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Posnjak G, Yin X, Butler P, Bienek O, Dass M, Lee S, Sharp ID, Liedl T. Diamond-lattice photonic crystals assembled from DNA origami. Science 2024; 384:781-785. [PMID: 38753795 PMCID: PMC7616107 DOI: 10.1126/science.adl2733] [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: 10/27/2023] [Accepted: 03/01/2024] [Indexed: 05/18/2024]
Abstract
Colloidal self-assembly allows rational design of structures on the micrometer and submicrometer scale. One architecture that can generate complete three-dimensional photonic bandgaps is the diamond cubic lattice, which has remained difficult to realize at length scales comparable with the wavelength of visible or ultraviolet light. In this work, we demonstrate three-dimensional photonic crystals self-assembled from DNA origami that act as precisely programmable patchy colloids. Our DNA-based nanoscale tetrapods crystallize into a rod-connected diamond cubic lattice with a periodicity of 170 nanometers. This structure serves as a scaffold for atomic-layer deposition of high-refractive index materials such as titanium dioxide, yielding a tunable photonic bandgap in the near-ultraviolet.
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Affiliation(s)
- Gregor Posnjak
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, Schellingstraße 4, München, 80539, Bayern, Germany
| | - Xin Yin
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, Schellingstraße 4, München, 80539, Bayern, Germany
| | - Paul Butler
- Walter Schottky Institute, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
- Physics Department, TUM School of Natural Sciences, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
| | - Oliver Bienek
- Walter Schottky Institute, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
- Physics Department, TUM School of Natural Sciences, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
| | - Mihir Dass
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, Schellingstraße 4, München, 80539, Bayern, Germany
| | - Seungwoo Lee
- Department of Integrative Energy Engineering (College of Engineering), KU-KIST Graduate School of Converging Science and Technology, Department of Biomicrosystem Technology, and KU Photonics Center, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02481, Republic of Korea
- Center for Opto-Electronic Materials and Devices, Post-Silicon Semiconductor Institute, Korea Institute of Science and Technology (KIST), 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Ian D. Sharp
- Walter Schottky Institute, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
- Physics Department, TUM School of Natural Sciences, Technical University of Munich, Am Coulombwall 4, Garching bei München, 85748, Bayern, Germany
| | - Tim Liedl
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, Schellingstraße 4, München, 80539, Bayern, Germany
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2
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Duque CM, Hall DM, Tyukodi B, Hagan MF, Santangelo CD, Grason GM. Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra. Proc Natl Acad Sci U S A 2024; 121:e2315648121. [PMID: 38669182 PMCID: PMC11067059 DOI: 10.1073/pnas.2315648121] [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: 09/08/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. Inspired by a recent class of programmable DNA origami colloids, we demonstrate that the economy of design in these crystalline assemblies-in terms of the growth of the number of distinct particle species required with the increased size-scale (e.g., periodicity)-is comparable to viral shells. We further test the role of geometric specificity in these assemblies via dynamical assembly simulations, which show that conditions for simultaneously efficient and high-fidelity assembly require an intermediate degree of flexibility of local angles and lengths in programmed assembly. Off-target misassembly occurs via incorporation of a variant of disclination defects, generalized to the case of hyperbolic crystals. The possibility of these topological defects is a direct consequence of the very same symmetry principles that underlie the economical design, exposing a basic tradeoff between design economy and fidelity of programmable, size controlled assembly.
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Affiliation(s)
- Carlos M. Duque
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
- Department of Physics, University of Massachusetts, Amherst, MA01003
| | - Douglas M. Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
| | - Botond Tyukodi
- Department of Physics, Babes-Bolyai University, Cluj-Napoca400084, Romania
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Christian D. Santangelo
- Department of Physics, University of Massachusetts, Amherst, MA01003
- Department of Physics, Syracuse University, Syracuse, NY13210
| | - Gregory M. Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
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3
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Chen Y, Zhang HA, El-Ghazaly A. Tuning the dimensional order in self-assembled magnetic nanostructures: theory, simulations, and experiments. NANOSCALE 2024. [PMID: 38525804 DOI: 10.1039/d3nr06299f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
A major obstacle to building nanoscale magnetic devices or even experimentally studying novel nanomagnetic spin textures is the present lack of a simple and robust method to fabricate various nano-structured alloys. Here, theoretical and experimental investigations were conducted to understand the underlying physical mechanisms of magnetic particle self-assembly in zero applied magnetic field. By changing the amount of NaOH added during the synthesis, we demonstrate that the resulting morphology of the assembled FeCo structure can be tuned from zero-dimensional (0D) nanoparticles to one-dimensional (1D) chains, and even three-dimensional (3D) networks. Two numerical simulations were developed to predict aspects of nanostructure formation by accounting for the magnetic interactions between individual magnetic nanoparticles. The first utilized the Boltzmann distribution to determine the equilibrium structure of a nanochain, iteratively predicting the local deviation angle θ of each particle as it attaches to a forming chain. The second simulation illustrates the differences in nanostructure arrangement and dimensionality (0D, 1D, or 3D) that arise from random interactions at various nanoparticle densities. The simulation results closely match the experimental findings, as seen from SEM images, demonstrating their ability to capture the system's structural properties. In addition, magnetic hysteresis measurements of the samples were performed along two orthogonal directions to show the influence of dimensional order on the magnetic behavior. The normalized remanence (MR/MS||) of the FeCo alloys increases as the dimensions of nanostructures are increased. Of the three cases, the FeCo 3D network structures exhibit the highest normalized nanostructure remanence of 0.33 and an increased coercivity to above 200 Oe at 300 K. This combined numerical and experimental investigation aims to shed light on the preparation of FeCo nanostructures with tailorable dimensional order and it opens new avenues for exploring the complex spin textures and coercive behavior of these multi-dimensional nanomagnetic structures.
