 2023; 120:e2219558120. [PMID: 37364104 PMCID: PMC10319023 DOI: 10.1073/pnas.2219558120] [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: 11/19/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Evolution in time-varying environments naturally leads to adaptable biological systems that can easily switch functionalities. Advances in the synthesis of environmentally responsive materials therefore open up the possibility of creating a wide range of synthetic materials which can also be trained for adaptability. We consider high-dimensional inverse problems for materials where any particular functionality can be realized by numerous equivalent choices of design parameters. By periodically switching targets in a given design algorithm, we can teach a material to perform incompatible functionalities with minimal changes in design parameters. We exhibit this learning strategy for adaptability in two simulated settings: elastic networks that are designed to switch deformation modes with minimal bond changes and heteropolymers whose folding pathway selections are controlled by a minimal set of monomer affinities. The resulting designs can reveal physical principles, such as nucleation-controlled folding, that enable such adaptability.
Collapse
Affiliation(s)
- Martin J. Falk
- Department of Physics, The University of Chicago, Chicago, IL60637
| | - Jiayi Wu
- Department of Physics, The University of Chicago, Chicago, IL60637
| | - Ayanna Matthews
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL60637
| | - Vedant Sachdeva
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL60637
| | - Nidhi Pashine
- School of Engineering and Applied Science, Yale University, New Haven, CT06511
| | - Margaret L. Gardel
- Department of Physics, The University of Chicago, Chicago, IL60637
- James Franck Institute, The University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL60637
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL60637
| | - Sidney R. Nagel
- Department of Physics, The University of Chicago, Chicago, IL60637
- James Franck Institute, The University of Chicago, Chicago, IL60637
| | - Arvind Murugan
- Department of Physics, The University of Chicago, Chicago, IL60637
- James Franck Institute, The University of Chicago, Chicago, IL60637
| |
Collapse
|
16
|
He Z, Shi K, Li J, Chao J. Self-assembly of DNA origami for nanofabrication, biosensing, drug delivery, and computational storage. iScience 2023; 26:106638. [PMID: 37187699 PMCID: PMC10176269 DOI: 10.1016/j.isci.2023.106638] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Since the pioneering work of immobile DNA Holliday junction by Ned Seeman in the early 1980s, the past few decades have witnessed the development of DNA nanotechnology. In particular, DNA origami has pushed the field of DNA nanotechnology to a new level. It obeys the strict Watson-Crick base pairing principle to create intricate structures with nanoscale accuracy, which greatly enriches the complexity, dimension, and functionality of DNA nanostructures. Benefiting from its high programmability and addressability, DNA origami has emerged as versatile nanomachines for transportation, sensing, and computing. This review will briefly summarize the recent progress of DNA origami, two-dimensional pattern, and three-dimensional assembly based on DNA origami, followed by introduction of its application in nanofabrication, biosensing, drug delivery, and computational storage. The prospects and challenges of assembly and application of DNA origami are also discussed.
Collapse
Affiliation(s)
- Zhimei He
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Kejun Shi
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Jinggang Li
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Jie Chao
- Key Laboratory for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors Institute of Advanced Materials (IAM) and School of Materials Science and Engineering, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Smart Health Big Data Analysis and Location Services Engineering Research Center of Jiangsu Province, School of Geographic and Biologic Information, Nanjing University of Posts & Telecommunications, Nanjing 210023, China
- Corresponding author
| |
Collapse
|
17
|
Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
Collapse
Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
| |
Collapse
|
18
|
Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang K, Pullen KM, Chiu W, Rouskin S, Bathe M. 3D RNA-scaffolded wireframe origami. Nat Commun 2023; 14:382. [PMID: 36693871 PMCID: PMC9872083 DOI: 10.1038/s41467-023-36156-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
Collapse
Affiliation(s)
- Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Matthew F Allan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shanshan Li
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Inscripta, Inc., Boulder, CO, 80027, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Krista M Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
19
|
Bednarz A, Sønderskov SM, Dong M, Birkedal V. Ion-mediated control of structural integrity and reconfigurability of DNA nanostructures. NANOSCALE 2023; 15:1317-1326. [PMID: 36545884 DOI: 10.1039/d2nr05780h] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Nucleic acid-based biomolecular self-assembly enables the creation of versatile functional architectures. Electrostatic screening of the negative charges of nucleic acids is essential for their folding and stability; thus, ions play a critical role in nucleic acid self-assembly in both biology and nanotechnology. However, the ion-DNA interplay and the resulting ion-specific structural integrity and responsiveness of DNA constructs are underexploited. Here, we harness a wide range of mono- and divalent ions to control the structural features of DNA origami constructs. Using atomic force microscopy and Förster resonance energy transfer (FRET) spectroscopy down to the single-molecule level, we report on the global and local structural performance and responsiveness of DNA origami constructs following self-assembly, upon post-assembly ion exchange and post-assembly ion-mediated reconfiguration. We determined the conditions for highly efficient DNA origami folding in the presence of several mono- (Li+, Na+, K+, Cs+) and divalent (Ca2+, Sr2+, Ba2+) ions, expanding the range where DNA origami structures can be exploited for custom-specific applications. We then manipulated fully folded constructs by exposing them to unfavorable ionic conditions that led to the emergence of substantial disintegrity but not to unfolding. Moreover, we found that poorly assembled nanostructures at low ion concentrations undergo substantial self-repair upon ion addition in the absence of free staple strands. This reconfigurability occurs in an ion type- and concentration-specific manner. Our findings provide a fundamental understanding of the ion-mediated structural responsiveness of DNA origami at the nanoscale enabling applications under a wide range of ionic conditions.
