1
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Enlund E, Julin S, Linko V, Kostiainen MA. Structural stability of DNA origami nanostructures in organic solvents. NANOSCALE 2024; 16:13407-13415. [PMID: 38910453 PMCID: PMC11256221 DOI: 10.1039/d4nr02185a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/18/2024] [Indexed: 06/25/2024]
Abstract
DNA origami nanostructures have attracted significant attention as an innovative tool in a variety of research areas, spanning from nanophotonics to bottom-up nanofabrication. However, the use of DNA origami is often restricted by their rather limited structural stability in application-specific conditions. The structural integrity of DNA origami is known to be superstructure-dependent, and the integrity is influenced by various external factors, for example cation concentration, temperature, and presence of nucleases. Given the necessity to functionalize DNA origami also with non-water-soluble entities, it is important to acquire knowledge of the structural stability of DNA origami in various organic solvents. Therefore, we herein systematically investigate the post-folding DNA origami stability in a variety of polar, water-miscible solvents, including acetone, ethanol, DMF, and DMSO. Our results suggest that the structural integrity of DNA origami in organic solvents is both superstructure-dependent and dependent on the properties of the organic solvent. In addition, DNA origami are generally more resistant to added organic solvents in folding buffer compared to that in deionized water. DNA origami stability can be maintained in up to 25-40% DMF or DMSO and up to 70-90% acetone or ethanol, with the highest overall stability observed in acetone. By rationally selecting both the DNA origami design and the solvent, the DNA origami stability can be maintained in high concentrations of organic solvents, which paves the way for more extensive use of non-water-soluble compounds for DNA origami functionalization and complexation.
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Affiliation(s)
- Eeva Enlund
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
| | - Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
- LIBER Center of Excellence, Aalto University, 00076 Aalto, Finland
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2
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Gavrilović S, Brüggenthies GA, Weck JM, Heuer-Jungemann A, Schwille P. Protein-Assisted Large-Scale Assembly and Differential Patterning of DNA Origami Lattices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309680. [PMID: 38229553 DOI: 10.1002/smll.202309680] [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: 10/24/2023] [Revised: 11/20/2023] [Indexed: 01/18/2024]
Abstract
Nanofabrication has experienced a big boost with the invention of DNA origami, enabling the production and assembly of complex nanoscale structures that may be able to unlock fully new functionalities in biology and beyond. The remarkable precision with which these structures can be designed and produced is, however, not yet matched by their assembly dynamics, which can be extremely slow, particularly when attached to biological templates, such as membranes. Here, the rapid and controlled formation of DNA origami lattices on the scale of hundreds of micrometers in as little as 30 minutes is demonstrated, utilizing active patterning by the E.coli Min protein system, thereby yielding a remarkable improvement over conventional passive diffusion-based assembly methods. Various patterns, including spots, inverse spots, mazes, and meshes can be produced at different scales, tailored through the shape and density of the assembled structures. The differential positioning accomplished by Min-induced diffusiophoresis even allows the introduction of "pseudo-colors", i.e., complex core-shell patterns, by simultaneously patterning different DNA origami species. Beyond the targeted functionalization of biological surfaces, this approach may also be promising for applications in plasmonics, catalysis, and molecular sensing.
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Affiliation(s)
- Svetozar Gavrilović
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | | | - Johann Moritz Weck
- Research Group DNA Hybridnanomaterials, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Amelie Heuer-Jungemann
- Research Group DNA Hybridnanomaterials, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
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3
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Sala L, Zerolová A, Vizcaino V, Mery A, Domaracka A, Rothard H, Boduch P, Pinkas D, Kocišek J. Ion beam processing of DNA origami nanostructures. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2024; 15:207-214. [PMID: 38379932 PMCID: PMC10877082 DOI: 10.3762/bjnano.15.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024]
Abstract
DNA origami nanostructures are emerging as a bottom-up nanopatterning approach. Direct combination of this approach with top-down nanotechnology, such as ion beams, has not been considered because of the soft nature of the DNA material. Here we demonstrate that the shape of 2D DNA origami nanostructures deposited on Si substrates is well preserved upon irradiation by ion beams, modeling ion implantation, lithography, and sputtering conditions. Structural changes in 2D DNA origami nanostructures deposited on Si are analyzed using AFM imaging. The observed effects on DNA origami include structure height decrease or increase upon fast heavy ion irradiation in vacuum and in air, respectively. Slow- and medium-energy heavy ion irradiation results in the cutting of the nanostructures or crater formation with ion-induced damage in the 10 nm range around the primary ion track. In all these cases, the designed shape of the 2D origami nanostructure remains unperturbed. Present stability and nature of damages on DNA origami nanostructures enable fusion of DNA origami advantages such as shape and positioning control into novel ion beam nanofabrication approaches.
