1
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Mogheiseh M, Hasanzadeh Ghasemi R. Design and simulation of a wireframe DNA origami nanoactuator. J Chem Phys 2024; 161:045101. [PMID: 39037143 DOI: 10.1063/5.0214313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/30/2024] [Indexed: 07/23/2024] Open
Abstract
This paper explores the use of deoxyribonucleic acid (DNA) origami structures as nanorobot components. Investigating the functional properties of DNA origami structures can facilitate the fabrication of DNA origami-based nanorobots. The wireframe structure stands out as one of the most interesting DNA origami structures. Hence, the present study aims to employ these structures to create DNA origami nanoactuators. The research delves into the design of DNA origami structures with the aim of opening under specific temperature conditions. Short DNA strands (staples) are one of the crucial parts of DNA origami structures, and the appropriate design of these strands can lead to the creation of structures with different properties. Thus, the components of the DNA origami nanoactuator are tailored to enable intentional opening at specific temperatures while maintaining stability at lower temperatures. This structural modification showcases the functional property of the DNA origami structure. The engineered DNA origami nanoactuator holds potential applications in medicine. By carrying drugs under specific temperature conditions and releasing them under different temperature conditions, it can serve as a platform for smart drug delivery purposes.
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Affiliation(s)
- Maryam Mogheiseh
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
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2
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Elonen A, Wimbes L, Mohammed A, Orponen P. DNAforge: a design tool for nucleic acid wireframe nanostructures. Nucleic Acids Res 2024; 52:W13-W18. [PMID: 38747339 PMCID: PMC11223811 DOI: 10.1093/nar/gkae367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/09/2024] [Accepted: 04/29/2024] [Indexed: 07/06/2024] Open
Abstract
DNAforge is an online tool that provides a unified, user-friendly interface to several recent design methods for DNA and RNA wireframe nanostructures, with the possibility of integrating additional methods into the same framework. Currently, DNAforge supports three design methods for DNA nanostructures and two for RNA nanostructures. The tool enables the design, visualisation and sequence generation for highly complex wireframe nanostructures with a simple fully automated process. DNAforge is freely accessible at https://dnaforge.org/.
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Affiliation(s)
- Antti Elonen
- Department of Computer Science, Aalto University, Finland
| | - Leon Wimbes
- Department of Computer Science, Aalto University, Finland
- Department of Mathematics and Computer Science, Philipps University of Marburg, Germany
| | | | - Pekka Orponen
- Department of Computer Science, Aalto University, Finland
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3
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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.
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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.
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4
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van Galen M, Bok A, Peshkovsky T, van der Gucht J, Albada B, Sprakel J. De novo DNA-based catch bonds. Nat Chem 2024:10.1038/s41557-024-01571-4. [PMID: 38914727 DOI: 10.1038/s41557-024-01571-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/06/2024] [Indexed: 06/26/2024]
Abstract
All primary chemical interactions weaken under mechanical stress, which imposes fundamental mechanical limits on the materials constructed from them. Biological materials combine plasticity with strength, for which nature has evolved a unique solution-catch bonds, supramolecular interactions that strengthen under tension. Biological catch bonds use force-gated conformational switches to convert weak bonds into strong ones. So far, catch bonds remain exclusive to nature, leaving their potential as mechanoadaptive elements in synthetic systems untapped. Here we report the design and realization of artificial catch bonds. Starting from a minimal set of thermodynamic design requirements, we created a molecular motif capable of catch bonding. It consists of a DNA duplex featuring a cryptic domain that unfolds under tension to strengthen the interaction. We show that these catch bonds recreate force-enhanced rolling adhesion, a hallmark feature of biological catch bonds in bacteria and leukocytes. This Article introduces catch bonds into the synthetic domain, and could lead to the creation of artificial catch-bonded materials.
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Affiliation(s)
- Martijn van Galen
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen, Netherlands
| | - Annemarie Bok
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands
| | - Taieesa Peshkovsky
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen, Netherlands
| | - Jasper van der Gucht
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen, Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen, Netherlands.
| | - Joris Sprakel
- Laboratory of Biochemistry, Wageningen University & Research, Wageningen, Netherlands.
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5
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Ji W, Xiong X, Cao M, Zhu Y, Li L, Wang F, Fan C, Pei H. Encoding signal propagation on topology-programmed DNA origami. Nat Chem 2024:10.1038/s41557-024-01565-2. [PMID: 38886615 DOI: 10.1038/s41557-024-01565-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 05/24/2024] [Indexed: 06/20/2024]
Abstract
Biological systems often rely on topological transformation to reconfigure connectivity between nodes to guide the flux of molecular information. Here we develop a topology-programmed DNA origami system that encodes signal propagation at the nanoscale, analogous to topologically efficient information processing in cellular systems. We present a systematic molecular implementation of topological operations involving 'glue-cut' processes that can prompt global conformational change of DNA origami structures, with demonstrated major topological properties including genus, number of boundary components and orientability. By spatially arranging reactive DNA hairpins, we demonstrate signal propagation across transmission paths of varying lengths and orientations, and curvatures on the curved surfaces of three-dimensional origamis. These DNA origamis can also form dynamic scaffolds for regulating the spatial and temporal signal propagations whereby topological transformations spontaneously alter the location of nodes and boundary of signal propagation network. We anticipate that our strategy for topological operations will provide a general route to manufacture dynamic DNA origami nanostructures capable of performing global structural transformations under programmable control.