Collapse
Affiliation(s)
- Aleksandra Bednarz
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark.
| | | | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark.
| |
Collapse
|
20
|
Razbin M, Benetatos P. Elasticity of Semiflexible ZigZag Nanosprings with a Point Magnetic Moment. Polymers (Basel) 2022; 15:polym15010044. [PMID: 36616394 PMCID: PMC9823424 DOI: 10.3390/polym15010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Kinks can appear along the contour of semiflexible polymers (biopolymers or synthetic ones), and they affect their elasticity and function. A regular sequence of alternating kink defects can form a semiflexible nanospring. In this article, we theoretically analyze the elastic behavior of such a nanospring with a point magnetic dipole attached to one end while the other end is assumed to be grafted to a rigid substrate. The rod-like segments of the nanospring are treated as weakly bending wormlike chains, and the propagator (Green's function) method is used in order to calculate the conformational and elastic properties of this system. We analytically calculate the distribution of orientational and positional fluctuations of the free end, the force-extension relation, as well as the compressional force that such a spring can exert on a planar wall. Our results show how the magnetic interaction affects the elasticity of the semiflexible nanospring. This sensitivity, which is based on the interplay of positional and orientational degrees of freedom, may prove useful in magnetometry or other applications.
Collapse
Affiliation(s)
- Mohammadhosein Razbin
- Department of Energy Engineering and Physics, Amirkabir University of Technology, Tehran 14588, Iran
- Correspondence: (M.R.); (P.B.)
| | - Panayotis Benetatos
- Department of Physics, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
- Correspondence: (M.R.); (P.B.)
| |
Collapse
|
21
|
Ijäs H, Liedl T, Linko V, Posnjak G. A label-free light-scattering method to resolve assembly and disassembly of DNA nanostructures. Biophys J 2022; 121:4800-4809. [PMID: 36811525 PMCID: PMC9811603 DOI: 10.1016/j.bpj.2022.10.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/06/2022] [Accepted: 10/24/2022] [Indexed: 11/02/2022] Open
Abstract
DNA self-assembly, and in particular DNA origami, has evolved into a reliable workhorse for organizing organic and inorganic materials with nanometer precision and with exactly controlled stoichiometry. To ensure the intended performance of a given DNA structure, it is beneficial to determine its folding temperature, which in turn yields the best possible assembly of all DNA strands. Here, we show that temperature-controlled sample holders and standard fluorescence spectrometers or dynamic light-scattering setups in a static light-scattering configuration allow for monitoring the assembly progress in real time. With this robust label-free technique, we determine the folding and melting temperatures of a set of different DNA origami structures without the need for more tedious protocols. In addition, we use the method to follow digestion of DNA structures in the presence of DNase I and find strikingly different resistances toward enzymatic degradation depending on the structural design of the DNA object.
Collapse
Affiliation(s)
- Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland; Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland; LIBER Center of Excellence, Aalto University, Aalto, Finland.
| | - Gregor Posnjak
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany.
| |
Collapse
|
22
|
Confederat S, Sandei I, Mohanan G, Wälti C, Actis P. Nanopore fingerprinting of supramolecular DNA nanostructures. Biophys J 2022; 121:4882-4891. [PMID: 35986518 PMCID: PMC9808562 DOI: 10.1016/j.bpj.2022.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilizing the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale, complex, multi-tile arrays. This technique relies on the binding of hundreds of short DNA staple strands to a long single-stranded DNA scaffold that drives the folding of well-defined nanostructures. Such DNA nanostructures have enabled new applications in biosensing, drug delivery, and other multifunctional materials. In this study, we take advantage of the enhanced sensitivity of a solid-state nanopore that employs a poly-ethylene glycol enriched electrolyte to deliver real-time, non-destructive, and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures with single-entity resolution. This approach enables the quantification of the assembly yields for complex DNA origami nanostructures using the nanostructure-induced equivalent charge surplus as a discriminant. We compare the assembly yield of four supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and atomic force microscopy imaging. We demonstrate that the nanopore system can provide analytical quantification of the complex supramolecular nanostructures within minutes, without any need for labeling and with single-molecule resolution. We envision that the nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real time.
Collapse
Affiliation(s)
- Samuel Confederat
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Ilaria Sandei
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Gayathri Mohanan
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Christoph Wälti
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
| |
Collapse
|
23
|
Wang J, Wei Y, Zhang P, Wang Y, Xia Q, Liu X, Luo S, Shi J, Hu J, Fan C, Li B, Wang L, Zhou X, Li J. Probing Heterogeneous Folding Pathways of DNA Origami Self-Assembly at the Molecular Level with Atomic Force Microscopy. NANO LETTERS 2022; 22:7173-7179. [PMID: 35977401 DOI: 10.1021/acs.nanolett.2c02447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A myriad of DNA origami nanostructures have been demonstrated in various intriguing applications. In pursuit of facile yet high-yield synthesis, the mechanisms underlying DNA origami folding need to be resolved. Here, we visualize the folding processes of several multidomain DNA origami structures under ambient annealing conditions in solution using atomic force microscopy with submolecular resolution. We reveal the coexistence of diverse transitional structures that might result in the same prescribed products. Based on the experimental observations and the simulation of the energy landscapes, we propose the heterogeneity of the folding pathways of multidomain DNA origami structures. Our findings may contribute to understanding the high-yield folding mechanism of DNA origami.