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Affiliation(s)
- Leo Sala
- Dynamics of Molecules and Clusters Department, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, Prague, 182 23, Czech Republic
| | - Agnes Zerolová
- Dynamics of Molecules and Clusters Department, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, Prague, 182 23, Czech Republic
| | - Violaine Vizcaino
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Boulevard Henri Becquerel, BP 5133, 14070, Caen cedex 5, France
| | - Alain Mery
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Boulevard Henri Becquerel, BP 5133, 14070, Caen cedex 5, France
| | - Alicja Domaracka
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Boulevard Henri Becquerel, BP 5133, 14070, Caen cedex 5, France
| | - Hermann Rothard
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Boulevard Henri Becquerel, BP 5133, 14070, Caen cedex 5, France
| | - Philippe Boduch
- Normandie Univ, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Boulevard Henri Becquerel, BP 5133, 14070, Caen cedex 5, France
| | - Dominik Pinkas
- Electron Microscopy Center, Institute of Molecular Genetics of the CAS, Vídenská 1083, 142 20, Prague, Czech Republic
| | - Jaroslav Kocišek
- Dynamics of Molecules and Clusters Department, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3, Prague, 182 23, Czech Republic
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4
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Kim D, Kim SJ, Jeong J, Han S, Kim H, Lee S, Choi I, Hong J, Jin JO, Lee JB. Multimodal Golden DNA Superstructures (GDSs) for Highly Efficient Photothermal Immunotherapy. ACS NANO 2024; 18:1744-1755. [PMID: 38174995 DOI: 10.1021/acsnano.3c12535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
DNA-templated metallization has emerged as an efficient strategy for creating nanoscale-metal DNA hybrid structures with a desirable conformation and function. Despite the potential of DNA-metal hybrids, their use as combinatory therapeutic agents has rarely been examined. Herein, we present a simple approach for fabricating a multipurpose DNA superstructure that serves as an efficient photoimmunotherapy agent. Specifically, we adsorb and locally concentrate Au ions onto DNA superstructures through induced local reduction, resulting in the formation of Au nanoclusters. The mechanical and optical properties of these metallic nanoclusters can be rationally controlled by their conformations and metal ions. The resulting golden DNA superstructures (GDSs) exhibit significant photothermal effects that induce cancer cell apoptosis. When sequence-specific immunostimulatory effects of DNA are combined, GDSs provide a synergistic effect to eradicate cancer and inhibit metastasis, demonstrating potential as a combinatory therapeutic agent for tumor treatment. Altogether, the DNA superstructure-templated metal casting system offers promising materials for future biomedical applications.
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Affiliation(s)
- Dajeong Kim
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - So-Jung Kim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jaepil Jeong
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Sangwoo Han
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Hyejin Kim
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Seungki Lee
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea
| | - Inhee Choi
- Department of Life Science, University of Seoul, Seoul 02504, Republic of Korea
| | - Jinkee Hong
- Department of Chemical & Biomolecular Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jun-O Jin
- Department of Microbiology, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jong Bum Lee
- Department of Chemical Engineering, University of Seoul, Seoul 02504, Republic of Korea
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5
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Nguyen-Thi PT, Ho TT, Nguyen TT, Vo GV. Nanotechnology-based Drug Delivery for Alzheimer's and Parkinson's Diseases. Curr Drug Deliv 2024; 21:917-931. [PMID: 37424345 DOI: 10.2174/1567201820666230707113405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 05/03/2023] [Accepted: 05/12/2023] [Indexed: 07/11/2023]
Abstract
The delivery of drugs to the brain is quite challenging in the treatment of the central nervous system (CNS) diseases due to the blood-brain barrier and the blood-cerebrospinal fluid barrier. However, significant developments in nanomaterials employed by nanoparticle drug-delivery systems have substantial potential to cross or bypass these barriers leading to enhanced therapeutic efficacies. Advances in nanoplatform, nanosystems based on lipids, polymers and inorganic materials have been extensively studied and applied in treating Alzheimer's and Parkinson's diseases. In this review, various types of brain drug delivery nanocarriers are classified, summarized, and their potential as drug delivery systems in Alzheimer's and Parkinson's diseases is discussed. Finally, challenges facing the clinical translation of nanoparticles from bench to bedside are highlighted.
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Affiliation(s)
| | - Thanh-Tam Ho
- Institute for Global Health Innovations, Duy Tan University, Da Nang 550000, Vietnam
- Faculty of Pharmacy, Duy Tan University, Da Nang 550000, Vietnam
| | - Thuy Trang Nguyen
- Faculty of Chemical Engineering, Industrial University of Ho Chi Minh City, Ho Chi Minh City 71420, Vietnam
| | - Giau Van Vo
- Department of Biomedical Engineering, School of Medicine, Vietnam National University, Ho Chi Minh City [VNU-HCM], Ho Chi Minh City 700000, Vietnam
- Research Center for Genetics and Reproductive Health [CGRH], School of Medicine, Vietnam National University, Ho Chi Minh City [VNU-HCM], Ho Chi Minh City 70000, Vietnam
- Vietnam National University, Ho Chi Minh City [VNU-HCM], Ho Chi Minh City 700000, Vietnam
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6
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Kannappan S, Jo K, Kim KK, Lee JH. Utilizing peptide-anchored DNA templates for novel programmable nanoparticle assemblies in biological macromolecules: A review. Int J Biol Macromol 2024; 256:128427. [PMID: 38016615 DOI: 10.1016/j.ijbiomac.2023.128427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 11/30/2023]
Abstract
Biological macromolecules such as proteins and DNA are known to self-assemble into various structural moieties with distinct functions. While nucleic acids are the structural building blocks, peptides exemplify diversity as tailorable biochemical units. Thus, combining the scaffold properties of the biomacromolecule DNA and the functionality of peptides could evolve into a powerful method to obtain tailorable nano assemblies. In this review, we discuss the assembly of non-DNA-coated colloidal NPs on DNA/peptide templates using functional anchors. We begin with strategies for directly attaching metallic NPs to DNA templates to ascertain the functional role of DNA as a scaffold. Followed by methods to assemble peptides onto DNA templates to emphasize the functional versatility of biologically abundant DNA-binding peptides. Next, we focus on studies corroborating peptide self-assembling into macromolecular templates onto which NPs can attach to emphasize the properties of NP-binding peptides. Finally, we discuss the assembly of NPs on a DNA template with a focus on the bifunctional DNA-binding peptides with NP-binding affinity (peptide anchors). This review aims to highlight the immense potential of combining the functional power of DNA scaffolds and tailorable functionalities of peptides for NP assembly and the need to utilize them effectively to obtain tailorable hierarchical NP assemblies.