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Affiliation(s)
- Wei Ji
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Xiewei Xiong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Mengyao Cao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Yun Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes; Shanghai Center of Brain-inspired Intelligent Materials and Devices; Shanghai Frontiers Science Center of Molecule Intelligent Syntheses; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
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6
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Liu H, Matthies M, Russo J, Rovigatti L, Narayanan RP, Diep T, McKeen D, Gang O, Stephanopoulos N, Sciortino F, Yan H, Romano F, Šulc P. Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments. Science 2024; 384:776-781. [PMID: 38753798 DOI: 10.1126/science.adl5549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/19/2024] [Indexed: 05/18/2024]
Abstract
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility of self-assembling complex lattices or finite-size constructs. However, attempts so far have mostly only been successful in silico and often fail in experiment because of unpredicted traps associated with kinetic slowing down (gelation, glass transition) and competing ordered structures. Theoretical predictions also face the difficulty of encoding the desired interparticle interaction potential with the experimentally available nano- and micrometer-sized particles. To overcome these issues, we combine SAT assembly (a patchy-particle interaction design algorithm based on constrained optimization) with coarse-grained simulations of DNA nanotechnology to experimentally realize trap-free self-assembly pathways. We use this approach to assemble a pyrochlore three-dimensional lattice, coveted for its promise in the construction of optical metamaterials, and characterize it with small-angle x-ray scattering and scanning electron microscopy visualization.
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Affiliation(s)
- Hao Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Michael Matthies
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Raghu Pradeep Narayanan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Department of Cellular and Molecular Pharmacology, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Thong Diep
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Daniel McKeen
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, 817 SW Mudd, New York, NY 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Flavio Romano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30171 Venezia-Mestre, Italy
- European Centre for Living Technology (ECLT), Ca' Bottacin, 3911 Dorsoduro Calle Crosera, 30123 Venice, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
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7
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Adžić N, Jochum C, Likos CN, Stiakakis E. Engineering Ultrasoft Interactions in Stiff All-DNA Dendrimers by Site-Specific Control of Scaffold Flexibility. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308763. [PMID: 38183376 DOI: 10.1002/smll.202308763] [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: 10/01/2023] [Revised: 12/10/2023] [Indexed: 01/08/2024]
Abstract
A combined experimental and theoretical study of the structural correlations in moderately concentrated suspensions of all-DNA dendrimers of the second generation (G2) with controlled scaffold rigidity is reported here. Small-angle X-ray scattering experiments in concentrated aqueous saline solutions of stiff all-DNA G2 dendritic constructs reveal a novel anomalous liquid-like phase behavior which is reflected in the calculated structure factors as a two-step increase at low scattering wave vectors. By developing a new design strategy for adjusting the particle's internal flexibility based on site-selective incorporation of single-stranded DNA linkers into the dendritic scaffold, it is shown that this unconventional type of self-organization is strongly contingent on the dendrimer's stiffness. A comprehensive computer simulation study employing dendritic models with different levels of coarse-graining, and two theoretical approaches based on effective, pair-potential interactions, remarkably confirmed the origin of this unusual liquid-like behavior. The results demonstrate that the precise control of the internal structure of the dendritic scaffold conferred by the DNA can be potentially used to engineer a rich palette of novel ultrasoft interaction potentials that could offer a route for directed self-assembly of intriguing soft matter phases and experimental realizations of a host of unusual phenomena theoretically predicted for ultrasoft interacting systems.
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Affiliation(s)
- Nataša Adžić
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Vienna, A-1090, Austria
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, Belgrade, 11080, Serbia
| | - Clemens Jochum
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10, Vienna, A-1040, Austria
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Vienna, A-1090, Austria
| | - Emmanuel Stiakakis
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425, Jülich, Germany
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8
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Piantanida L, Liddle JA, Hughes WL, Majikes JM. DNA nanostructure decoration: a how-to tutorial. NANOTECHNOLOGY 2024; 35:273001. [PMID: 38373400 DOI: 10.1088/1361-6528/ad2ac5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/18/2024] [Indexed: 02/21/2024]
Abstract
DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.