Collapse
Affiliation(s)
- Jianhua Wang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yuhui Wei
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Ping Zhang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Yue Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Qinglin Xia
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules and National Centre for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shihua Luo
- Department of Traumatology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200025, China
| | - Jiye Shi
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Jun Hu
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules and National Centre for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bin Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | - Xingfei Zhou
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Jiang Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| |
Collapse
|
24
|
Cumberworth A, Frenkel D, Reinhardt A. Simulations of DNA-Origami Self-Assembly Reveal Design-Dependent Nucleation Barriers. NANO LETTERS 2022; 22:6916-6922. [PMID: 36037484 PMCID: PMC9479157 DOI: 10.1021/acs.nanolett.2c01372] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding of the scaffold strand, is unclear. Here, using Monte Carlo simulations of a lattice model of DNA origami, we find that some, but not all, designs can have a nucleation barrier and that this barrier disappears at lower temperatures, rationalizing the success of isothermal assembly. We show that the height of the nucleation barrier depends primarily on the coaxial stacking of staples that are adjacent on the same helix, a parameter that can be modified with staple design. Creating a nucleation barrier to DNA-origami assembly could be useful in optimizing assembly times and yields, while eliminating the barrier may allow for fast molecular sensors that can assemble/disassemble without hysteresis in response to changes in the environment.
Collapse
Affiliation(s)
| | - Daan Frenkel
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Aleks Reinhardt
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| |
Collapse
|
25
|
A Parallel DNA Algorithm for Solving the Quota Traveling Salesman Problem Based on Biocomputing Model. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:1450756. [PMID: 36093485 PMCID: PMC9451995 DOI: 10.1155/2022/1450756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022]
Abstract
The quota traveling salesman problem (QTSP) is a variant of the traveling salesman problem (TSP), which is a classical optimization problem. In the QTSP, the salesman visits some of the n cities to meet a given sales quota Q while having minimized travel costs. In this paper, we develop a DNA algorithm based on Adleman-Lipton model to solve the quota traveling salesman problem. Its time complexity is O(n2+Q), which is a significant improvement over previous algorithms with exponential complexity. A coding scheme of element information is pointed out, and a reasonable biological algorithm is raised by using limited conditions, whose feasibility is verified by simulation experiments. The innovation of this study is to propose a polynomial time complexity algorithm to solve the QTSP. This advantage will become more obvious as the problem scale increases compared with the algorithm of exponential computational complexity. The proposed DNA algorithm also has the significant advantages of having a large storage capacity and consuming less energy during the operation. With the maturity of DNA manipulation technology, DNA computing, as one of the parallel biological computing methods, has the potential to solve more complex NP-hard problems.
Collapse
|
26
|
You Z, Huang Q, Xu L, Liu X, Fu J, Li B, Yang Y, Li S, Qian H, Wang G. Framework nucleic acids enabled pulmonary artery endothelial cell growth inhibition by targeting microRNA-152. Chembiochem 2022; 23:e202200344. [PMID: 35904008 DOI: 10.1002/cbic.202200344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/28/2022] [Indexed: 11/11/2022]
Abstract
Pulmonary artery vascular endothelial dysfunction plays a pivotal role in the occurrence and progression of pulmonary vascular remodeling (PVR). To address this, aberrantly expressed non-coding microRNAs (miRNAs) are excellent therapeutic targets in human pulmonary artery endothelial cells (HPAECs). Here, we discovered and validated the overexpression of miRNA-152 in HPAECs under hypoxia and its role in endothelial cell dysfunction. We constructed a framework nucleic acids nanostructure that harbors six protruding single-stranded DNA segments that can fully hybridize with miRNA-152 (DNT-152). DNT-152 was efficiently taken up by HPAECs with increasing time and concentration; it markedly induced apoptosis, and inhibited HPAEC growth under hypoxic conditions. Mechanistically, DNT-152 silenced miRNA-152 expression and upregulated its target gene Meox2, which subsequently inhibited the AKT/mTOR signaling pathway. These results indicate that miRNA-152 in HPAECs may be an excellent therapeutic target against PVR, and that framework nucleic acids with carefully designed sequences are promising nanomedicines for noncancerous cells and diseases.
Collapse
Affiliation(s)
- Zaichun You
- Third Military Medical University Second Affiliated Hospital: Xinqiao Hospital, Institute of Respiratory Diseases,Department of General Practice, CHINA
| | - Qiuhong Huang
- Third Military Medical University Second Affiliated Hospital: Xinqiao Hospital, Department of General Practice, CHINA
| | - Lilin Xu
- Third Military Medical University Second Affiliated Hospital: Xinqiao Hospital, Department of General Practice, CHINA
| | - Xueping Liu
- Third Military Medical University Second Affiliated Hospital: Xinqiao Hospital, Institute of Respiratory Diseases, CHINA
| | - Juan Fu
- Third Military Medical University Second Affiliated Hospital: Xinqiao Hospital, Department of General Practice, CHINA
| | - Boxuan Li
- Changzhi Medical College, Department of Pharmacy, CHINA
| | - Yi Yang
- Third Military Medical University Second Affiliated Hospital: Xinqiao Hospital, Department of General Practice, CHINA
| | - Shuyi Li
- Third Military Medical University Second Affiliated Hospital: Xinqiao Hospital, Department of General Practice, CHINA
| | - Hang Qian
- Third Military Medical University, Institute of Respiratory Diseases, 183 Xinqiao Street, 400037, Chongqing, CHINA
| | - Guansong Wang
- Third Military Medical University Second Affiliated Hospital: Xinqiao Hospital, Institute of Respiratory Diseases, CHINA
| |
Collapse
|
27
|
Mannattil M, Schwarz JM, Santangelo CD. Thermal Fluctuations of Singular Bar-Joint Mechanisms. PHYSICAL REVIEW LETTERS 2022; 128:208005. [PMID: 35657887 DOI: 10.1103/physrevlett.128.208005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/01/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
A bar-joint mechanism is a deformable assembly of freely rotating joints connected by stiff bars. Here we develop a formalism to study the equilibration of common bar-joint mechanisms with a thermal bath. When the constraints in a mechanism cease to be linearly independent, singularities can appear in its shape space, which is the part of its configuration space after discarding rigid motions. We show that the free-energy landscape of a mechanism at low temperatures is dominated by the neighborhoods of points that correspond to these singularities. We consider two example mechanisms with shape-space singularities and find that they are more likely to be found in configurations near the singularities than others. These findings are expected to help improve the design of nanomechanisms for various applications.