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Affiliation(s)
- Shrute Kannappan
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Mapo-gu, Seoul 04107, Republic of Korea.
| | - Kyeong Kyu Kim
- Department of Precision Medicine, School of Medicine, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Department of Metabiohealth, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Jung Heon Lee
- Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Department of Metabiohealth, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
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7
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Julin S, Best N, Anaya-Plaza E, Enlund E, Linko V, Kostiainen MA. Assembly and optically triggered disassembly of lipid-DNA origami fibers. Chem Commun (Camb) 2023; 59:14701-14704. [PMID: 37997149 DOI: 10.1039/d3cc04677j] [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: 11/25/2023]
Abstract
The co-assembly of lipids and other compounds has recently gained increasing interest. Here, we report the formation of stimuli-responsive lipid-DNA origami fibers through the electrostatic co-assembly of cationic lipids and 6-helix bundle (6HB) DNA origami. The photosensitive lipid degrades when exposed to UV-A light, which allows a photoinduced, controlled release of the 6HBs from the fibers. The presented complexation strategy may find uses in developing responsive nanomaterials e.g. for therapeutics.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
| | - Nadine Best
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
- Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Fraunhofer Institute for Microengineering and Microsystems IMM, 55129 Mainz, Germany
| | - Eduardo Anaya-Plaza
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
| | - Eeva Enlund
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.
- LIBER Center of Excellence, Aalto University, 00076 Aalto, Finland
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8
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Torigoe H, Arakawa F. Importance of isothermal titration calorimetry for the detection of the direct binding of metal ions to mismatched base pairs in duplex DNA. Dalton Trans 2023; 52:13089-13096. [PMID: 37661915 DOI: 10.1039/d2dt02097a] [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: 09/05/2023]
Abstract
Metal ion-nucleic acid interactions contribute substantially to the structure and biological activity of nucleic acids and have a wide range of potential applications in nanotechnology. In this study, we examined the interactions between metal ions and mismatched base pairs in duplex DNA to reveal the underlying molecular mechanism. UV melting analyses showed that the melting temperature (Tm) of a 21-base pair duplex DNA with each of the C-A, C-C and C-T mismatched base pairs increased upon the addition of Ag+. However, isothermal titration calorimetry (ITC) demonstrated that Ag+ only bound to the C-C mismatched base pair of the duplex DNA to form C-Ag-C bonds, without binding to the C-A and C-T mismatches. These results showed that Tm increased even when metal ions did not bind to the mismatched base pairs of the duplex DNA. Although the increase in Tm upon the addition of the metal ions is often used to detect metal ion binding to mismatched base pairs of duplex DNA, these results indicated that UV melting analyses are unable to detect the direct binding of metal ions to the mismatched base pairs. Because ITC analyses directly detect the heat derived from metal ion binding to mismatched base pairs of duplex DNA, we concluded that this may be an effective detection approach.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Fumihiro Arakawa
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
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9
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Pothineni BK, Grundmeier G, Keller A. Cation-dependent assembly of hexagonal DNA origami lattices on SiO 2 surfaces. NANOSCALE 2023; 15:12894-12906. [PMID: 37462427 DOI: 10.1039/d3nr02926c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO2 surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca2+ is found to be superior to Mg2+ in promoting the assembly of ordered lattices, while the presence of Mg2+ rather results in DNA origami aggregation and multilayer formation at the comparably high Na+ concentrations of 200 to 600 mM. Furthermore, Na+ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na+ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO2 surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.