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Affiliation(s)
- Luca Piantanida
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| | - William L Hughes
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
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9
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Chen T, Mao S, Ma J, Tang X, Zhu R, Mao D, Zhu X, Pan Q. Proximity-Enhanced Functional Imaging Analysis of Engineered Tumors. Angew Chem Int Ed Engl 2024; 63:e202319117. [PMID: 38305848 DOI: 10.1002/anie.202319117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/03/2024]
Abstract
Functional imaging (FI) techniques have revolutionized tumor imaging by providing information on specific tumor functions, such as glycometabolism. However, tumor cells lack unique molecular characteristics at the molecular level and metabolic pathways, resulting in limited metabolic differences compared to normal cells and increased background signals from FI. To address this limitation, we developed a novel imaging technique termed proximity-enhanced functional imaging (PEFI) for accurate visualization of tumors. By using "two adjacent chemically labeled glycoproteins" as output signals, we significantly enhance the metabolic differences between tumor and normal cells by PEFI, thereby reducing the background signals for analysis and improving the accuracy of tumor functional imaging. Our results demonstrate that PEFI can accurately identify tumors at the cellular, tissue, and animal level, and has potential value in clinical identification and analysis of tumor cells and tissues, as well as in the guidance of clinical tumor resection surgery.
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Affiliation(s)
- Tianshu Chen
- Clinical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Siwei Mao
- Clinical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Ji Ma
- Clinical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Xiaochen Tang
- Clinical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Rui Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Dongsheng Mao
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Qiuhui Pan
- Clinical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
- Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center, Sanya, 572000, P. R. China
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10
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Ma Y, Guo W, Mou Q, Shao X, Lyu M, Garcia V, Kong L, Lewis W, Ward C, Yang Z, Pan X, Yi SS, Lu Y. Spatial imaging of glycoRNA in single cells with ARPLA. Nat Biotechnol 2024; 42:608-616. [PMID: 37217750 PMCID: PMC10663388 DOI: 10.1038/s41587-023-01801-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
Little is known about the biological roles of glycosylated RNAs (glycoRNAs), a recently discovered class of glycosylated molecules, because of a lack of visualization methods. We report sialic acid aptamer and RNA in situ hybridization-mediated proximity ligation assay (ARPLA) to visualize glycoRNAs in single cells with high sensitivity and selectivity. The signal output of ARPLA occurs only when dual recognition of a glycan and an RNA triggers in situ ligation, followed by rolling circle amplification of a complementary DNA, which generates a fluorescent signal by binding fluorophore-labeled oligonucleotides. Using ARPLA, we detect spatial distributions of glycoRNAs on the cell surface and their colocalization with lipid rafts as well as the intracellular trafficking of glycoRNAs through SNARE protein-mediated secretory exocytosis. Studies in breast cell lines suggest that surface glycoRNA is inversely associated with tumor malignancy and metastasis. Investigation of the relationship between glycoRNAs and monocyte-endothelial cell interactions suggests that glycoRNAs may mediate cell-cell interactions during the immune response.
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Affiliation(s)
- Yuan Ma
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Weijie Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Quanbing Mou
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xiangli Shao
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Mingkuan Lyu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Valeria Garcia
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Linggen Kong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Whitney Lewis
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Carson Ward
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Zhenglin Yang
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xingxin Pan
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - S Stephen Yi
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA.
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA.
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11
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Casiraghi L, Mambretti F, Tovo A, Paraboschi EM, Suweis S, Bellini T. Synthetic eco-evolutionary dynamics in simple molecular environment. eLife 2024; 12:RP90156. [PMID: 38530348 PMCID: PMC10965223 DOI: 10.7554/elife.90156] [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] [Indexed: 03/27/2024] Open
Abstract
The understanding of eco-evolutionary dynamics, and in particular the mechanism of coexistence of species, is still fragmentary and in need of test bench model systems. To this aim we developed a variant of SELEX in vitro selection to study the evolution of a population of ∼1015 single-strand DNA oligonucleotide 'individuals'. We begin with a seed of random sequences which we select via affinity capture from ∼1012 DNA oligomers of fixed sequence ('resources') over which they compete. At each cycle ('generation'), the ecosystem is replenished via PCR amplification of survivors. Massive parallel sequencing indicates that across generations the variety of sequences ('species') drastically decreases, while some of them become populous and dominate the ecosystem. The simplicity of our approach, in which survival is granted by hybridization, enables a quantitative investigation of fitness through a statistical analysis of binding energies. We find that the strength of individual resource binding dominates the selection in the first generations, while inter- and intra-individual interactions become important in later stages, in parallel with the emergence of prototypical forms of mutualism and parasitism.