Collapse
Affiliation(s)
- Manu Mannattil
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA
| | - J M Schwarz
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA
- Indian Creek Farm, Ithaca, New York 14850, USA
| | | |
Collapse
|
28
|
Xin Y, Piskunen P, Suma A, Li C, Ijäs H, Ojasalo S, Seitz I, Kostiainen MA, Grundmeier G, Linko V, Keller A. Environment-Dependent Stability and Mechanical Properties of DNA Origami Six-Helix Bundles with Different Crossover Spacings. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107393. [PMID: 35363419 DOI: 10.1002/smll.202107393] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/14/2022] [Indexed: 05/25/2023]
Abstract
The internal design of DNA nanostructures defines how they behave in different environmental conditions, such as endonuclease-rich or low-Mg2+ solutions. Notably, the inter-helical crossovers that form the core of such DNA objects have a major impact on their mechanical properties and stability. Importantly, crossover design can be used to optimize DNA nanostructures for target applications, especially when developing them for biomedical environments. To elucidate this, two otherwise identical DNA origami designs are presented that have a different number of staple crossovers between neighboring helices, spaced at 42- and 21- basepair (bp) intervals, respectively. The behavior of these structures is then compared in various buffer conditions, as well as when they are exposed to enzymatic digestion by DNase I. The results show that an increased number of crossovers significantly improves the nuclease resistance of the DNA origami by making it less accessible to digestion enzymes but simultaneously lowers its stability under Mg2+ -free conditions by reducing the malleability of the structures. Therefore, these results represent an important step toward rational, application-specific DNA nanostructure design.
Collapse
Affiliation(s)
- Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Antonio Suma
- Dipartimento di Fisica, Università di Bari and Sezione INFN di Bari, Bari, 70126, Italy
| | - Changyong Li
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Iris Seitz
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| |
Collapse
|
29
|
Dey S, Dorey A, Abraham L, Xing Y, Zhang I, Zhang F, Howorka S, Yan H. A reversibly gated protein-transporting membrane channel made of DNA. Nat Commun 2022; 13:2271. [PMID: 35484117 PMCID: PMC9051096 DOI: 10.1038/s41467-022-28522-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/14/2022] [Indexed: 01/14/2023] Open
Abstract
Controlled transport of biomolecules across lipid bilayer membranes is of profound significance in biological processes. In cells, cargo exchange is mediated by dedicated channels that respond to triggers, undergo a nanomechanical change to reversibly open, and thus regulate cargo flux. Replicating these processes with simple yet programmable chemical means is of fundamental scientific interest. Artificial systems that go beyond nature's remit in transport control and cargo are also of considerable interest for biotechnological applications but challenging to build. Here, we describe a synthetic channel that allows precisely timed, stimulus-controlled transport of folded and functional proteins across bilayer membranes. The channel is made via DNA nanotechnology design principles and features a 416 nm2 opening cross-section and a nanomechanical lid which can be controllably closed and re-opened via a lock-and-key mechanism. We envision that the functional DNA device may be used in highly sensitive biosensing, drug delivery of proteins, and the creation of artificial cell networks.
Collapse
Affiliation(s)
- Swarup Dey
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Adam Dorey
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Leeza Abraham
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Yongzheng Xing
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK
| | - Irene Zhang
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural Molecular Biology, University College London, London, UK.
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ, 85287, USA.
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
| |
Collapse
|
30
|
Hanke M, Hansen N, Chen R, Grundmeier G, Fahmy K, Keller A. Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate. Int J Mol Sci 2022; 23:ijms23052817. [PMID: 35269959 PMCID: PMC8911265 DOI: 10.3390/ijms23052817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/16/2022] Open
Abstract
DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out.
Collapse
Affiliation(s)
- Marcel Hanke
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Niklas Hansen
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Ruiping Chen
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, 01328 Dresden, Germany;
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; (M.H.); (N.H.); (R.C.); (G.G.)
- Correspondence: ; Tel.: +49-5251-605722
| |
Collapse
|
31
|
Zhang C, Yuan Y, Wu K, Wang Y, Zhu S, Shi J, Wang L, Li Q, Zuo X, Fan C, Chang C, Li J. Driving DNA Origami Assembly with a Terahertz Wave. NANO LETTERS 2022; 22:468-475. [PMID: 34968055 DOI: 10.1021/acs.nanolett.1c04369] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Terahertz (THz) waves show nontrivial interactions with living systems, but the underlying molecular mechanisms have yet to be explored. Here, we employ DNA origami as a model system to study the interactions between THz waves and DNA structures. We find that a 3-min THz illumination (35.2 THz) can drive the unwinding of DNA duplexes at ∼10 °C below their melting point. Computational study reveals that the THz wave can resonate with the vibration of DNA bases, provoking the hydrogen bond breaking. The cooperation of thermal and nonthermal effects allows the unfolding of undesired secondary structures and the THz illumination can generate diverse DNA origami assemblies with the yield (>80%) ∼ 4-fold higher than that by the contact heating at similar temperatures. We also demonstrate the in situ assembly of DNA origami in cell lysate. This method enables remotely controllable assembly of intact biomacromolecules, providing new insight into the bioeffects of THz waves.