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Affiliation(s)
- Bhanu Kiran Pothineni
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
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10
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Tan Y, Zhou J, Xing X, Wang J, Huang J, Liu H, Chen J, Dong M, Xiang Q, Dong H, Zhang X. DNA Assembly of Plasmonic Nanostructures Enables In Vivo SERS-Based MicroRNA Detection and Tumor Photoacoustic Imaging. Anal Chem 2023. [PMID: 37467354 DOI: 10.1021/acs.analchem.3c00775] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Controllable self-assembly of the DNA-linked gold nanoparticle (AuNP) architecture for in vivo biomedical applications remains a key challenge. Here, we describe the use of the programmed DNA tetrahedral structure to control the assembly of three different types of AuNPs (∼20, 10, and 5 nm) by organizing them into defined positioning and arrangement. A DNA-assembled "core-satellite" architecture is built by DNA sequencing where satellite AuNPs (10 and 5 nm) surround a central core AuNP (20 nm). The density and arrangement of the AuNP satellites around the core AuNP were controlled by tuning the size and amount of the DNA tetrahedron functionalized on the core AuNPs, resulting in strong electromagnetic field enhancement derived from hybridized plasmonic coupling effects. By conjugating with the Raman molecule, strong surface-enhanced Raman scattering photoacoustic imaging signals could be generated, which were able to image microRNA-21 and tumor tissues in vivo. These results provided an efficient strategy to build precision plasmonic superstructures in plasmonic-based bioanalysis and imaging.
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Affiliation(s)
- Yan Tan
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Jianxing Zhou
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen 518060, China
| | - Xiaotong Xing
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Junren Wang
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Jinkun Huang
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Huiyu Liu
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Jiajie Chen
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronics Engineering, Shenzhen University, Shenzhen 518060, China
| | - Mingjie Dong
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Qin Xiang
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Haifeng Dong
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Xueji Zhang
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Research Center for Biosensor and Nanotheranostic, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen 518060, China
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11
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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: 6] [Impact Index Per Article: 6.0] [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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12
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Abstract
DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations ("open" and "closed" states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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13
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Kabusure KM, Piskunen P, Yang J, Linko V, Hakala TK. Raman enhancement in bowtie-shaped aperture-particle hybrid nanostructures fabricated with DNA-assisted lithography. NANOSCALE 2023; 15:8589-8596. [PMID: 37097163 DOI: 10.1039/d3nr00616f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We report on efficient surface-enhanced Raman spectroscopy (SERS) supporting substrates, which are based on deoxyribonucleic acid (DNA)-assisted lithography (DALI) and a layered configuration of materials. In detail, we used nanoscopic DNA origami bowtie templates to form hybrid nanostructures consisting of aligned silver bowtie-shaped particles and apertures of similar shape in a silver film. We hypothesized that this particular geometry could facilitate a four-fold advantage in Raman enhancement compared to common particle-based SERS substrates, and further, we verified these hypotheses experimentally and by finite difference time domain simulations. In summary, our DALI-fabricated hybrid structures suppress the background emission, allow emission predominantly from the areas of high field enhancement, and support additional resonances associated with the nanoscopic apertures. Finally, these nanoapertures also enhance the fields associated with the resonances of the underlying bowtie particles. The versatility and parallel nature of our DNA origami-based nanofabrication scheme and all of the above-mentioned features of the hybrid structures therefore make our optically resonant substrates attractive for various SERS-based applications.
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Affiliation(s)
- Kabusure M Kabusure
- Center for Photonics Sciences, University of Eastern Finland, Yliopistokatu 2, P.O. Box 111, FI-80101, Joensuu, Finland.
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
| | - Jiaqi Yang
- Center for Photonics Sciences, University of Eastern Finland, Yliopistokatu 2, P.O. Box 111, FI-80101, Joensuu, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia.
| | - Tommi K Hakala
- Center for Photonics Sciences, University of Eastern Finland, Yliopistokatu 2, P.O. Box 111, FI-80101, Joensuu, Finland.
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14
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Torigoe H, Kondo J, Arakawa F. Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA. J Inorg Biochem 2023; 241:112125. [PMID: 36716510 DOI: 10.1016/j.jinorgbio.2023.112125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 01/07/2023] [Accepted: 01/08/2023] [Indexed: 01/13/2023]
Abstract
Metal ion-nucleic acid interactions contribute significantly to nucleic acid structure and biological activity and have potential applications in nanotechnology. Hg2+ specifically binds to the natural T-T mismatched base pair in duplex DNA to form a T-Hg-T base pair. Metal ions may enhance DNA damage induced by DNA-damaging agents, such as oxidative agents. The interactions between metal ions and damaged DNAs, such as mismatched oxidized bases, have not been well characterized. Here, we examined the possibility of Hg2+ binding to an asymmetric mismatched base pair involving thymine and 5-hydroxyuracil (OHdU), an oxidized base produced by the oxidative deamination of cytosine. UV melting analyses showed that only the melting temperature of the single T-OHdU mismatched duplex DNA increased upon Hg2+ addition. CD spectra indicated no significant change in the higher-order structure of the single T-OHdU mismatched duplex DNA upon Hg2+ addition. X-ray crystallographic structure with two consecutive T-OHdU mismatched base pairs and isothermal titration calorimetric analyses with the single T-OHdU mismatched base pair showed that Hg2+ specifically binds to the N3 positions of both T and OHdU in T-OHdU at 1:1 molar ratio, with a 5×105 M-1 binding constant of to form the T-Hg-OHdU base pair. The Hg2+-bound structure and the Hg2+-binding affinity for T-OHdU was similar to those for T-T. This study on T-Hg-OHdU metal-mediated base pair could aid in studying the molecular mechanism of metal ion-mediated DNA damage and their potential applications in nanotechnology.
