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Li Z, Lim Y, Tanriover I, Zhou W, Li Y, Zhang Y, Aydin K, Glotzer SC, Mirkin CA. DNA-mediated assembly of Au bipyramids into anisotropic light emitting kagome superlattices. SCIENCE ADVANCES 2024; 10:eadp3756. [PMID: 39028823 PMCID: PMC11259166 DOI: 10.1126/sciadv.adp3756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
Abstract
Colloidal crystal engineering with DNA allows one to design diverse superlattices with tunable lattice symmetry, composition, and spacing. Most of these structures follow the complementary contact model, maximizing DNA hybridization on building blocks and producing relatively close-packed lattices. Here, low-symmetry kagome superlattices are assembled from DNA-modified gold bipyramids that can engage only in partial DNA surface matching. The bipyramid dimensions and DNA length can be engineered for two different superlattices with rhombohedral unit cells, including one composed of a periodic stacking of kagome lattices. Enabled by the partial facet alignment, the kagome lattices exhibit lattice distortion, bipyramid twisting, and planar chirality. When conjugated with Cy-5 dyes, the kagome lattices serve as cavities with high-density optical states and large Purcell factors along lateral directions, leading to strong dipole radiation along the z axis and facet-dependent light emission. Such complex optical properties make these materials attractive for lasers, displays, and quantum sensing constructs.
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Affiliation(s)
- Zhiwei Li
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
| | - Yein Lim
- Department of Chemical Engineering, University of Michigan, Michigan, Ann Arbor, MI 48109, USA
| | - Ibrahim Tanriover
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
- Department of Electrical and Computer Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Wenjie Zhou
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
| | - Yuanwei Li
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Ye Zhang
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
| | - Koray Aydin
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
- Department of Electrical and Computer Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Sharon C. Glotzer
- Department of Chemical Engineering, University of Michigan, Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
- International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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Wei X, Chen C, Popov AV, Bathe M, Hernandez R. Binding Site Programmable Self-Assembly of 3D Hierarchical DNA Origami Nanostructures. J Phys Chem A 2024; 128:4999-5008. [PMID: 38875485 DOI: 10.1021/acs.jpca.4c02603] [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: 06/16/2024]
Abstract
DNA nanotechnology has broad applications in biomedical drug delivery and programmable materials. Characterization of the self-assembly of DNA origami and quantum dots (QDs) is necessary for the development of new DNA-based nanostructures. We use computation and experiment to show that the self-assembly of 3D hierarchical nanostructures can be controlled by programming the binding site number and their positions on DNA origami. Using biotinylated pentagonal pyramid wireframe DNA origamis and streptavidin capped QDs, we demonstrate that DNA origami with 1 binding site at the outer vertex can assemble multimeric origamis with up to 6 DNA origamis on 1 QD, and DNA origami with 1 binding site at the inner center can only assemble monomeric and dimeric origamis. Meanwhile, the yield percentages of different multimeric origamis are controlled by the QD:DNA-origami stoichiometric mixing ratio. DNA origamis with 2 binding sites at the αγ positions (of the pentagon) make larger nanostructures than those with binding sites at the αβ positions. In general, increasing the number of binding sites leads to increases in the nanostructure size. At high DNA origami concentration, the QD number in each cluster becomes the limiting factor for the growth of nanostructures. We find that reducing the QD size can also affect the self-assembly because of the reduced access to the binding sites from more densely packed origamis.
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Affiliation(s)
- Xingfei Wei
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Chi Chen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alexander V Popov
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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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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Vo T. Theory and simulation of ligand functionalized nanoparticles - a pedagogical overview. SOFT MATTER 2024; 20:3554-3576. [PMID: 38646950 DOI: 10.1039/d4sm00177j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Synthesizing reconfigurable nanoscale synthons with predictive control over shape, size, and interparticle interactions is a holy grail of bottom-up self-assembly. Grand challenges in their rational design, however, lie in both the large space of experimental synthetic parameters and proper understanding of the molecular mechanisms governing their formation. As such, computational and theoretical tools for predicting and modeling building block interactions have grown to become integral in modern day self-assembly research. In this review, we provide an in-depth discussion of the current state-of-the-art strategies available for modeling ligand functionalized nanoparticles. We focus on the critical role of how ligand interactions and surface distributions impact the emergent, pre-programmed behaviors between neighboring particles. To help build insights into the underlying physics, we first define an "ideal" limit - the short ligand, "hard" sphere approximation - and discuss all experimental handles through the lens of perturbations about this reference point. Finally, we identify theories that are capable of bridging interparticle interactions to nanoscale self-assembly and conclude by discussing exciting new directions for this field.