Collapse
Affiliation(s)
- Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yifang Yuan
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 700071, China
| | - Kaijie Wu
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- Key Laboratory of Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yue Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shitai Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Chao Chang
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- School of Physics, Peking University, Beijing 100084, China
- Key Laboratory of Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Jiang Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| |
Collapse
|
32
|
Cazenille L, Baccouche A, Aubert-Kato N. Automated exploration of DNA-based structure self-assembly networks. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210848. [PMID: 34754499 PMCID: PMC8493194 DOI: 10.1098/rsos.210848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Finding DNA sequences capable of folding into specific nanostructures is a hard problem, as it involves very large search spaces and complex nonlinear dynamics. Typical methods to solve it aim to reduce the search space by minimizing unwanted interactions through restrictions on the design (e.g. staples in DNA origami or voxel-based designs in DNA Bricks). Here, we present a novel methodology that aims to reduce this search space by identifying the relevant properties of a given assembly system to the emergence of various families of structures (e.g. simple structures, polymers, branched structures). For a given set of DNA strands, our approach automatically finds chemical reaction networks (CRNs) that generate sets of structures exhibiting ranges of specific user-specified properties, such as length and type of structures or their frequency of occurrence. For each set, we enumerate the possible DNA structures that can be generated through domain-level interactions, identify the most prevalent structures, find the best-performing sequence sets to the emergence of target structures, and assess CRNs' robustness to the removal of reaction pathways. Our results suggest a connection between the characteristics of DNA strands and the distribution of generated structure families.
Collapse
Affiliation(s)
- L. Cazenille
- Department of Information Sciences, Ochanomizu University, Tokyo, Japan
| | | | - N. Aubert-Kato
- Department of Information Sciences, Ochanomizu University, Tokyo, Japan
| |
Collapse
|
33
|
Sigl C, Willner EM, Engelen W, Kretzmann JA, Sachenbacher K, Liedl A, Kolbe F, Wilsch F, Aghvami SA, Protzer U, Hagan MF, Fraden S, Dietz H. Programmable icosahedral shell system for virus trapping. NATURE MATERIALS 2021; 20:1281-1289. [PMID: 34127822 PMCID: PMC7611604 DOI: 10.1038/s41563-021-01020-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/26/2021] [Indexed: 05/21/2023]
Abstract
Broad-spectrum antiviral platforms that can decrease or inhibit viral infection would alleviate many threats to global public health. Nonetheless, effective technologies of this kind are still not available. Here, we describe a programmable icosahedral canvas for the self-assembly of icosahedral shells that have viral trapping and antiviral properties. Programmable triangular building blocks constructed from DNA assemble with high yield into various shell objects with user-defined geometries and apertures. We have created shells with molecular masses ranging from 43 to 925 MDa (8 to 180 subunits) and with internal cavity diameters of up to 280 nm. The shell interior can be functionalized with virus-specific moieties in a modular fashion. We demonstrate this virus-trapping concept by engulfing hepatitis B virus core particles and adeno-associated viruses. We demonstrate the inhibition of hepatitis B virus core interactions with surfaces in vitro and the neutralization of infectious adeno-associated viruses exposed to human cells.
Collapse
Affiliation(s)
- Christian Sigl
- Department of Physics, Technical University of Munich, Munich, Germany
| | - Elena M Willner
- Department of Physics, Technical University of Munich, Munich, Germany
| | - Wouter Engelen
- Department of Physics, Technical University of Munich, Munich, Germany
| | | | - Ken Sachenbacher
- Department of Physics, Technical University of Munich, Munich, Germany
| | - Anna Liedl
- Department of Physics, Technical University of Munich, Munich, Germany
| | - Fenna Kolbe
- Institute of Virology, School of Medicine, Technical University of Munich and Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research, Munich, Germany
| | - Florian Wilsch
- Institute of Virology, School of Medicine, Technical University of Munich and Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research, Munich, Germany
| | - S Ali Aghvami
- Department of Physics, Brandeis University, Waltham, MA, USA
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich and Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research, Munich, Germany
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, MA, USA
| | - Seth Fraden
- Department of Physics, Brandeis University, Waltham, MA, USA
| | - Hendrik Dietz
- Department of Physics, Technical University of Munich, Munich, Germany.
| |
Collapse
|
34
|
Abstract
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent kinetics, but this has received considerably less attention. Using recent advances in automatic differentiation, we show how kinetic pathways can be precisely designed by directly differentiating through statistical physics models, namely free energy calculations and molecular dynamics simulations. We consider two systems that are crucial to our understanding of structural self-assembly: bulk crystallization and small nanoclusters. In each case, we are able to assemble precise dynamical features. Using gradient information, we manipulate interactions among constituent particles to tune the rate at which these systems yield specific structures of interest. Moreover, we use this approach to learn nontrivial features about the high-dimensional design space, allowing us to accurately predict when multiple kinetic features can be simultaneously and independently controlled. These results provide a concrete and generalizable foundation for studying nonstructural self-assembly, including kinetic properties as well as other complex emergent properties, in a vast array of systems.
Collapse
|
35
|
Green CM, Hughes WL, Graugnard E, Kuang W. Correlative Super-Resolution and Atomic Force Microscopy of DNA Nanostructures and Characterization of Addressable Site Defects. ACS NANO 2021; 15:11597-11606. [PMID: 34137595 DOI: 10.1021/acsnano.1c01976] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To bring real-world applications of DNA nanostructures to fruition, advanced microscopy techniques are needed to shed light on factors limiting the availability of addressable sites. Correlative microscopy, where two or more microscopies are combined to characterize the same sample, is an approach to overcome the limitations of individual techniques, yet it has seen limited use for DNA nanotechnology. We have developed an accessible strategy for high resolution, correlative DNA-based points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution and atomic force microscopy (AFM) of DNA nanostructures, enabled by a simple and robust method to selectively bind DNA origami to cover glass. Using this technique, we examined addressable "docking" sites on DNA origami to distinguish between two defect scenarios-structurally incorporated but inactive docking sites, and unincorporated docking sites. We found that over 75% of defective docking sites were incorporated but inactive, suggesting unincorporated strands played a minor role in limiting the availability of addressable sites. We further explored the effects of strand purification, UV irradiation, and photooxidation on availability, providing insight on potential sources of defects and pathways toward improving the fidelity of DNA nanostructures.
