1
|
Wang Y, Baars I, Berzina I, Rocamonde-Lago I, Shen B, Yang Y, Lolaico M, Waldvogel J, Smyrlaki I, Zhu K, Harris RA, Högberg B. A DNA robotic switch with regulated autonomous display of cytotoxic ligand nanopatterns. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01676-4. [PMID: 38951595 DOI: 10.1038/s41565-024-01676-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/10/2024] [Indexed: 07/03/2024]
Abstract
The clustering of death receptors (DRs) at the membrane leads to apoptosis. With the goal of treating tumours, multivalent molecular tools that initiate this mechanism have been developed. However, DRs are also ubiquitously expressed in healthy tissue. Here we present a stimuli-responsive robotic switch nanodevice that can autonomously and selectively turn on the display of cytotoxic ligand patterns in tumour microenvironments. We demonstrate a switchable DNA origami that normally hides six ligands but displays them as a hexagonal pattern 10 nm in diameter once under higher acidity. This can effectively cluster DRs and trigger apoptosis of human breast cancer cells at pH 6.5 while remaining inert at pH 7.4. When administered to mice bearing human breast cancer xenografts, this nanodevice decreased tumour growth by up to 70%. The data demonstrate the feasibility and opportunities for developing ligand pattern switches as a path for targeted treatment.
Collapse
Affiliation(s)
- Yang Wang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Igor Baars
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ieva Berzina
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Iris Rocamonde-Lago
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Boxuan Shen
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, Aalto, Finland
| | - Yunshi Yang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Marco Lolaico
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Janine Waldvogel
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ioanna Smyrlaki
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Keying Zhu
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Robert A Harris
- Applied Immunology and Immunotherapy, Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
2
|
Kim T, Lee C, Lee JY, Kim DN. Controlling Chiroptical Responses via Chemo-Mechanical Deformation of DNA Origami Structures. ACS NANO 2024; 18:3414-3423. [PMID: 38236130 DOI: 10.1021/acsnano.3c10386] [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: 01/19/2024]
Abstract
DNA origami-based templates have been widely used to fabricate chiral plasmonic metamaterials due to their precise control of the placement of nanoparticles (NPs) in a desired configuration. However, achieving various chiroptical responses inevitably requires a change in the structure of DNA origami-based templates or binding sites on them, leading to the use of significantly different sets of DNA strands. Here, we propose an approach to controlling various chiroptical responses with a single DNA origami design using its chemo-mechanical deformation induced by DNA intercalators. The chiroptical response could be finely tuned by altering the concentration of intercalators only. The silver (Ag) enhancement was used to amplify the chiroptical signal by enlarging NPs and to maintain it by stiffening the template DNA structure. Furthermore, the sensitivity in the chiroptical signal change to the concentration of intercalators could be modulated by the type of intercalator, the mixture of two intercalators, and the stiffness of DNA origami structures. This approach would be useful in a variety of optical applications that require programmed spatial modification of chiroptical responses.
Collapse
Affiliation(s)
- Taehwi Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Chanseok Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Do-Nyun Kim
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| |
Collapse
|
3
|
Chandrasekaran AR. A DNA rotary nanodevice operated by enzyme-initiated strand resetting. Chem Commun (Camb) 2024; 60:534-537. [PMID: 38038977 PMCID: PMC10843534 DOI: 10.1039/d3cc05487j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
DNA nanostructures that respond to external stimuli have found applications in several areas such as biosensing, drug delivery and molecular computation. The use of different types of stimuli in a single operation provides another layer of control for the reconfiguration of nucleic acid nanostructures. This work demonstrates the use of a ribonuclease to "unset" a nucleic acid nanodevice based on the paranemic crossover (PX) DNA and specific DNA inputs to "reset" the structure into a juxtaposed DNA (JX2) configuration, resulting in a 180° rotation of the helical domains. Such operations would be useful in translational applications where DNA nanostructures can be designed to reconfigure on the basis of more than one stimulus.