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Affiliation(s)
- Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan.
| | - Jiro Kondo
- Department of Materials and Life Sciences, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan
| | - Fumihiro Arakawa
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601, Japan
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15
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Bohlin J, Turberfield AJ, Louis AA, Šulc P. Designing the Self-Assembly of Arbitrary Shapes Using Minimal Complexity Building Blocks. ACS NANO 2023; 17:5387-5398. [PMID: 36763807 DOI: 10.1021/acsnano.2c09677] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The design space for self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. We develop a pipeline to explore the design spaces for a set of structures of various sizes and complexities. To understand the implications of the different solutions, we analyze their assembly dynamics using patchy particle simulations and study the influence of the number of distinct building blocks, and the angular and spatial tolerances on their interactions, on the kinetics and yield of the target assembly. We show that the resource-saving solution with a minimum number of distinct blocks can often assemble just as well (or faster) than designs where each building block is unique. We further use our methods to design multifarious structures, where building blocks are shared between different target structures. Finally, we use coarse-grained DNA simulations to investigate the realization of multicomponent shapes using DNA nanostructures as building blocks.
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Affiliation(s)
- Joakim Bohlin
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, U.K
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, U.K
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Keble Road, Oxford OX1 3NP, U.K
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
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16
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Kemper U, Ye J, Poppitz D, Gläser R, Seidel R. DNA Mold-Based Fabrication of Palladium Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2206438. [PMID: 36960479 DOI: 10.1002/smll.202206438] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/03/2023] [Indexed: 06/18/2023]
Abstract
DNA origami molds allow a shape-controlled growth of metallic nanoparticles. So far, this approach is limited to gold and silver. Here, the fabrication of linear palladium nanostructures with controlled lengths and patterns is demonstrated. To obtain nucleation centers for a seeded growth, a synthesis procedure of palladium nanoparticles (PdNPs) using Bis(p-sulfonatophenyl)phenylphosphine (BSPP) both as reductant and stabilizer is developed to establish an efficient functionalization protocol of the particles with single-stranded DNA. Attaching the functionalized particles to complementary DNA strands inside DNA mold cavities supports subsequently a highly specific seeded palladium deposition. This provides rod-like PdNPs with diameters of 20-35 nm of grainy morphology. Using an annealing procedure and a post-reduction step with hydrogen, homogeneous palladium nanostructures can be obtained. With the adaptation of the procedure to palladium the capabilities of the mold-based tool-box are expanded. In the future, this may allow a facile adaptation of the mold approach to less noble metals including magnetic materials such as Ni and Co.
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Affiliation(s)
- Ulrich Kemper
- Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - Jingjing Ye
- Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
| | - David Poppitz
- Heterogeneous Catalysis, Institute of Chemical Technology, Universität Leipzig, 04103, Leipzig, Germany
| | - Roger Gläser
- Heterogeneous Catalysis, Institute of Chemical Technology, Universität Leipzig, 04103, Leipzig, Germany
| | - Ralf Seidel
- Molecular Biophysics group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany
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17
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Williamson P, Piskunen P, Ijäs H, Butterworth A, Linko V, Corrigan DK. Signal Amplification in Electrochemical DNA Biosensors Using Target-Capturing DNA Origami Tiles. ACS Sens 2023; 8:1471-1480. [PMID: 36914224 PMCID: PMC10152479 DOI: 10.1021/acssensors.2c02469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Electrochemical DNA (e-DNA) biosensors are feasible tools for disease monitoring, with their ability to translate hybridization events between a desired nucleic acid target and a functionalized transducer, into recordable electrical signals. Such an approach provides a powerful method of sample analysis, with a strong potential to generate a rapid time to result in response to low analyte concentrations. Here, we report a strategy for the amplification of electrochemical signals associated with DNA hybridization, by harnessing the programmability of the DNA origami method to construct a sandwich assay to boost charge transfer resistance (RCT) associated with target detection. This allowed for an improvement in the sensor limit of detection by two orders of magnitude compared to a conventional label-free e-DNA biosensor design and linearity for target concentrations between 10 pM and 1 nM without the requirement for probe labeling or enzymatic support. Additionally, this sensor design proved capable of achieving a high degree of strand selectivity in a challenging DNA-rich environment. This approach serves as a practical method for addressing strict sensitivity requirements necessary for a low-cost point-of-care device.