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Affiliation(s)
- Yulan Chen
- Department of Materials Science and Engineering, Cornell University, Ithaca, New York 14853, USA.
| | - Hanyu Alice Zhang
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Amal El-Ghazaly
- School of Electrical and Computer Engineering, Cornell University, Ithaca, New York 14853, USA.
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4
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Michelson A, Subramanian A, Kisslinger K, Tiwale N, Xiang S, Shen E, Kahn JS, Nykypanchuk D, Yan H, Nam CY, Gang O. Three-dimensional nanoscale metal, metal oxide, and semiconductor frameworks through DNA-programmable assembly and templating. SCIENCE ADVANCES 2024; 10:eadl0604. [PMID: 38198553 PMCID: PMC10780874 DOI: 10.1126/sciadv.adl0604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024]
Abstract
Controlling the three-dimensional (3D) nanoarchitecture of inorganic materials is imperative for enabling their novel mechanical, optical, and electronic properties. Here, by exploiting DNA-programmable assembly, we establish a general approach for realizing designed 3D ordered inorganic frameworks. Through inorganic templating of DNA frameworks by liquid- and vapor-phase infiltrations, we demonstrate successful nanofabrication of diverse classes of inorganic frameworks from metal, metal oxide and semiconductor materials, as well as their combinations, including zinc, aluminum, copper, molybdenum, tungsten, indium, tin, and platinum, and composites such as aluminum-doped zinc oxide, indium tin oxide, and platinum/aluminum-doped zinc oxide. The open 3D frameworks have features on the order of nanometers with architecture prescribed by the DNA frames and self-assembled lattice. Structural and spectroscopic studies reveal the composition and organization of diverse inorganic frameworks, as well as the optoelectronic properties of selected materials. The work paves the road toward establishing a 3D nanoscale lithography.
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Affiliation(s)
- Aaron Michelson
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA
| | - Ashwanth Subramanian
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Kim Kisslinger
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nikhil Tiwale
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Shuting Xiang
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
| | - Eric Shen
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
| | - Jason S. Kahn
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Dmytro Nykypanchuk
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hanfei Yan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Chang-Yong Nam
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
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5
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Wang S, Lin PA, DeLuca M, Zauscher S, Arya G, Ke Y. Controlling Silicification on DNA Origami with Polynucleotide Brushes. J Am Chem Soc 2024; 146:358-367. [PMID: 38117542 PMCID: PMC10785815 DOI: 10.1021/jacs.3c09310] [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: 08/27/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However, the silicification reaction is sensitive to the reaction conditions and often results in uncontrolled DNA origami aggregation, especially when growth of thicker silica layers is desired. Here, we investigated how site-specifically placed polynucleotide brushes influence the silicification of DNA origami. Our experiments showed that long DNA brushes, in the form of single- or double-stranded DNA, significantly suppress the aggregation of DNA origami during the silicification process. Furthermore, we found that double-stranded DNA brushes selectively promote silica growth on DNA origami surfaces. These observations were supported and explained by coarse-grained molecular dynamics simulations. This work provides new insights into our understanding of the silicification process on DNA and provides a powerful toolset for the development of novel DNA-based organic-inorganic nanomaterials.
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Affiliation(s)
- Shuang Wang
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Po-An Lin
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Marcello DeLuca
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Stefan Zauscher
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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6
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Mao R, Minevich B, McKeen D, Chen Q, Lu F, Gang O, Mittal J. Regulating phase behavior of nanoparticle assemblies through engineering of DNA-mediated isotropic interactions. Proc Natl Acad Sci U S A 2023; 120:e2302037120. [PMID: 38109548 PMCID: PMC10756293 DOI: 10.1073/pnas.2302037120] [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: 02/06/2023] [Accepted: 11/14/2023] [Indexed: 12/20/2023] Open
Abstract
Self-assembly of isotropically interacting particles into desired crystal structures could allow for creating designed functional materials via simple synthetic means. However, the ability to use isotropic particles to assemble different crystal types remains challenging, especially for generating low-coordinated crystal structures. Here, we demonstrate that isotropic pairwise interparticle interactions can be rationally tuned through the design of DNA shells in a range that allows transition from common, high-coordinated FCC-CuAu and BCC-CsCl lattices, to more exotic symmetries for spherical particles such as the SC-NaCl lattice and to low-coordinated crystal structures (i.e., cubic diamond, open honeycomb). The combination of computational and experimental approaches reveals such a design strategy using DNA-functionalized nanoparticles and successfully demonstrates the realization of BCC-CsCl, SC-NaCl, and a weakly ordered cubic diamond phase. The study reveals the phase behavior of isotropic nanoparticles for DNA-shell tunable interaction, which, due to the ease of synthesis is promising for the practical realization of non-close-packed lattices.
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Affiliation(s)
- Runfang Mao
- Department of Chemical Engineering and Materials Science, University of Minnesota–Twin Cities, Minneapolis, MN55455
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, NY10027
| | - Daniel McKeen
- Department of Chemical Engineering, Columbia University, New York, NY10027
| | - Qizan Chen
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX77843
| | - Fang Lu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY11973
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, NY10027
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY11973
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY10027
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX77843
- Department of Chemistry, Texas A&M University, College Station, TX77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX77843
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7
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Adhikari S, Minevich B, Redeker D, Michelson AN, Emamy H, Shen E, Gang O, Kumar SK. Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions. J Am Chem Soc 2023; 145:19578-19587. [PMID: 37651692 DOI: 10.1021/jacs.3c03181] [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: 09/02/2023]
Abstract
Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or "material voxels" and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. X-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.