Collapse
Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, D.C. 20375, United States
- National Research Council, 500 fifth St NW, Washington, D.C. 20001, United States
| | | | | | | |
Collapse
|
36
|
Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
Collapse
Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| |
Collapse
|
37
|
Johnson JA, Kolliopoulos V, Castro CE. Co-self-assembly of multiple DNA origami nanostructures in a single pot. Chem Commun (Camb) 2021; 57:4795-4798. [PMID: 33982710 DOI: 10.1039/d1cc00049g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simultaneous self-assembly of two distinct DNA origami nanostructures folded with the same scaffold strand was achieved in a single pot. Relative yields were tuned by adjusting concentrations of the competing strands, correlating well with folding kinetics of individual structures. These results can faciliate efficient fabrication of multi-structure systems and materials.
Collapse
Affiliation(s)
- Joshua A Johnson
- Biophysics Graduate Program, The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA.
| | - Vasiliki Kolliopoulos
- Department of Chemical and Biomolecular Engineering, The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA
| | - Carlos E Castro
- Biophysics Graduate Program, The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA. and Department of Mechanical and Aerospace Engineering, The Ohio State University, 281 W Lane Ave, Columbus, OH 43210, USA
| |
Collapse
|
38
|
Glaser M, Deb S, Seier F, Agrawal A, Liedl T, Douglas S, Gupta MK, Smith DM. The Art of Designing DNA Nanostructures with CAD Software. Molecules 2021; 26:molecules26082287. [PMID: 33920889 PMCID: PMC8071251 DOI: 10.3390/molecules26082287] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.
Collapse
Affiliation(s)
- Martin Glaser
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany;
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
| | - Sourav Deb
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
| | - Florian Seier
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
| | - Amay Agrawal
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539 München, Germany;
| | - Shawn Douglas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA;
| | - Manish K. Gupta
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
- Correspondence: (M.K.G.); (D.M.S.)
| | - David M. Smith
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany;
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany; (F.S.); (A.A.)
- Dhirubhai Ambani Institute of Information and Communication Technology, Gandhinagar 382 007, India;
- Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany
- Correspondence: (M.K.G.); (D.M.S.)
| |
Collapse
|
39
|
Li R, Chen H, Choi JH. Topological Assembly of a Deployable Hoberman Flight Ring from DNA. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2007069. [PMID: 33615664 DOI: 10.1002/smll.202007069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Deployable geometries are finite auxetic structures that preserve their overall shapes during expansion and contraction. The topological behaviors emerge from intricately arranged elements and their connections. Despite the considerable utility of such configurations in nature and in engineering, deployable nanostructures have never been demonstrated. Here a deployable flight ring, a simplified planar structure of Hoberman sphere is shown, using DNA origami. The DNA flight ring consists of topologically assembled six triangles in two layers that can slide against each other, thereby switching between two distinct (open and closed) states. The origami topology is a trefoil knot, and its auxetic reconfiguration results in negative Poisson's ratios. This work shows the feasibility of deployable nanostructures, providing a versatile platform for topological studies and opening new opportunities for bioengineering.
Collapse
Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Haorong Chen
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
40
|
Majikes JM, Patrone PN, Kearsley AJ, Zwolak M, Liddle JA. Failure Mechanisms in DNA Self-Assembly: Barriers to Single-Fold Yield. ACS NANO 2021; 15:3284-3294. [PMID: 33565312 PMCID: PMC11005093 DOI: 10.1021/acsnano.0c10114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding the folding process of DNA origami is a critical stepping stone to the broader implementation of nucleic acid nanofabrication technology but is notably nontrivial. Origami are formed by several hundred cooperative hybridization events-folds-between spatially separate domains of a scaffold, derived from a viral genome, and oligomeric staples. Individual events are difficult to detect. Here, we present a real-time probe of the unit operation of origami assembly, a single fold, across the scaffold as a function of hybridization domain separation-fold distance-and staple/scaffold ratio. This approach to the folding problem elucidates a predicted but previously unobserved blocked state that acts as a limit on yield for single folds, which may manifest as a barrier in whole origami assembly.
Collapse
Affiliation(s)
- Jacob M. Majikes
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - Paul N. Patrone
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - Anthony J. Kearsley
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - Michael Zwolak
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - J. Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| |
Collapse
|
41
|
Cabello-Garcia J, Bae W, Stan GBV, Ouldridge TE. Handhold-Mediated Strand Displacement: A Nucleic Acid Based Mechanism for Generating Far-from-Equilibrium Assemblies through Templated Reactions. ACS NANO 2021; 15:3272-3283. [PMID: 33470806 DOI: 10.1021/acsnano.0c10068] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The use of templates is a well-established method for the production of sequence-controlled assemblies, particularly long polymers. Templating is canonically envisioned as akin to a self-assembly process, wherein sequence-specific recognition interactions between a template and a pool of monomers favor the assembly of a particular polymer sequence at equilibrium. However, during the biogenesis of sequence-controlled polymers, template recognition interactions are transient; RNA and proteins detach spontaneously from their templates to perform their biological functions and allow template reuse. Breaking template recognition interactions puts the product sequence distribution far from equilibrium, since specific product formation can no longer rely on an equilibrium dominated by selective copy-template bonds. The rewards of engineering artificial polymer systems capable of spontaneously exhibiting nonequilibrium templating are large, but fields like DNA nanotechnology lack the requisite tools; the specificity and drive of conventional DNA reactions rely on product stability at equilibrium, sequestering any recognition interaction in products. The proposed alternative is handhold-mediated strand displacement (HMSD), a DNA-based reaction mechanism suited to producing out-of-equilibrium products. HMSD decouples the drive and specificity of the reaction by introducing a transient recognition interaction, the handhold. We measure the kinetics of 98 different HMSD systems to prove that handholds can accelerate displacement by 4 orders of magnitude without being sequestered in the final product. We then use HMSD to template the selective assembly of any one product DNA duplex from an ensemble of equally stable alternatives, generating a far-from-equilibrium output. HMSD thus brings DNA nanotechnology closer to the complexity of out-of-equilibrium biological systems.