Collapse
|
4
|
Kim J, Choi YS, Park G, Kim M, Myung JS, Choi WJ, Park SM, Yoon DK. On-Demand Aligned DNA Hydrogel Via Light Scanning. ACS NANO 2023; 17:22778-22787. [PMID: 37947399 DOI: 10.1021/acsnano.3c07493] [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: 11/12/2023]
Abstract
DNA is an anisotropic, water-attracting, and biocompatible material, an ideal building block for hydrogel. The alignment of the anisotropic DNA chains is essential to maximize hydrogel properties, which has been little explored. Here, we present a method to fabricate the anisotropic DNA hydrogel that allows precise control for the polymerization process of photoreactive cationic monomers. Scanning ultraviolet light enables the uniaxial alignment of DNA chains through the polymerization-induced diffusive mass flow using a concentration gradient. While studying anisotropic mechanical properties and orientation recovery according to the DNA chain alignment direction, we demonstrate the potential of directionally controlled DNA hydrogels as smart materials.
Collapse
Affiliation(s)
- Juri Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yun-Seok Choi
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos 87545, New Mexico, USA
| | - Geonhyeong Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Mingeun Kim
- Chemical Materials Solutions Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Jin Suk Myung
- Chemical Materials Solutions Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Woo Jin Choi
- Chemical Materials Solutions Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Soon Mo Park
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Department of Chemical and Biomolecular Engineering, Cornell University, Ithaca 14853, New York, USA
| | - Dong Ki Yoon
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| |
Collapse
|
5
|
Lee JY, Koh H, Kim DN. A computational model for structural dynamics and reconfiguration of DNA assemblies. Nat Commun 2023; 14:7079. [PMID: 37925463 PMCID: PMC10625641 DOI: 10.1038/s41467-023-42873-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
Abstract
Recent advances in constructing a structured DNA assembly whose configuration can be dynamically changed in response to external stimuli have demanded the development of an efficient computational modeling approach to expedite its design process. Here, we present a computational framework capable of analyzing both equilibrium and non-equilibrium dynamics of structured DNA assemblies at the molecular level. The framework employs Langevin dynamics with structural and hydrodynamic finite element models that describe mechanical, electrostatic, base stacking, and hydrodynamic interactions. Equilibrium dynamic analysis for various problems confirms the solution accuracy at a near-atomic resolution, comparable to molecular dynamics simulations and experimental measurements. Furthermore, our model successfully simulates a long-time-scale close-to-open-to-close dynamic reconfiguration of the switch structure in response to changes in ion concentration. We expect that the proposed model will offer a versatile way of designing responsive and reconfigurable DNA machines.
Collapse
Affiliation(s)
- Jae Young Lee
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Heeyuen Koh
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Do-Nyun Kim
- Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Soft Foundry Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
- Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
| |
Collapse
|
6
|
Pfeifer WG, Huang CM, Poirier MG, Arya G, Castro CE. Versatile computer-aided design of free-form DNA nanostructures and assemblies. SCIENCE ADVANCES 2023; 9:eadi0697. [PMID: 37494445 PMCID: PMC10371015 DOI: 10.1126/sciadv.adi0697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 07/28/2023]
Abstract
Recent advances in structural DNA nanotechnology have been facilitated by design tools that continue to push the limits of structural complexity while simplifying an often-tedious design process. We recently introduced the software MagicDNA, which enables design of complex 3D DNA assemblies with many components; however, the design of structures with free-form features like vertices or curvature still required iterative design guided by simulation feedback and user intuition. Here, we present an updated design tool, MagicDNA 2.0, that automates the design of free-form 3D geometries, leveraging design models informed by coarse-grained molecular dynamics simulations. Our GUI-based, stepwise design approach integrates a high level of automation with versatile control over assembly and subcomponent design parameters. We experimentally validated this approach by fabricating a range of DNA origami assemblies with complex free-form geometries, including a 3D Nozzle, G-clef, and Hilbert and Trifolium curves, confirming excellent agreement between design input, simulation, and structure formation.