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Affiliation(s)
- Sabin Adhikari
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Daniel Redeker
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Aaron Noam Michelson
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Hamed Emamy
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Eric Shen
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Sanat K Kumar
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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8
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Yang S, Wang Y, Wang Q, Li F, Ling D. DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:340-355. [PMID: 37501793 PMCID: PMC10369495 DOI: 10.1021/cbmi.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 04/07/2023] [Indexed: 07/29/2023]
Abstract
DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.
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Affiliation(s)
- Shengfei Yang
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuqi Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Qiyue Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Fangyuan Li
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
| | - Daishun Ling
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
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9
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Kasyanenko N, Baryshev A, Artamonova D, Sokolov P. Packaging of DNA Integrated with Metal Nanoparticles in Solution. ENTROPY (BASEL, SWITZERLAND) 2023; 25:1052. [PMID: 37509999 PMCID: PMC10378076 DOI: 10.3390/e25071052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023]
Abstract
The transformation of high-molecular DNA from a random swollen coil in a solution to a discrete nanosized particle with the ordered packaging of a rigid and highly charged double-stranded molecule is one of the amazing phenomena of polymer physics. DNA condensation is a well-known phenomenon in biological systems, yet its molecular mechanism is not clear. Understanding the processes occurring in vivo is necessary for the usage of DNA in the fabrication of new biologically significant nanostructures. Entropy plays a very important role in DNA condensation. DNA conjugates with metal nanoparticles are useful in various fields of nanotechnology. In particular, they can serve as a basis for creating multicomponent nanoplatforms for theranostics. DNA must be in a compact state in such constructions. In this paper, we tested the methods of DNA integration with silver, gold and palladium nanoparticles and analyzed the properties of DNA conjugates with metal nanoparticles using the methods of atomic force microscopy, spectroscopy, viscometry and dynamic light scattering. DNA size, stability and rigidity (persistence length), as well as plasmon resonance peaks in the absorption spectra of systems were studied. The methods for DNA condensation with metal nanoparticles were analyzed.
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Affiliation(s)
- Nina Kasyanenko
- Faculty of Physics, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Andrei Baryshev
- Faculty of Physics, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Daria Artamonova
- Faculty of Physics, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Petr Sokolov
- Faculty of Physics, Saint Petersburg State University, Saint Petersburg 199034, Russia
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10
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Dai L, Hu X, Ji M, Ma N, Xing H, Zhu JJ, Min Q, Tian Y. Programming the morphology of DNA origami crystals by magnesium ion strength. Proc Natl Acad Sci U S A 2023; 120:e2302142120. [PMID: 37399399 PMCID: PMC10334761 DOI: 10.1073/pnas.2302142120] [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: 02/07/2023] [Accepted: 05/31/2023] [Indexed: 07/05/2023] Open
Abstract
Harnessing the programmable nature of DNA origami for controlling structural features in crystalline materials affords opportunities to bring crystal engineering to a remarkable level. However, the challenge of crystallizing a single type of DNA origami unit into varied structural outcomes remains, given the requirement for specific DNA designs for each targeted structure. Here, we show that crystals with distinct equilibrium phases and shapes can be realized using a single DNA origami morphology with an allosteric factor to modulate the binding coordination. As a result, origami crystals undergo phase transitions from a simple cubic lattice to a simple hexagonal (SH) lattice and eventually to a face-centered cubic (FCC) lattice. After selectively removing internal nanoparticles from DNA origami building blocks, the body-centered tetragonal and chalcopyrite lattice are derived from the SH and FCC lattices, respectively, revealing another phase transition involving crystal system conversions. The rich phase space was realized through the de novo synthesis of crystals under varying solution environments, followed by the individual characterizations of the resulting products. Such phase transitions can lead to associated transitions in the shape of the resulting products. Hexagonal prism crystals, crystals characterized by triangular facets, and twinned crystals are observed to form from SH and FCC systems, which have not previously been experimentally realized by DNA origami crystallization. These findings open a promising pathway toward accessing a rich phase space with a single type of building block and wielding other instructions as tools to develop crystalline materials with tunable properties.
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Affiliation(s)
- Lizhi Dai
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Xiaoxue Hu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Min Ji
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Ningning Ma
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
| | - Jun-Jie Zhu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Qianhao Min
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
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11
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Vecchioni S, Lu B, Livernois W, Ohayon YP, Yoder JB, Yang CF, Woloszyn K, Bernfeld W, Anantram MP, Canary JW, Hendrickson WA, Rothschild LJ, Mao C, Wind SJ, Seeman NC, Sha R. Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210938. [PMID: 37268326 DOI: 10.1002/adma.202210938] [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: 11/03/2022] [Revised: 03/06/2023] [Indexed: 06/04/2023]
Abstract
DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.
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Affiliation(s)
- Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Livernois
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, IL, 60439, USA
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Bernfeld
- Department of Chemistry, New York University, New York, NY, 10003, USA
- ASPIRE Program, King School, Stamford, CT, 06905, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, CA, 94035, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Math, Columbia University, New York, NY, 10027, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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12
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Wassermann LM, Scheckenbach M, Baptist AV, Glembockyte V, Heuer-Jungemann A. Full Site-Specific Addressability in DNA Origami-Templated Silica Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2212024. [PMID: 36932052 DOI: 10.1002/adma.202212024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Indexed: 06/09/2023]
Abstract
DNA nanotechnology allows for the fabrication of nanometer-sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site-specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA-PAINT super-resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site-specifically addressable silica nanostructure with complete control over size and shape.