Collapse
Affiliation(s)
- Javier Cabello-Garcia
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, SW7 2AZ London, U.K
| | - Wooli Bae
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, SW7 2AZ London, U.K
| | - Guy-Bart V Stan
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, SW7 2AZ London, U.K
| | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, SW7 2AZ London, U.K
| |
Collapse
|
42
|
Menssen RJ, Kimmel GJ, Tokmakoff A. Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations. J Chem Phys 2021; 154:045101. [PMID: 33514113 DOI: 10.1063/5.0035187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this work, we present a kinetic Markov state Monte Carlo model designed to complement temperature-jump (T-jump) infrared spectroscopy experiments probing the kinetics and dynamics of short DNA oligonucleotides. The model is designed to be accessible to experimental researchers in terms of both computational simplicity and expense while providing detailed insights beyond those provided by experimental methods. The model is an extension of a thermodynamic lattice model for DNA hybridization utilizing the formalism of the nucleation-zipper mechanism. Association and dissociation trajectories were generated utilizing the Gillespie algorithm and parameters determined via fitting the association and dissociation timescales to previously published experimental data. Terminal end fraying, experimentally observed following a rapid T-jump, in the sequence 5'-ATATGCATAT-3' was replicated by the model that also demonstrated that experimentally observed fast dynamics in the sequences 5'-C(AT)nG-3', where n = 2-6, were also due to terminal end fraying. The dominant association pathways, isolated by transition pathway theory, showed two primary motifs: initiating at or next to a G:C base pair, which is enthalpically favorable and related to the increased strength of G:C base pairs, and initiating in the center of the sequence, which is entropically favorable and related to minimizing the penalty associated with the decrease in configurational entropy due to hybridization.
Collapse
Affiliation(s)
- Ryan J Menssen
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Gregory J Kimmel
- Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, Florida 33612, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| |
Collapse
|
43
|
|
44
|
Razbin M, Mashaghi A. Elasticity of connected semiflexible quadrilaterals. SOFT MATTER 2021; 17:102-112. [PMID: 33150925 DOI: 10.1039/d0sm01719a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Using the positional-orientational propagator of a semiflexible filament in the weakly bending regime, we analytically calculate the probability densities associated with the fluctuating tip and the corners of a grafted system of connected quadrilaterals. We calculate closed analytic expressions for the probability densities within the framework of the worm-like chain model, which are valid in the weakly bending regime. The probability densities give the physical quantities related to the elasticity of the system such as the force-extension relation in the fixed extension ensemble, the Poisson's ratio and the average of the force exerted to a confining stiff planar wall by the fluctuating tip of the system. Our analysis reveals that the force-extension relations depend on the contour length of the system (material content), the bending stiffness (chemical nature), the geometrical angle and the number of the quadrilaterals, while the Poisson's ratio depends only on the geometrical angle and the number of the quadrilaterals, and is thus a purely geometric property of the system.
Collapse
Affiliation(s)
- Mohammadhosein Razbin
- Department of Energy Engineering and Physics, Amirkabir University of Technology, 14588 Tehran, Iran.
| | | |
Collapse
|
45
|
Berengut JF, Wong CK, Berengut JC, Doye JPK, Ouldridge TE, Lee LK. Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation. ACS NANO 2020; 14:17428-17441. [PMID: 33232603 DOI: 10.1021/acsnano.0c07696] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biology demonstrates how a near infinite array of complex systems and structures at many scales can originate from the self-assembly of component parts on the nanoscale. But to fully exploit the benefits of self-assembly for nanotechnology, a crucial challenge remains: How do we rationally encode well-defined global architectures in subunits that are much smaller than their assemblies? Strain accumulation via geometric frustration is one mechanism that has been used to explain the self-assembly of global architectures in diverse and complex systems a posteriori. Here we take the next step and use strain accumulation as a rational design principle to control the length distributions of self-assembling polymers. We use the DNA origami method to design and synthesize a molecular subunit known as the PolyBrick, which perturbs its shape in response to local interactions via flexible allosteric blocking domains. These perturbations accumulate at the ends of polymers during growth, until the deformation becomes incompatible with further extension. We demonstrate that the key thermodynamic factors for controlling length distributions are the intersubunit binding free energy and the fundamental strain free energy, both which can be rationally encoded in a PolyBrick subunit. While passive polymerization yields geometrical distributions, which have the highest statistical length uncertainty for a given mean, the PolyBrick yields polymers that approach Gaussian length distributions whose variance is entirely determined by the strain free energy. We also show how strain accumulation can in principle yield length distributions that become tighter with increasing subunit affinity and approach distributions with uniform polymer lengths. Finally, coarse-grained molecular dynamics and Monte Carlo simulations delineate and quantify the dominant forces influencing strain accumulation in a molecular system. This study constitutes a fundamental investigation of the use of strain accumulation as a rational design principle in molecular self-assembly.
Collapse
Affiliation(s)
- Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales Sydney 2052, Australia
| | - Chak Kui Wong
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Julian C Berengut
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales Sydney 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
| |
Collapse
|
46
|
Insights into the Structure and Energy of DNA Nanoassemblies. Molecules 2020; 25:molecules25235466. [PMID: 33255286 PMCID: PMC7727707 DOI: 10.3390/molecules25235466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.