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Affiliation(s)
- Thi Vo
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
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Wang W, Li X, Zeng K, Lu Y, Jia B, Lv J, Wu C, Wang X, Zhang X, Zhang Z. Improved Catalytic Activity of Spherical Nucleic Acid Enzymes by Hybridization Chain Reaction and Its Application for Sensitive Analysis of Aflatoxin B1. SENSORS (BASEL, SWITZERLAND) 2024; 24:2325. [PMID: 38610537 PMCID: PMC11014268 DOI: 10.3390/s24072325] [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: 02/26/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024]
Abstract
Conventional spherical nucleic acid enzymes (SNAzymes), made with gold nanoparticle (AuNPs) cores and DNA shells, are widely applied in bioanalysis owing to their excellent physicochemical properties. Albeit important, the crowded catalytic units (such as G-quadruplex, G4) on the limited AuNPs surface inevitably influence their catalytic activities. Herin, a hybridization chain reaction (HCR) is employed as a means to expand the quantity and spaces of G4 enzymes for their catalytic ability enhancement. Through systematic investigations, we found that when an incomplete G4 sequence was linked at the sticky ends of the hairpins with split modes (3:1 and 2:2), this would significantly decrease the HCR hybridization capability due to increased steric hindrance. In contrast, the HCR hybridization capability was remarkably enhanced after the complete G4 sequence was directly modified at the non-sticky end of the hairpins, ascribed to the steric hindrance avoided. Accordingly, the improved SNAzymes using HCR were applied for the determination of AFB1 in food samples as a proof-of-concept, which exhibited outstanding performance (detection limit, 0.08 ng/mL). Importantly, our strategy provided a new insight for the catalytic activity improvement in SNAzymes using G4 as a signaling molecule.
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Affiliation(s)
- Wenjun Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Xuesong Li
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Kun Zeng
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Yanyan Lu
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Boyuan Jia
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Jianxia Lv
- National Narcotics Laboratory Beijing Regional Center, Beijing 100164, China; (J.L.); (C.W.)
| | - Chenghao Wu
- National Narcotics Laboratory Beijing Regional Center, Beijing 100164, China; (J.L.); (C.W.)
| | - Xinyu Wang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Xinshuo Zhang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
| | - Zhen Zhang
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China (K.Z.); (Y.L.); (B.J.); (X.W.); (X.Z.)
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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [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: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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Tao Z, Zhang H, Wu S, Zhang J, Cheng Y, Lei L, Qin Y, Wei H, Yu CY. Spherical nucleic acids: emerging amplifiers for therapeutic nanoplatforms. NANOSCALE 2024; 16:4392-4406. [PMID: 38289178 DOI: 10.1039/d3nr05971e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Gene therapy is a revolutionary treatment approach in the 21st century, offering significant potential for disease prevention and treatment. However, the efficacy of gene delivery is often compromised by the inherent challenges of gene properties and vector-related defects. It is crucial to explore ways to enhance the curative effect of gene drugs and achieve safer, more widespread, and more efficient utilization, which represents a significant challenge in amplification gene therapy advancements. Spherical nucleic acids (SNAs), with their unique physicochemical properties, are considered an innovative solution for scalable gene therapy. This review aims to comprehensively explore the amplifying contributions of SNAs in gene therapy and emphasize the contribution of SNAs to the amplification effect of gene therapy from the aspects of structure, application, and recent clinical translation - an aspect that has been rarely reported or explored thus far. We begin by elucidating the fundamental characteristics and scaling-up properties of SNAs that distinguish them from traditional linear nucleic acids, followed by an analysis of combined therapy treatment strategies, theranostics, and clinical translation amplified by SNAs. We conclude by discussing the challenges of SNAs and provide a prospect on the amplification characteristics. This review seeks to update the current understanding of the use of SNAs in gene therapy amplification and promote further research into their clinical translation and amplification of gene therapy.
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Affiliation(s)
- Zhenghao Tao
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, P. R. China.
| | - Haitao Zhang
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, P. R. China.
| | - Shang Wu
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, P. R. China.
| | - Jiaheng Zhang
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, P. R. China.
| | - Yao Cheng
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, P. R. China.
| | - Longtianyang Lei
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, P. R. China.
| | - Yang Qin
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, P. R. China.
| | - Hua Wei
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, P. R. China.
| | - Cui-Yun Yu
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, 421001, Hengyang, P. R. China.
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Quantum dots make it big at last. NATURE MATERIALS 2024; 23:159. [PMID: 38307978 DOI: 10.1038/s41563-024-01807-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
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