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Affiliation(s)
- Lea M Wassermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Michael Scheckenbach
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Anna V Baptist
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
| | - Viktorija Glembockyte
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried and Center for NanoScience (CeNS), Ludwig-Maximilians-University, 81377, Munich, Germany
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13
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Zhao Y, Chandrasekaran AR, Rusling DA, Woloszyn K, Hao Y, Hernandez C, Vecchioni S, Ohayon YP, Mao C, Seeman NC, Sha R. The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA Crystals. J Am Chem Soc 2023; 145:3599-3605. [PMID: 36731121 PMCID: PMC10032566 DOI: 10.1021/jacs.2c12667] [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: 02/04/2023]
Abstract
Reconfigurable structures engineered through DNA hybridization and self-assembly offer both structural and dynamic applications in nanotechnology. Here, we have demonstrated that strand displacement of triplex-forming oligonucleotides (TFOs) can be translated to a robust macroscopic DNA crystal by coloring the crystals with covalently attached fluorescent dyes. We show that three different types of triplex strand displacement are feasible within the DNA crystals and the bound TFOs can be removed and/or replaced by (a) changing the pH from 5 to 7, (b) the addition of the Watson-Crick complement to a TFO containing a short toehold, and (c) the addition of a longer TFO that uses the duplex edge as a toehold. We have also proved by X-ray diffraction that the structure of the crystals remains as designed in the presence of the TFOs.
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Affiliation(s)
- Yue Zhao
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Arun Richard Chandrasekaran
- The RNA Institute, University of Albany, State University of New York, Albany, New York 12222, United States
| | - David A Rusling
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yudong Hao
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Carina Hernandez
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
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14
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Lu B, Woloszyn K, Ohayon YP, Yang B, Zhang C, Mao C, Seeman NC, Vecchioni S, Sha R. Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles. Angew Chem Int Ed Engl 2023; 62:e202213451. [PMID: 36520622 DOI: 10.1002/anie.202213451] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson-Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Bena Yang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
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15
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Ober MF, Baptist A, Wassermann L, Heuer-Jungemann A, Nickel B. In situ small-angle X-ray scattering reveals strong condensation of DNA origami during silicification. Nat Commun 2022; 13:5668. [PMID: 36167861 PMCID: PMC9515200 DOI: 10.1038/s41467-022-33083-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Silicification of DNA origami structures increases their stability and provides chemical protection. Yet, it is unclear whether the whole DNA framework is embedded or if silica just forms an outer shell and how silicification affects the origami's internal structure. Employing in situ small-angle X-ray scattering (SAXS), we show that addition of silica precursors induces substantial condensation of the DNA origami at early reaction times by almost 10 %. Subsequently, the overall size of the silicified DNA origami increases again due to increasing silica deposition. We further identify the SAXS Porod invariant as a reliable, model-free parameter for the evaluation of the amount of silica formation at a given time. Contrast matching of the DNA double helix Lorentzian peak reveals silica growth also inside the origami. The less polar silica forming within the origami structure, replacing more than 40 % of the internal hydration water, causes a hydrophobic effect: condensation. DNA origami objects with flat surfaces show a strong tendency towards aggregation during silicification, presumably driven by the same entropic forces causing condensation. Maximally condensed origami displayed thermal stability up to 60 °C. Our studies provide insights into the silicification reaction allowing for the formulation of optimized reaction protocols.
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Affiliation(s)
- Martina F Ober
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Anna Baptist
- Max Planck Institute of Biochemistry and CeNS, Ludwig-Maximilians-Universität München, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Lea Wassermann
- Max Planck Institute of Biochemistry and CeNS, Ludwig-Maximilians-Universität München, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry and CeNS, Ludwig-Maximilians-Universität München, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Bert Nickel
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
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16
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Vargas-Lara F, Starr FW, Douglas JF. Solution properties of spherical gold nanoparticles with grafted DNA chains from simulation and theory. NANOSCALE ADVANCES 2022; 4:4144-4161. [PMID: 36285224 PMCID: PMC9514572 DOI: 10.1039/d2na00377e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/30/2022] [Indexed: 06/16/2023]
Abstract
There has been a rapidly growing interest in the use of functionalized Au nanoparticles (NPs) as platforms in multiple applications in medicine and manufacturing. The sensing and targeting characteristics of these NPs, and the realization of precisely organized structures in manufacturing applications using such NPs, depend on the control of their surface functionalization. NP functionalization typically takes the form of polymer grafted layers, and a detailed knowledge of the chemical and structural properties of these layers is required to molecularly engineer the particle characteristics for specific applications. However, the prediction and experimental determination of these properties to enable the rational engineering of these particles is a persistent problem in the development of this class of materials. To address this situation, molecular dynamic simulations were performed based on a previously established coarse-grained single-stranded DNA (ssDNA) model to determine basic solution properties of model ssDNA-grafted NP-layers under a wide range of conditions. In particular, we emphasize the calculation of the hydrodynamic radius for ssDNA-grafted Au NPs as a function of structural parameters such as ssDNA length, NP core size, and surface coverage. We also numerically estimate the radius of gyration and the intrinsic viscosity of these NPs, which in combination with hydrodynamic radius estimates, provide valuable information about the fluctuating structure of the grafted polymer layers. We may then understand the origin of the commonly reported variation in effective NP "size" by different measurement methods, and then exploit this information in connection to material design and characterization in connection with the ever-growing number of applications utilizing polymer-grafted NPs.