Collapse
Affiliation(s)
- Wolfgang G. Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
7
|
Matsubara H, Fukunaga H, Saito T, Ikezaki K, Iwaki M. A Programmable DNA Origami Nanospring That Reports Dynamics of Single Integrin Motion, Force Magnitude and Force Orientation in Living Cells. ACS NANO 2023. [PMID: 37394270 PMCID: PMC10373515 DOI: 10.1021/acsnano.2c12545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Mechanical forces are critical for regulating many biological processes such as cell differentiation, proliferation, and death. Probing the continuously changing molecular force through integrin receptors provides insights into the molecular mechanism of rigidity sensing in cells; however, the force information is still limited. Here, we built a coil-shaped DNA origami (DNA nanospring, NS) as a force sensor that reports the dynamic motion of single integrins as well as the magnitude and orientation of the force through integrins in living cells. We monitored the extension with nanometer accuracy and the orientation of the NS linked with a single integrin by the shape of the fluorescence spots. We used acoustic force spectroscopy to estimate the force-extension curve of the NS and determined the force with an ∼10% force error at a broad detectable range from subpicoNewtons (pN) to ∼50 pN. We found single integrins tethered with the NS moved several tens of nanometers, and the contraction and relaxation speeds were load dependent at less than ∼20 pN but robust over ∼20 pN. Fluctuations of the traction force orientation were suppressed with increasing load. Our assay system is a potentially powerful tool for studying mechanosensing at the molecular level.
Collapse
Affiliation(s)
- Hitomi Matsubara
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 5650874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 5650871, Japan
| | - Hiroki Fukunaga
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 5650874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 5650871, Japan
| | - Takahiro Saito
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 5650871, Japan
| | - Keigo Ikezaki
- Department of Physics, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 1130033, Japan
| | - Mitsuhiro Iwaki
- RIKEN Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 5650874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 5650871, Japan
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo 6512492, Japan
| |
Collapse
|
8
|
Xing Y, Dorey A, Howorka S. Multi-Stimuli-Responsive and Mechano-Actuated Biomimetic Membrane Nanopores Self-Assembled from DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2300589. [PMID: 37029712 DOI: 10.1002/adma.202300589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/31/2023] [Indexed: 06/04/2023]
Abstract
In bioinspired design, biological templates are mimicked in structure and function by highly controllable synthetic means. Of interest are static barrel-like nanopores that enable molecular transport across membranes for use in biosensing, sequencing, and biotechnology. However, biological ion channels offer additional functions such as dynamic changes of the entire pore shape between open and closed states, and triggering of dynamic processes with biochemical and physical stimuli. To better capture this complexity, this report presents multi-stimuli and mechano-responsive biomimetic nanopores which are created with DNA nanotechnology. The nanopores switch between open and closed states, whereby specific binding of DNA and protein molecules as stimuli locks the pores in the open state. Furthermore, the physical stimulus of high transmembrane voltage switches the pores into a closed state. In addition, the pore diameters are larger and more tunable than those of natural templates. These multi-stimuli-responsive and mechanically actuated nanopores mimic several aspects of complex biological channels yet offer easier control over pore size, shape and stimulus response. The designer pores are expected to be applied in biosensing and synthetic biology.
Collapse
Affiliation(s)
- Yongzheng Xing
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Adam Dorey
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| |
Collapse
|
9
|
Zhang XL, Li SS, Liu WW, Kong LQ, Chai YQ, Yuan R. Programmable mismatch-fueled high-efficiency DNA signal amplifier. Chem Sci 2022; 13:11926-11935. [PMID: 36320909 PMCID: PMC9580486 DOI: 10.1039/d2sc04814k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/23/2022] [Indexed: 08/11/2023] Open
Abstract
Herein, by introducing mismatches, a high-efficiency mismatch-fueled catalytic multiple-arm DNA junction assembly (M-CMDJA) with high-reactivity and a high-threshold is developed as a programmable DNA signal amplifier for rapid detection and ultrasensitive intracellular imaging of miRNA. Compared with traditional nucleic acid signal amplification (NASA) with a perfect complement, the M-CMDJA possesses larger kinetic and thermodynamic favorability owing to the more negative reaction standard free energy (ΔG) as driving force, resulting in much higher efficiency and rates. Once traces of the input initiator react with the mismatched substrate DNA, it could be converted into amounts of output multiple-arm DNA junctions via the M-CMDJA as the functional DNA conversion nanodevice. Impressively, the mismatch-fueled catalytic four-arm DNA junction assembly (M-CFDJA) exhibits high conversion efficiency up to 1.05 × 108 in 30 min, which is almost ten times more than those of conventional methods. Therefore, the M-CMDJA could easily address the challenges of traditional methods: slow rates and low efficiency. In application, the M-CFDJA as a DNA signal amplifier was successfully used to develop a biosensing platform for rapid miRNA detection with a LOD of 6.11 aM and the ultrasensitive intracellular imaging of miRNA, providing a basis for the next-generation of versatile DNA signal amplification methods for ultimate applications in DNA nanobiotechnology, biosensing assay, and clinical diagnoses.