Collapse
|
47
|
Young KG, Najafi B, Sant WM, Contera S, Louis AA, Doye JPK, Turberfield AJ, Bath J. Reconfigurable T‐junction DNA Origami. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Behnam Najafi
- Department of Physics University of Oxford Parks Road Oxford OX1 3PU UK
| | - William M. Sant
- Department of Chemistry University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Sonia Contera
- Department of Physics University of Oxford Parks Road Oxford OX1 3PU UK
| | - Ard A. Louis
- Department of Physics University of Oxford Parks Road Oxford OX1 3PU UK
| | - Jonathan P. K. Doye
- Department of Chemistry University of Oxford South Parks Road Oxford OX1 3QZ UK
| | | | - Jonathan Bath
- Department of Physics University of Oxford Parks Road Oxford OX1 3PU UK
| |
Collapse
|
48
|
Young KG, Najafi B, Sant WM, Contera S, Louis AA, Doye JPK, Turberfield AJ, Bath J. Reconfigurable T-junction DNA Origami. Angew Chem Int Ed Engl 2020; 59:15942-15946. [PMID: 32524699 DOI: 10.1002/anie.202006281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Indexed: 01/24/2023]
Abstract
DNA self-assembly allows the construction of nanometre-scale structures and devices. Structures with thousands of unique components are routinely assembled in good yield. Experimental progress has been rapid, based largely on empirical design rules. Herein, we demonstrate a DNA origami technique designed as a model system with which to explore the mechanism of assembly. The origami fold is controlled through single-stranded loops embedded in a double-stranded DNA template and is programmed by a set of double-stranded linkers that specify pairwise interactions between loop sequences. Assembly is via T-junctions formed by hybridization of single-stranded overhangs on the linkers with the loops. The sequence of loops on the template and the set of interaction rules embodied in the linkers can be reconfigured with ease. We show that a set of just two interaction rules can be used to assemble simple T-junction origami motifs and that assembly can be performed at room temperature.
Collapse
Affiliation(s)
- Katherine G Young
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Behnam Najafi
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - William M Sant
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Sonia Contera
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Ard A Louis
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| | - Jonathan P K Doye
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | | | - Jonathan Bath
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
| |
Collapse
|
49
|
Majikes JM, Patrone PN, Schiffels D, Zwolak M, Kearsley AJ, Forry SP, Liddle JA. Revealing thermodynamics of DNA origami folding via affine transformations. Nucleic Acids Res 2020; 48:5268-5280. [PMID: 32347943 PMCID: PMC7261180 DOI: 10.1093/nar/gkaa283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 04/07/2020] [Accepted: 04/28/2020] [Indexed: 01/25/2023] Open
Abstract
Structural DNA nanotechnology, as exemplified by DNA origami, has enabled the design and construction of molecularly-precise objects for a myriad of applications. However, limitations in imaging, and other characterization approaches, make a quantitative understanding of the folding process challenging. Such an understanding is necessary to determine the origins of structural defects, which constrain the practical use of these nanostructures. Here, we combine careful fluorescent reporter design with a novel affine transformation technique that, together, permit the rigorous measurement of folding thermodynamics. This method removes sources of systematic uncertainty and resolves problems with typical background-correction schemes. This in turn allows us to examine entropic corrections associated with folding and potential secondary and tertiary structure of the scaffold. Our approach also highlights the importance of heat-capacity changes during DNA melting. In addition to yielding insight into DNA origami folding, it is well-suited to probing fundamental processes in related self-assembling systems.
Collapse
Affiliation(s)
- Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Paul N Patrone
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Daniel Schiffels
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Michael Zwolak
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Anthony J Kearsley
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Samuel P Forry
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| |
Collapse
|
50
|
Cao HH, Abel GR, Gu Q, Gueorguieva GAV, Zhang Y, Nanney WA, Provencio ET, Ye T. Seeding the Self-Assembly of DNA Origamis at Surfaces. ACS NANO 2020; 14:5203-5212. [PMID: 32053349 DOI: 10.1021/acsnano.9b09348] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Unlike supramolecular self-assembly methods that can organize many distinct components into designer shapes in a homogeneous solution (e.g., DNA origami), only relatively simple, symmetric structures consisting of a few distinct components have been self-assembled at solid surfaces. As the self-assembly process is confined to the surface/interface by mostly nonspecific attractive interactions, an open question is how these interfacial interactions affect multicomponent self-assembly. To gain a mechanistic understanding of the roles of the surface environment in DNA origami self-assembly, here we studied the oligonucleotide-assisted folding of a long single-stranded DNA (ssDNA scaffold) that was end-tethered to a dynamic surface, which could actively regulate the DNA-surface interactions. The results showed that even weak surface attractions can lead to defective structures by inhibiting the merging of multiple domains into complete structures. A combination of surface anchoring and deliberate regulation of DNA-surface interactions allowed us to depart from the existing paradigm of surface confinement via nonspecific interactions and enabled DNA origami folding to proceed in a solution-like environment. Importantly, our strategy retains the key advantages of surface-mediated self-assembly. For example, surface-anchored oligonucleotides could sequence-specifically initiate the growth of DNA origamis of specific sizes and shapes. Our work enables information to be encoded into a surface and expressed into complex DNA surface architectures for potential nanoelectronic and nanophotonic applications. In addition, our approach to surface confinement may facilitate the 2D self-assembly of other molecular components, such as proteins, as maintaining conformational freedom may be a general challenge in the self-assembly of complex structures at surfaces.
Collapse
Affiliation(s)
- Huan H Cao
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Gary R Abel
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Qufei Gu
- Materials and Biomaterials Science and Engineering, University of California, Merced, California 95343, United States
| | | | - Yehan Zhang
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Warren A Nanney
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Eric T Provencio
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Tao Ye
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
- Materials and Biomaterials Science and Engineering, University of California, Merced, California 95343, United States
| |
Collapse
|