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Affiliation(s)
- Paul Williamson
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1QE, United Kingdom
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.,Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Adrian Butterworth
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1QE, United Kingdom
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland.,LIBER Center of Excellence, Aalto University, 00076 Aalto, Finland.,Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Damion K Corrigan
- Department of Biomedical Engineering, University of Strathclyde, Glasgow G1 1QE, United Kingdom.,Department of Pure & Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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18
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Ouyang X, Wu Y, Gao Y, Li L, Li L, Liu T, Jing X, Fu Y, Luo J, Xie G, Jia S, Li M, Li Q, Fan C, Liu X. Micron-Scale Fabrication of Ultrathin Amorphous Copper Nanosheets Templated by DNA Scaffolds. J Am Chem Soc 2023; 145:4553-4563. [PMID: 36802526 DOI: 10.1021/jacs.2c12009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Two-dimensional (2D) amorphous materials could outperform their crystalline counterparts toward various applications because they have more defects and reactive sites and thus could exhibit a unique surface chemical state and provide an advanced electron/ion transport path. Nevertheless, it is challenging to fabricate ultrathin and large-sized 2D amorphous metallic nanomaterials in a mild and controllable manner due to the strong metallic bonds between metal atoms. Here, we reported a simple yet fast (10 min) DNA nanosheet (DNS)-templated method to synthesize micron-scale amorphous copper nanosheets (CuNSs) with a thickness of 1.9 ± 0.4 nm in aqueous solution at room temperature. We demonstrated the amorphous feature of the DNS/CuNSs by transmission electron microscopy (TEM) and X-ray diffraction (XRD). Interestingly, we found that they could transform to crystalline forms under continuous electron beam irradiation. Of note, the amorphous DNS/CuNSs exhibited much stronger photoemission (∼62-fold) and photostability than dsDNA-templated discrete Cu nanoclusters due to the elevation of both the conduction band (CB) and valence band (VB). Such ultrathin amorphous DNS/CuNSs hold great potential for practical applications in biosensing, nanodevices, and photodevices.
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Affiliation(s)
- Xiangyuan Ouyang
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Yongli Wu
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Yanjing Gao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingyun Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Le Li
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Ting Liu
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Xinxin Jing
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yue Fu
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Jing Luo
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Gang Xie
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, National Demonstration Center for Experimental Chemistry Education, Northwest University, Xi'an 710127, China
| | - Sisi Jia
- Zhangjiang Laboratory, 100 Haike Road, Shanghai 201210, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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19
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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 2023; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/11/2022] [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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20
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Dunn KE, Elfick A. Harnessing DNA Nanotechnology and Chemistry for Applications in Photonics and Electronics. Bioconjug Chem 2023; 34:97-104. [PMID: 36121896 PMCID: PMC9853499 DOI: 10.1021/acs.bioconjchem.2c00286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/30/2022] [Indexed: 01/24/2023]
Abstract
Many photonic and electronic devices rely on nanotechnology and nanofabrication, but DNA-based approaches have yet to make a significant commercial impact in these fields even though DNA molecules are now well-established as versatile building blocks for nanostructures. As we describe here, DNA molecules can be chemically modified with a wide variety of functional groups enabling nanocargoes to be attached at precisely determined locations. DNA nanostructures can also be used as templates for the growth of inorganic structures. Together, these factors enable the use of DNA nanotechnology for the construction of many novel devices and systems. In this topical review, we discuss four case studies of potential applications in photonics and electronics: carbon nanotube transistors, devices for quantum computing, artificial electromagnetic materials, and enzymatic fuel cells. We conclude by speculating about the barriers to the exploitation of these technologies in real-world settings.
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Affiliation(s)
- Katherine E. Dunn
- School of
Engineering, Institute for
Bioengineering, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3DW, Scotland, U.K.
| | - Alistair Elfick
- School of
Engineering, Institute for
Bioengineering, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3DW, Scotland, U.K.
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21
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Abstract
Hierarchical assembly of programmable DNA frameworks─such as DNA origami─paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.
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Affiliation(s)
- Sofia Julin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Adrian Keller
- Paderborn
University, Technical and Macromolecular
Chemistry, Warburger
Str. 100, 33098 Paderborn, Germany
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- LIBER
Center of Excellence, Aalto University, 00076 Aalto, Finland
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22
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Ijäs H, Liedl T, Linko V, Posnjak G. A label-free light-scattering method to resolve assembly and disassembly of DNA nanostructures. Biophys J 2022; 121:4800-4809. [PMID: 36811525 PMCID: PMC9811603 DOI: 10.1016/j.bpj.2022.10.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/06/2022] [Accepted: 10/24/2022] [Indexed: 11/02/2022] Open
Abstract
DNA self-assembly, and in particular DNA origami, has evolved into a reliable workhorse for organizing organic and inorganic materials with nanometer precision and with exactly controlled stoichiometry. To ensure the intended performance of a given DNA structure, it is beneficial to determine its folding temperature, which in turn yields the best possible assembly of all DNA strands. Here, we show that temperature-controlled sample holders and standard fluorescence spectrometers or dynamic light-scattering setups in a static light-scattering configuration allow for monitoring the assembly progress in real time. With this robust label-free technique, we determine the folding and melting temperatures of a set of different DNA origami structures without the need for more tedious protocols. In addition, we use the method to follow digestion of DNA structures in the presence of DNase I and find strikingly different resistances toward enzymatic degradation depending on the structural design of the DNA object.
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Affiliation(s)
- Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland; Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland; LIBER Center of Excellence, Aalto University, Aalto, Finland.
| | - Gregor Posnjak
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany.