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Affiliation(s)
- Fernando Vargas-Lara
- Departments of Physics & Molecular Biology & Biochemistry, Wesleyan University Middletown CT 06459 USA
| | - Francis W Starr
- Departments of Physics & Molecular Biology & Biochemistry, Wesleyan University Middletown CT 06459 USA
| | - Jack F Douglas
- Materials Science & Engineering Division, National Institute of Standards and Technology Gaithersburg Maryland 20899 USA
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17
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Zhang L, Chu M, Ji C, Tan J, Yuan Q. Preparation, applications, and challenges of functional DNA nanomaterials. NANO RESEARCH 2022; 16:3895-3912. [PMID: 36065175 PMCID: PMC9430014 DOI: 10.1007/s12274-022-4793-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
As a carrier of genetic information, DNA is a versatile module for fabricating nanostructures and nanodevices. Functional molecules could be integrated into DNA by precise base complementary pairing, greatly expanding the functions of DNA nanomaterials. These functions endow DNA nanomaterials with great potential in the application of biomedical field. In recent years, functional DNA nanomaterials have been rapidly investigated and perfected. There have been reviews that classified DNA nanomaterials from the perspective of functions, while this review primarily focuses on the preparation methods of functional DNA nanomaterials. This review comprehensively introduces the preparation methods of DNA nanomaterials with functions such as molecular recognition, nanozyme catalysis, drug delivery, and biomedical material templates. Then, the latest application progress of functional DNA nanomaterials is systematically reviewed. Finally, current challenges and future prospects for functional DNA nanomaterials are discussed.
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Affiliation(s)
- Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Mengge Chu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
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18
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Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2022; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
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Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,
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19
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Feng J, Feng L, Xu S, Zhu C, Pan G, Yao L. Universal Preparation Strategy for Ultradurable Antibacterial Fabrics through Coating an Adhesive Nanosilver Glue. NANOMATERIALS 2022; 12:nano12142429. [PMID: 35889656 PMCID: PMC9323275 DOI: 10.3390/nano12142429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022]
Abstract
Microbiological protection textile materials played an important role in the battle against the epidemic. However, the traditional active antimicrobial treatment of textiles suffers from narrow textile applicability, low chemical stability, and poor washability. Here, a high-strength adhesive nanosilver glue was synthesized by introducing nontoxic water-soluble polyurethane glue as a protectant. The as-prepared nanosilver glue could adhere firmly to the fiber surfaces by forming a flexible polymer film and could encapsulate nanosilver inside the glue. The as-prepared nanosilver had a torispherical structure with diameter of ~22 nm, zeta potential of −42.7 mV, and good dispersibility in water, and it could be stored for one year. Further studies indicated that the nanosilver glue had wide applicability to the main fabric species, such as cotton and polyester fabric, surgical mask, latex paint, and wood paint. The antimicrobial cotton and polyester fabrics were prepared by a simple impregnation–padding–baking process. The corresponding antimicrobial activity was positively correlated with nanosilver content. The treated fabrics (500 mg/kg) exhibited ultrahigh washing resistance (maintained over 99% antibacterial rates for 100 times of standard washing) and wear resistance (99% antibacterial rates for 8000 times of standard wearing), equivalent breathability to untreated fabric, improved mechanical properties, and good flexibility, demonstrating a potential in cleanable and reusable microbiological protection textiles.
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Affiliation(s)
- Jundan Feng
- National & Local Joint Engineering Research Center of Technical Fiber Composites for Safety and Protection, Nantong University, Nantong 226019, China; (J.F.); (L.F.); (G.P.); (L.Y.)
| | - Lingling Feng
- National & Local Joint Engineering Research Center of Technical Fiber Composites for Safety and Protection, Nantong University, Nantong 226019, China; (J.F.); (L.F.); (G.P.); (L.Y.)
| | - Sijun Xu
- National & Local Joint Engineering Research Center of Technical Fiber Composites for Safety and Protection, Nantong University, Nantong 226019, China; (J.F.); (L.F.); (G.P.); (L.Y.)
- Correspondence:
| | - Chunhong Zhu
- Faculty of Textile Science and Technology, Shinshu University, Nagano 386-8567, Japan;
| | - Gangwei Pan
- National & Local Joint Engineering Research Center of Technical Fiber Composites for Safety and Protection, Nantong University, Nantong 226019, China; (J.F.); (L.F.); (G.P.); (L.Y.)
| | - Lirong Yao
- National & Local Joint Engineering Research Center of Technical Fiber Composites for Safety and Protection, Nantong University, Nantong 226019, China; (J.F.); (L.F.); (G.P.); (L.Y.)
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20
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Dwivedi M, Singh SL, Bharadwaj AS, Kishore V, Singh AV. Self-Assembly of DNA-Grafted Colloids: A Review of Challenges. MICROMACHINES 2022; 13:mi13071102. [PMID: 35888919 PMCID: PMC9324607 DOI: 10.3390/mi13071102] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/05/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023]
Abstract
DNA-mediated self-assembly of colloids has emerged as a powerful tool to assemble the materials of prescribed structure and properties. The uniqueness of the approach lies in the sequence-specific, thermo-reversible hybridization of the DNA-strands based on Watson–Crick base pairing. Grafting particles with DNA strands, thus, results into building blocks that are fully programmable, and can, in principle, be assembled into any desired structure. There are, however, impediments that hinder the DNA-grafted particles from realizing their full potential, as building blocks, for programmable self-assembly. In this short review, we focus on these challenges and highlight the research around tackling these challenges.
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Affiliation(s)
- Manish Dwivedi
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India; (M.D.); (V.K.)
| | - Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
- Correspondence: (S.L.S.); (A.V.S.)
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India;
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India; (M.D.); (V.K.)
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR), Maxdohrnstrasse 8-10, 10589 Berlin, Germany
- Correspondence: (S.L.S.); (A.V.S.)