Collapse
Affiliation(s)
- Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Sha-Sha Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Wei-Wei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ling-Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China
| |
Collapse
|
10
|
Liu L, Xiong Q, Xie C, Pincet F, Lin C. Actuating tension-loaded DNA clamps drives membrane tubulation. SCIENCE ADVANCES 2022; 8:eadd1830. [PMID: 36223466 PMCID: PMC9555772 DOI: 10.1126/sciadv.add1830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Membrane dynamics in living organisms can arise from proteins adhering to, assembling on, and exerting force on cell membranes. Programmable synthetic materials, such as self-assembled DNA nanostructures, offer the capability to drive membrane-remodeling events that resemble protein-mediated dynamics but with user-defined outcomes. An illustrative example is the tubular deformation of liposomes by DNA nanostructures with purposely designed shapes, surface modifications, and self-assembling properties. However, stimulus-responsive membrane tubulation mediated by DNA reconfiguration remains challenging. Here, we present the triggered formation of membrane tubes in response to specific DNA signals that actuate membrane-bound DNA clamps from an open state to various predefined closed states, releasing prestored energy to activate membrane deformation. We show that the timing and efficiency of vesicle tubulation, as well as the membrane tube widths, are modulated by the conformational change of DNA clamps, marking a solid step toward spatiotemporal control of membrane dynamics in an artificial system.
Collapse
Affiliation(s)
- Longfei Liu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Qiancheng Xiong
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Chun Xie
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Frederic Pincet
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Laboratoire de Physique de l’Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| |
Collapse
|
11
|
Zhang J, Song C, Wang L. DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications. Phys Chem Chem Phys 2022; 24:23959-23979. [PMID: 36168789 DOI: 10.1039/d2cp02100e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.
Collapse
Affiliation(s)
- Jingjing Zhang
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Chunyuan Song
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Lianhui Wang
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| |
Collapse
|
12
|
Dai Z, Xie X, Gao Z, Li Q. DNA‐PAINT Super‐Resolution Imaging for Characterization of Nucleic Acid Nanostructures. Chempluschem 2022; 87:e202200127. [DOI: 10.1002/cplu.202200127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Zheze Dai
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Xiaodong Xie
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Zhaoshuai Gao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Qian Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering Dongchuan Road 800中国 200240 Shanghai CHINA
| |
Collapse
|
13
|
Cervantes-Salguero K, Biaggne A, Youngsman JM, Ward BM, Kim YC, Li L, Hall JA, Knowlton WB, Graugnard E, Kuang W. Strategies for Controlling the Spatial Orientation of Single Molecules Tethered on DNA Origami Templates Physisorbed on Glass Substrates: Intercalation and Stretching. Int J Mol Sci 2022; 23:ijms23147690. [PMID: 35887059 PMCID: PMC9323263 DOI: 10.3390/ijms23147690] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/08/2022] [Accepted: 07/10/2022] [Indexed: 11/18/2022] Open
Abstract
Nanoarchitectural control of matter is crucial for next-generation technologies. DNA origami templates are harnessed to accurately position single molecules; however, direct single molecule evidence is lacking regarding how well DNA origami can control the orientation of such molecules in three-dimensional space, as well as the factors affecting control. Here, we present two strategies for controlling the polar (θ) and in-plane azimuthal (ϕ) angular orientations of cyanine Cy5 single molecules tethered on rationally-designed DNA origami templates that are physically adsorbed (physisorbed) on glass substrates. By using dipolar imaging to evaluate Cy5′s orientation and super-resolution microscopy, the absolute spatial orientation of Cy5 is calculated relative to the DNA template. The sequence-dependent partial intercalation of Cy5 is discovered and supported theoretically using density functional theory and molecular dynamics simulations, and it is harnessed as our first strategy to achieve θ control for a full revolution with dispersion as small as ±4.5°. In our second strategy, ϕ control is achieved by mechanically stretching the Cy5 from its two tethers, being the dispersion ±10.3° for full stretching. These results can in principle be applied to any single molecule, expanding in this way the capabilities of DNA as a functional templating material for single-molecule orientation control. The experimental and modeling insights provided herein will help engineer similar self-assembling molecular systems based on polymers, such as RNA and proteins.