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23
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Stars, combs and bottlebrushes of elastic single-chain nanoparticles. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Agarwal NP, Chandrasekhar S, Prakash PS, Joffroy K, Schmidt TL. Block Copolymer Micellization of DNA Origami Promotes Solubility in Organic Solvents. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11650-11657. [PMID: 36103620 DOI: 10.1021/acs.langmuir.2c01508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The DNA origami technique allows the precise synthesis of complex, biocompatible nanomaterials containing small molecules, biomolecules, and inorganic nanoparticles. The negatively charged phosphates in the backbone make DNA highly water-soluble and require salts to shield its electrostatic repulsion. DNA origamis are therefore not soluble in most organic solvents. While this is not problematic for applications in biochemistry, biophysics, or nanomedicine, other potential applications, processes, and substrates are incompatible with saline solutions, which include the synthesis of many nanomaterials, and reactions in templated synthesis, the operation of nanoelectronic devices, or semiconductor fabrication. To overcome this limitation, we coated DNA origami with amphiphilic poly(ethylene glycol) polylysine block copolymers and transferred them into various organic solvents including chloroform, dichloromethane, acetone, or 1-propanol. Our approach maintains the shape of the nanostructures and protects functional elements bound to the structure, such as fluorophores, gold nanoparticles, or proteins. The DNA origami polyplex micellization (DOPM) strategy hence enables solubilization or a phase transfer of complex structures into various organic solvents, which significantly expands the use of DNA origami for a range of potential applications and technical processes.
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Affiliation(s)
- Nayan P Agarwal
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | | | | | - Kristin Joffroy
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany
| | - Thorsten L Schmidt
- Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany
- Department of Physics, Kent State University, Kent, Ohio 44242, United States
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25
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Seitz I, Ijäs H, Linko V, Kostiainen MA. Optically Responsive Protein Coating of DNA Origami for Triggered Antigen Targeting. ACS APPLIED MATERIALS & INTERFACES 2022; 14:38515-38524. [PMID: 35984232 PMCID: PMC9437894 DOI: 10.1021/acsami.2c10058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA nanostructures have emerged as modular building blocks in several research fields including biomedicine and nanofabrication. Their proneness to degradation in various environments has led to the development of a variety of nature-inspired protection strategies. Coating of DNA origami nanostructures with proteins can circumvent degradation and alter their properties. Here, we have used a single-chain variable antibody fragment and serum albumin to construct positively charged and stimuli-responsive protein-dendron conjugates, which were complexed with DNA origami through electrostatic interactions. Using a stepwise assembly approach, the coated nanostructures were studied for their interaction with the corresponding antigen in fluorescence-based immunoassays. The results suggest that the antibody-antigen interaction can be disturbed by the addition of the bulky serum albumin. However, this effect is fully reversible upon irradiation of the structures with an optical stimulus. This leads to a selective dissociation of the serum albumin from the nanostructure due to cleavage of a photolabile group integrated in the dendron structure, exposing the antibody fragment and enabling triggered binding to the antigen, demonstrating that serum albumin can be considered as an externally controlled "camouflaging" agent. The presented stimuli-responsive complexation approach is highly versatile regarding the choice of protein components and could, therefore, find use in DNA origami protection, targeting, and delivery as well as their spatiotemporal control.
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Affiliation(s)
- Iris Seitz
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Heini Ijäs
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Veikko Linko
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER
Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Department
of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER
Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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Kabusure KM, Piskunen P, Yang J, Kataja M, Chacha M, Ojasalo S, Shen B, Hakala TK, Linko V. Optical characterization of DNA origami-shaped silver nanoparticles created through biotemplated lithography. NANOSCALE 2022; 14:9648-9654. [PMID: 35718875 DOI: 10.1039/d1nr06256e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here, we study optically resonant substrates fabricated using the previously reported BLIN (biotemplated lithography of inorganic nanostructures) technique with single triangle and bowtie DNA origami as templates. We present the first optical characterization of BLIN-fabricated origami-shaped silver nanoparticle patterns on glass surfaces, comprising optical transmission measurements and surface-enhanced Raman spectroscopy. The formed nanoparticle patterns are examined by optical transmission measurements and used for surface enhanced Raman spectroscopy (SERS) of Rhodamine 6G (R6G) dye molecules. Polarization-resolved simulations reveal that the higher SERS enhancement observed for the bowties is primarily due to spectral overlap of the optical resonances with the Raman transitions of R6G. The results manifest the applicability of the BLIN method and substantiate its potential in parallel and high-throughput substrate manufacturing with engineered optical properties. While the results demonstrate the crucial role of the formed nanogaps for SERS, the DNA origami may enable even more complex nanopatterns for various optical applications.