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21
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The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly. Nat Commun 2022; 13:3112. [PMID: 35662248 PMCID: PMC9166708 DOI: 10.1038/s41467-022-30779-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/04/2022] [Indexed: 12/31/2022] Open
Abstract
The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context. Engineered crystal architectures from DNA have become a foundational goal for nanotechnological precise arrangement. Here, the authors systematically investigate the structures of 36 immobile Holliday junction sequences and identify the features allowing the crystallisation of most of them, while 6 are considered fatal.
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22
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Yin J, Xie M, Wang J, Cui M, Zhu D, Su S, Fan C, Chao J, Li Q, Wang L. Gold-Nanoparticle-Mediated Assembly of High-Order DNA Nano-Architectures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200824. [PMID: 35523735 DOI: 10.1002/smll.202200824] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Constructing high-order DNA nano-architectures in large sizes is of critical significance for the application of DNA nanotechnology. Robust and flexible design strategies together with easy protocols to construct high-order large-size DNA nano-architectures remain highly desirable. In this work, the authors report a simple and versatile one-pot strategy to fabricate DNA architectures with the assistance of spherical gold nanoparticles modified with thiolated oligonucleotide strands (SH-DNA-AuNPs), which serve as "power strips" to connect various DNA nanostructures carrying complementary ssDNA strands as "plugs". By modulating the plug numbers and positions on each DNA nanostructure and the ratios between DNA nanostructures and AuNPs, the desired architectures are formed via the stochastic co-assembly of different modules. This SH-DNA-AuNP-mediated plug-in assembly (SAMPA) strategy offers new opportunities to drive macroscopic self-assembly to meet the demand of the fabrication of well-defined nanomaterials and nanodevices.
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Affiliation(s)
- Jue Yin
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Mo Xie
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Junke Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Meirong Cui
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Dan Zhu
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
| | - Shao Su
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. 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, Shanghai, 200240, P. R. China
| | - Jie Chao
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. 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, Shanghai, 200240, P. R. China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, P. R. China
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23
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Michelson A, Minevich B, Emamy H, Huang X, Chu YS, Yan H, Gang O. Three-dimensional visualization of nanoparticle lattices and multimaterial frameworks. Science 2022; 376:203-207. [PMID: 35389786 DOI: 10.1126/science.abk0463] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Advances in nanoscale self-assembly have enabled the formation of complex nanoscale architectures. However, the development of self-assembly strategies toward bottom-up nanofabrication is impeded by challenges in revealing these structures volumetrically at the single-component level and with elemental sensitivity. Leveraging advances in nano-focused hard x-rays, DNA-programmable nanoparticle assembly, and nanoscale inorganic templating, we demonstrate nondestructive three-dimensional imaging of complexly organized nanoparticles and multimaterial frameworks. In a three-dimensional lattice with a size of 2 micrometers, we determined the positions of about 10,000 individual nanoparticles with 7-nanometer resolution, and identified arrangements of assembly motifs and a resulting multimaterial framework with elemental sensitivity. The real-space reconstruction permits direct three-dimensional imaging of lattices, which reveals their imperfections and interfaces and also clarifies the relationship between lattices and assembly motifs.
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Affiliation(s)
- Aaron Michelson
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Hamed Emamy
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Xiaojing Huang
- National Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yong S Chu
- National Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hanfei Yan
- National Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Oleg Gang
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY 10027, USA.,Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
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24
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Mahale P, Lee B, Cheng HY, Segad M, Mallouk TE. Small-Angle X-ray Scattering Analysis of Colloidal Crystals and Replica Materials Made from l-Arginine-Stabilized Silica Nanoparticles. ACS APPLIED MATERIALS & INTERFACES 2022; 14:9398-9407. [PMID: 35134294 DOI: 10.1021/acsami.1c19193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Colloidal crystals made from sub-100 nm silica nanoparticles have provided a versatile platform for the template-assisted synthesis of three-dimensionally interconnected semiconducting, metallic, and magnetic replicas. However, the detailed structure of these materials has not yet been characterized. In this study, we investigated the structures of colloidal crystalline films and germanium replicas by scanning electron microscopy and small angle X-ray scattering. The structures of colloidal crystals made by evaporative assembly depends on the size of l-arginine-capped silica nanoparticles. Particles smaller than ∼31 nm diameter assemble into non-close-packed arrangements (bcc) whereas particles larger than 31 nm assemble into random close-packed structures with disordered hexagonal phase. Polycrystalline films of these materials retain their structures and long-range order upon infiltration at high temperature and pressure, and the structure is preserved in Ge replicas. The shear force during deposition and dispersity of silica nanoparticles contributes to the size-based variation in the structure and to the size of crystal domains in the colloidal crystal films.
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Affiliation(s)
- Pratibha Mahale
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Byeongdu Lee
- Advanced Photon Source, Argonne National Laboratory, Argonne, Lemont, Illinois 60439, United States
| | - Hiu Yan Cheng
- Department of Chemistry, Pennsylvania State University, University Park, State College, Pennsylvania 16801, United States
| | - Mo Segad
- Materials Research Institute, Pennsylvania State University, University Park, State College, Pennsylvania 16801, United States
| | - Thomas E Mallouk
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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25
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Fabrini G, Minard A, Brady RA, Di Antonio M, Di Michele L. Cation-Responsive and Photocleavable Hydrogels from Noncanonical Amphiphilic DNA Nanostructures. NANO LETTERS 2022; 22:602-611. [PMID: 35026112 PMCID: PMC8796241 DOI: 10.1021/acs.nanolett.1c03314] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/01/2021] [Indexed: 05/26/2023]
Abstract
Thanks to its biocompatibility, versatility, and programmable interactions, DNA has been proposed as a building block for functional, stimuli-responsive frameworks with applications in biosensing, tissue engineering, and drug delivery. Of particular importance for in vivo applications is the possibility of making such nanomaterials responsive to physiological stimuli. Here, we demonstrate how combining noncanonical DNA G-quadruplex (G4) structures with amphiphilic DNA constructs yields nanostructures, which we termed "Quad-Stars", capable of assembling into responsive hydrogel particles via a straightforward, enzyme-free, one-pot reaction. The embedded G4 structures allow one to trigger and control the assembly/disassembly in a reversible fashion by adding or removing K+ ions. Furthermore, the hydrogel aggregates can be photo-disassembled upon near-UV irradiation in the presence of a porphyrin photosensitizer. The combined reversibility of assembly, responsiveness, and cargo-loading capabilities of the hydrophobic moieties make Quad-Stars a promising candidate for biosensors and responsive drug delivery carriers.