Collapse
Affiliation(s)
- Keitel Cervantes-Salguero
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Correspondence: (K.C.-S.); (W.K.)
| | - Austin Biaggne
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - John M. Youngsman
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Brett M. Ward
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
| | - Young C. Kim
- Materials Science and Technology Division, U.S. Naval Research Laboratory, Code 6300, Washington, DC 20375, USA;
| | - Lan Li
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - John A. Hall
- Division of Research and Economic Development, Boise State University, Boise, ID 83725, USA;
| | - William B. Knowlton
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
| | - Elton Graugnard
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; (A.B.); (J.M.Y.); (B.M.W.); (L.L.); (W.B.K.); (E.G.)
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Wan Kuang
- Department of Electrical and Computer Engineering, Boise State University, Boise, ID 83725, USA
- Correspondence: (K.C.-S.); (W.K.)
| |
Collapse
|
14
|
Yang Q, Chang X, Lee JY, Olivera TR, Saji M, Wisniewski H, Kim S, Zhang F. Recent Advances in Self-Assembled DNA Nanostructures for Bioimaging. ACS APPLIED BIO MATERIALS 2022; 5:4652-4667. [PMID: 35559619 DOI: 10.1021/acsabm.2c00128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA nanotechnology has been proven to be a powerful platform to assist the development of imaging probes for biomedical research. The attractive features of DNA nanostructures, such as nanometer precision, controllable size, programmable functions, and biocompatibility, have enabled researchers to design and customize DNA nanoprobes for bioimaging applications. However, DNA probes with low molecular weights (e.g., 10-100 nt) generally suffer from low stability in physiological buffer environments. To improve the stability of DNA nanoprobes in such environments, DNA nanostructures can be designed with relatively larger sizes and defined shapes. In addition, the established modification methods for DNA nanostructures are also essential in enhancing their properties and performances in a physiological environment. In this review, we begin with a brief recap of the development of DNA nanostructures including DNA tiles, DNA origami, and multifunctional DNA nanostructures with modifications. Then we highlight the recent advances of DNA nanostructures for bioimaging, emphasizing the latest developments in probe modifications and DNA-PAINT imaging. Multiple imaging modules for intracellular biomolecular imaging and cell membrane biomarkers recognition are also summarized. In the end, we discuss the advantages and challenges of applying DNA nanostructures in bioimaging research and speculate on its future developments.
Collapse
Affiliation(s)
- Qi Yang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Xu Chang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Jung Yeon Lee
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Tiffany R Olivera
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Minu Saji
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Henry Wisniewski
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Suchan Kim
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| |
Collapse
|
15
|
Wong CK, Tang C, Schreck JS, Doye JPK. Characterizing the free-energy landscapes of DNA origamis. NANOSCALE 2022; 14:2638-2648. [PMID: 35129570 DOI: 10.1039/d1nr05716b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We show how coarse-grained modelling combined with umbrella sampling using distance-based order parameters can be applied to compute the free-energy landscapes associated with mechanical deformations of large DNA nanostructures. We illustrate this approach for the strong bending of DNA nanotubes and the potentially bistable landscape of twisted DNA origami sheets. The homogeneous bending of the DNA nanotubes is well described by the worm-like chain model; for more extreme bending the nanotubes reversibly buckle with the bending deformations localized at one or two "kinks". For a twisted one-layer DNA origami, the twist is coupled to the bending of the sheet giving rise to a free-energy landscape that has two nearly-degenerate minima that have opposite curvatures. By contrast, for a two-layer origami, the increased stiffness with respect to bending leads to a landscape with a single free-energy minimum that has a saddle-like geometry. The ability to compute such landscapes is likely to be particularly useful for DNA mechanotechnology and for understanding stress accumulation during the self-assembly of origamis into higher-order structures.
Collapse
Affiliation(s)
- Chak Kui Wong
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Chuyan Tang
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - John S Schreck
- National Center for Atmospheric Research, Computational and Information Systems Laboratory, 850 Table Mesa Drive, Boulder, CO 80305, USA
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| |
Collapse
|