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Affiliation(s)
- Kabusure M Kabusure
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Jiaqi Yang
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mikko Kataja
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mwita Chacha
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Tommi K Hakala
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
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Linko V, Zhang H, Nonappa, Kostiainen MA, Ikkala O. From Precision Colloidal Hybrid Materials to Advanced Functional Assemblies. Acc Chem Res 2022; 55:1785-1795. [PMID: 35647700 PMCID: PMC9260957 DOI: 10.1021/acs.accounts.2c00093] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
ConspectusThe concept of colloids encompasses a wide range of isotropic and anisotropic particles with diverse sizes, shapes, and functions from synthetic nanoparticles, nanorods, and nanosheets to functional biological units. They are addressed in materials science for various functions, while they are ubiquitous in the biological world for multiple functions. A large variety of synthetic colloids have been researched due to their scientific and technological importance; still they characteristically suffer from finite size distributions, imperfect shapes and interactions, and not fully engineered functions. This contrasts with biological colloids that offer precision in their size, shape, and functionality. Materials science has searched for inspiration from the biological world to allow structural control by self-assembly and hierarchy and to identify novel routes for combinations of functions in bio-inspiration.Herein, we first discuss different approaches for highly defined structural control of technically relevant synthetic colloids based on guided assemblies of biological motifs. First, we describe how polydisperse nanoparticles can be assembled within hollow protein cages to allow well-defined assemblies and hierarchical packings. Another approach relies on DNA nanotechnology-based assemblies, where engineered DNA structures allow programmed assembly. Then we will discuss synthetic colloids that have either particularly narrow size dispersity or even atomically precise structures for new assemblies and potential functions. Such colloids can have well-defined packings for membranes allowing high modulus. They can be switchable using light-responsive moieties, and they can initiate packing of larger assemblies of different geometrical shapes. The emphasis is on atomically defined nanoclusters that allow well-defined assemblies by supramolecular interactions, such as directional hydrogen bonding. Finally, we will discuss stimulus-responsive colloids for new functions, even toward complex responsive functions inspired by life. Therein, stimulus-responsive materials inspired by biological learning could allow the next generation of such materials. Classical conditioning is among the simplest biological learning concepts, requiring two stimuli and triggerable memory. Therein we use thermoresponsive hydrogels with plasmonic gold nanoparticles and a spiropyran photoacid as a model. Heating is the unconditioned stimulus leading to melting of the thermoresponsive gel, whereas light (at a specified wavelength) originally leads to reduced pH without plasmonic or structural changes because of steric gel stabilization. Under heat-induced gel melting, light results in pH-decrease and chain-like aggregation of the gold nanoparticles, allowing a new plasmonic response. Thus, simultaneous heating and light irradiation allow conditioning for a newly derived stimulus, where the logic diagram is analogous to Pavlovian conditioning. The shown assemblies demonstrate the different functionalities achievable using colloids when the sizes and the dispersity are controlled.
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Affiliation(s)
- Veikko Linko
- Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, FI-00076 Espoo, Finland
| | - Hang Zhang
- Department of Applied Physics, Aalto University School of Science, FI-00076 Espoo, Finland
| | - Nonappa
- Faculty of Engineering and Natural Sciences, Tampere University, P.O. Box 541, FI-33101 Tampere, Finland
| | - Mauri A. Kostiainen
- Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, FI-00076 Espoo, Finland
| | - Olli Ikkala
- Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, FI-00076 Espoo, Finland
- Department of Applied Physics, Aalto University School of Science, FI-00076 Espoo, Finland
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Piskunen P, Latham R, West CE, Castronovo M, Linko V. Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond. iScience 2022; 25:104389. [PMID: 35633938 PMCID: PMC9130510 DOI: 10.1016/j.isci.2022.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Precise genome editing with CRISPR/Cas paves the way for many biochemical, biotechnological, and medical applications, and consequently, it may enable treatment of already known and still-to-be-found genetic diseases. Meanwhile, another rapidly emerging field—structural DNA nanotechnology—provides a customizable and modular platform for accurate positioning of nanoscopic materials, for e.g., biomedical uses. This addressability has just recently been applied in conjunction with the newly developed gene engineering tools to enable impactful, programmable nanotechnological applications. As of yet, self-assembled DNA nanostructures have been mainly employed to enhance and direct the delivery of CRISPR/Cas, but lately the groundwork has also been laid out for other intriguing and complex functions. These recent advances will be described in this perspective.
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Xin Y, Piskunen P, Suma A, Li C, Ijäs H, Ojasalo S, Seitz I, Kostiainen MA, Grundmeier G, Linko V, Keller A. Environment-Dependent Stability and Mechanical Properties of DNA Origami Six-Helix Bundles with Different Crossover Spacings. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107393. [PMID: 35363419 DOI: 10.1002/smll.202107393] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/14/2022] [Indexed: 05/25/2023]
Abstract
The internal design of DNA nanostructures defines how they behave in different environmental conditions, such as endonuclease-rich or low-Mg2+ solutions. Notably, the inter-helical crossovers that form the core of such DNA objects have a major impact on their mechanical properties and stability. Importantly, crossover design can be used to optimize DNA nanostructures for target applications, especially when developing them for biomedical environments. To elucidate this, two otherwise identical DNA origami designs are presented that have a different number of staple crossovers between neighboring helices, spaced at 42- and 21- basepair (bp) intervals, respectively. The behavior of these structures is then compared in various buffer conditions, as well as when they are exposed to enzymatic digestion by DNase I. The results show that an increased number of crossovers significantly improves the nuclease resistance of the DNA origami by making it less accessible to digestion enzymes but simultaneously lowers its stability under Mg2+ -free conditions by reducing the malleability of the structures. Therefore, these results represent an important step toward rational, application-specific DNA nanostructure design.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Antonio Suma
- Dipartimento di Fisica, Università di Bari and Sezione INFN di Bari, Bari, 70126, Italy
| | - Changyong Li
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Iris Seitz
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
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Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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