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Affiliation(s)
- Giacomo Fabrini
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Aisling Minard
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Ryan A. Brady
- Department
of Chemistry, King’s College London, London SE1 1DB, United Kingdom
| | - Marco Di Antonio
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
| | - Lorenzo Di Michele
- Department
of Chemistry, Imperial College London, London W12 0BZ, United Kingdom
- Department
of Physics—Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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26
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Affiliation(s)
- Jason S. Kahn
- Department of Chemical Engineering Columbia University New York NY 10027 USA
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton NY 11973 USA
| | - Oleg Gang
- Department of Chemical Engineering Columbia University New York NY 10027 USA
- Department of Applied Physics and Applied Mathematics Columbia University New York NY 10027 USA
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton NY 11973 USA
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27
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Narayanan RP, Abraham L. Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots. Curr Top Med Chem 2022; 22:668-685. [PMID: 35023457 DOI: 10.2174/1568026622666220112143401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 11/22/2022]
Abstract
DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the 'tile' based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.
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Affiliation(s)
- Raghu Pradeep Narayanan
- Centre for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe-85281, USA
| | - Leeza Abraham
- Centre for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe-85281, USA
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28
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Dai X, Chen X, Jing X, Zhang Y, Pan M, Li M, Li Q, Liu P, Fan C, Liu X. DNA Origami‐Encoded Integration of Heterostructures. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202114190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Xinpei Dai
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Division of Physical Biology CHINA
| | - Xiaoliang Chen
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Xinxin Jing
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Yinan Zhang
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Muchen Pan
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Mingqiang Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Qian Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Biodesign Center 300307 Tianjin CHINA
| | - Chunhai Fan
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering No. 800, Dongchuan Road 200240 Shanghai CHINA
| | - Xiaoguo Liu
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine No. 800 Dongchuan road 200240 Shanghai CHINA
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29
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Dai X, Chen X, Jing X, Zhang Y, Pan M, Li M, Li Q, Liu P, Fan C, Liu X. DNA Origami-Encoded Integration of Heterostructures. Angew Chem Int Ed Engl 2021; 61:e202114190. [PMID: 34962699 DOI: 10.1002/anie.202114190] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Indexed: 11/09/2022]
Abstract
Integrating dissimilar materials at the nanoscale is crucial for modern electronics and optoelectronics. The structural DNA nanotechnology provides a universal platform for precision assembly of materials; nevertheless, heterogeneous integration of dissimilar materials with DNA nanostructures has yet to be explored. Here we report a DNA origami-encoded strategy for integrating silica-metal heterostructures. Theoretical and experimental studies reveal distinctive mechanisms for the binding and aggregation of silica and metal clusters on protruding double-stranded DNA (dsDNA) strands that are prescribed on the DNA origami template. In particular, the binding energy differences of silica/metal clusters and DNA molecules underlies the accessibilities of dissimilar material areas on DNA origami. We find that, by programming the densities and lengths of protruding dsDNA strands on DNA origami, silica and metal materials can be independently deposited at their predefined areas with a high vertical precision of 2 nm. We demonstrate the integration of silica-gold and silica-silver heterostructures with high site addressability. This DNA nanotechnology-based strategy is thus applicable for integrating various types of dissimilar materials, which opens new routes for bottom-up electronics.
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Affiliation(s)
- Xinpei Dai
- Shanghai Institute of Applied Physics Chinese Academy of Sciences, Division of Physical Biology, CHINA
| | - Xiaoliang Chen
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Xinxin Jing
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Yinan Zhang
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Muchen Pan
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Mingqiang Li
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Qian Li
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, CHINA
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, Biodesign Center, 300307, Tianjin, CHINA
| | - Chunhai Fan
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, No. 800, Dongchuan Road, 200240, Shanghai, CHINA
| | - Xiaoguo Liu
- Shanghai Jiao Tong University, School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, No. 800 Dongchuan road, 200240, Shanghai, CHINA
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30
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Heuer-Jungemann A, Linko V. Engineering Inorganic Materials with DNA Nanostructures. ACS CENTRAL SCIENCE 2021; 7:1969-1979. [PMID: 34963890 PMCID: PMC8704036 DOI: 10.1021/acscentsci.1c01272] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Indexed: 05/25/2023]
Abstract
Nucleic acid nanotechnology lays a foundation for the user-friendly design and synthesis of DNA frameworks of any desirable shape with extreme accuracy and addressability. Undoubtedly, such features make these structures ideal modules for positioning and organizing molecules and molecular components into complex assemblies. One of the emerging concepts in the field is to create inorganic and hybrid materials through programmable DNA templates. Here, we discuss the challenges and perspectives of such DNA nanostructure-driven materials science engineering and provide insights into the subject by introducing various DNA-based fabrication techniques including metallization, mineralization, lithography, casting, and hierarchical self-assembly of metal nanoparticles.
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Affiliation(s)
- Amelie Heuer-Jungemann
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Center
for Nanoscience, Ludwig-Maximilians University, 80539 Munich, Germany
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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31
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De Fazio AF, Misatziou D, Baker YR, Muskens OL, Brown T, Kanaras AG. Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly. Chem Soc Rev 2021; 50:13410-13440. [PMID: 34792047 PMCID: PMC8628606 DOI: 10.1039/d1cs00632k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/26/2022]
Abstract
The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.
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Affiliation(s)
- Angela F De Fazio
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Doxi Misatziou
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Ysobel R Baker
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Otto L Muskens
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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32
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Zhao Y, Zhang C, Yang L, Xu X, Xu R, Ma Q, Tang Q, Yang Y, Han D. Programmable and Site-Specific Patterning on DNA Origami Templates with Heterogeneous Condensation of Silver and Silica. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2103877. [PMID: 34636168 DOI: 10.1002/smll.202103877] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/15/2021] [Indexed: 06/13/2023]
Abstract
DNA origami has been widely used as a modular platform for condensation of functional molecules to assemble optical, electronic, and biological components. However, the heterogeneous condensation with greater diversities in chemical composition templated with DNA origami is still challenging. Herein, a programmable deposition method is developed to precisely condense silver-silica nanohybrids on DNA origami templates. First, the site-specific metallization of Ag is achieved by thiol group-initiated silver reduction at the designed areas of DNA origami. Next, cysteamine is used to selectively modify the condensed Ag surface with positively charged amino groups for creating an electronically different environment for site-specific placement of silica by a modified Stöber method. Using these strategies, customized patterning of both silver and silica on tubular and rectangular DNA origami nanostructures is successfully achieved with nanoscale spatial resolution. These findings will greatly facilitate the development of DNA nanotechnology-based bottom-up nanofabrication.
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Affiliation(s)
- Yumeng Zhao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Linlin Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Xuemei Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Rui Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Qian Ma
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Qian Tang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
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33
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Martynenko IV, Ruider V, Dass M, Liedl T, Nickels PC. DNA Origami Meets Bottom-Up Nanopatterning. ACS NANO 2021; 15:10769-10774. [PMID: 34255962 PMCID: PMC8320526 DOI: 10.1021/acsnano.1c04297] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA origami has emerged as a powerful molecular breadboard with nanometer resolution that can integrate the world of bottom-up (bio)chemistry with large-scale, macroscopic devices created by top-down lithography. Substituting the top-down patterning with self-assembled colloidal nanoparticles now takes the manufacturing complexity of top-down lithography out of the equation. As a result, the deterministic positioning of single molecules or nanoscale objects on macroscopic arrays is benchtop ready and easily accessible.
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Affiliation(s)
- Irina V. Martynenko
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
| | - Veronika Ruider
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
| | - Philipp C. Nickels
- Faculty of Physics and Center for NanoScience (CeNS)
Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1,
80539 Munich, Germany
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34
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Wang S, Xie X, Chen Z, Ma N, Zhang X, Li K, Teng C, Ke Y, Tian Y. DNA-Grafted 3D Superlattice Self-Assembly. Int J Mol Sci 2021; 22:7558. [PMID: 34299179 PMCID: PMC8306452 DOI: 10.3390/ijms22147558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
The exploitation of new methods to control material structure has historically been dominating the material science. The bottom-up self-assembly strategy by taking atom/molecule/ensembles in nanoscale as building blocks and crystallization as a driving force bring hope for material fabrication. DNA-grafted nanoparticle has emerged as a "programmable atom equivalent" and was employed for the assembly of hierarchically ordered three-dimensional superlattice with novel properties and studying the unknown assembly mechanism due to its programmability and versatility in the binding capabilities. In this review, we highlight the assembly strategies and rules of DNA-grafted three-dimensional superlattice, dynamic assembly by different driving factors, and discuss their future applications.
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Affiliation(s)
- Shuang Wang
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen 518055, China; (S.W.); (K.L.)
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China; (X.X.); (Z.C.); (N.M.); (X.Z.)
| | - Xiaolin Xie
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China; (X.X.); (Z.C.); (N.M.); (X.Z.)
| | - Zhi Chen
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China; (X.X.); (Z.C.); (N.M.); (X.Z.)
| | - Ningning Ma
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China; (X.X.); (Z.C.); (N.M.); (X.Z.)
| | - Xue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China; (X.X.); (Z.C.); (N.M.); (X.Z.)
| | - Kai Li
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen 518055, China; (S.W.); (K.L.)
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China; (X.X.); (Z.C.); (N.M.); (X.Z.)
| | - Chao Teng
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen 518055, China; (S.W.); (K.L.)
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Ye Tian
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China
- College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
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35
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Kahn JS, Gang O. Designer Nanomaterials through Programmable Assembly. Angew Chem Int Ed Engl 2021; 61:e202105678. [PMID: 34128306 DOI: 10.1002/anie.202105678] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 11/08/2022]
Abstract
Nanoparticles have long been recognized for their unique properties, leading to exciting potential applications across optics, electronics, magnetism, and catalysis. These specific functions often require a designed organization of particles, which includes the type of order as well as placement and relative orientation of particles of the same or different kinds. DNA nanotechnology offers the ability to introduce highly addressable bonds, tailor particle interactions, and control the geometry of bindings motifs. Here, we discuss how developments in structural DNA nanotechnology have enabled greater control over 1D, 2D, and 3D particle organizations through programmable assembly. This Review focuses on how the use of DNA binding between nanocomponents and DNA structural motifs has progressively allowed the rational formation of prescribed particle organizations. We offer insight into how DNA-based motifs and elements can be further developed to control particle organizations and how particles and DNA can be integrated into nanoscale building blocks, so-called "material voxels", to realize designer nanomaterials with desired functions.
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Affiliation(s)
- Jason S Kahn
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.,Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.,Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA.,Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
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