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Affiliation(s)
- Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli CerviSegrateItaly
| | - Francesco Mambretti
- Dipartimento di Fisica e Astronomia, Università degli Studi di PadovaPadovaItaly
| | - Anna Tovo
- Dipartimento di Fisica e Astronomia, Università degli Studi di PadovaPadovaItaly
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi MontalciniPieve EmanueleItaly
- IRCCS, Humanitas Clinical and Research CenterRozzanoItaly
| | - Samir Suweis
- Dipartimento di Fisica e Astronomia, Università degli Studi di PadovaPadovaItaly
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Fratelli CerviSegrateItaly
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12
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Ratajczyk EJ, Šulc P, Turberfield AJ, Doye JPK, Louis AA. Coarse-grained modeling of DNA-RNA hybrids. J Chem Phys 2024; 160:115101. [PMID: 38497475 DOI: 10.1063/5.0199558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/26/2024] [Indexed: 03/19/2024] Open
Abstract
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids that is based on two previously developed coarse-grained models-oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes, including their structure, persistence length, and force-extension characteristics. By parameterizing the DNA-RNA hydrogen bonding interaction, we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability, we provide three examples of its use-calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop, and simulating RNA-scaffolded wireframe origami.
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Affiliation(s)
- Eryk J Ratajczyk
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - 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
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
| | - Andrew J Turberfield
- Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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13
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Chandrasekhar S, Swope TP, Fadaei F, Hollis DR, Bricker R, Houser D, Portman J, Schmidt TL. Bending Unwinds DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.579968. [PMID: 38405957 PMCID: PMC10888926 DOI: 10.1101/2024.02.14.579968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In biology, DNA is often tightly bent to small radii. Solely based on the groove asymmetry, a 30-year-old theoretical paper predicted that such bending should unwind DNA, but this effect has not been directly experimentally quantified so far. We developed a ligation-based assay with nicked DNA circles of variable length, thereby decoupling the twist-dependent ligation efficiency from the large bending strain which dominates conventional circularization assays. We demonstrate that tightly bent DNA indeed unwinds to over 11 base pairs/turn, exactly as predicted. Our discovery requires reassessing the molecular mechanisms and energetics of all processes where DNA is tightly bent or relaxed again, including DNA packaging, gene regulation and expression.
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Affiliation(s)
- Soumya Chandrasekhar
- Department of Physics, Kent State University, Kent, OH, 44242, USA
- Contributed equally
| | - Thomas P. Swope
- Department of Physics, Kent State University, Kent, OH, 44242, USA
- Contributed equally
| | - Fatemeh Fadaei
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Daniel R. Hollis
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Rachel Bricker
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Draven Houser
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - John Portman
- Department of Physics, Kent State University, Kent, OH, 44242, USA
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14
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Centola M, Poppleton E, Ray S, Centola M, Welty R, Valero J, Walter NG, Šulc P, Famulok M. A rhythmically pulsing leaf-spring DNA-origami nanoengine that drives a passive follower. NATURE NANOTECHNOLOGY 2024; 19:226-236. [PMID: 37857824 PMCID: PMC10873200 DOI: 10.1038/s41565-023-01516-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/31/2023] [Indexed: 10/21/2023]
Abstract
Molecular engineering seeks to create functional entities for modular use in the bottom-up design of nanoassemblies that can perform complex tasks. Such systems require fuel-consuming nanomotors that can actively drive downstream passive followers. Most artificial molecular motors are driven by Brownian motion, in which, with few exceptions, the generated forces are non-directed and insufficient for efficient transfer to passive second-level components. Consequently, efficient chemical-fuel-driven nanoscale driver-follower systems have not yet been realized. Here we present a DNA nanomachine (70 nm × 70 nm × 12 nm) driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates as fuel to generate a rhythmic pulsating motion of two rigid DNA-origami arms. Furthermore, we demonstrate actuation control and the simple coupling of the active nanomachine with a passive follower, to which it then transmits its motion, forming a true driver-follower pair.
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Affiliation(s)
- Mathias Centola
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany
| | - Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Max-Planck-Institute for Medical Research, Heidelberg, Germany
| | - Sujay Ray
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA
| | | | - Robb Welty
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA
| | - Julián Valero
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany
- Interdisciplinary Nanoscience Center - INANO-MBG, iNANO-huset, Århus, Denmark
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, Ann Arbor, MI, USA.
| | - Petr Šulc
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany.
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Bonn, Germany.
- Max-Planck Institute for Neurobiology of Behaviour, Bonn, Germany.
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15
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Li XQ, Jia YL, Zhang YW, Shi PF, Chen HY, Xu JJ. Simulation-Assisted DNA Nanodevice Serve as a General Optical Platform for Multiplexed Analysis of Micrornas. Adv Healthc Mater 2024; 13:e2302652. [PMID: 37794560 DOI: 10.1002/adhm.202302652] [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: 08/24/2023] [Revised: 09/29/2023] [Indexed: 10/06/2023]
Abstract
Small frame nucleic acids (FNAs) serve as excellent carrier materials for various functional nucleic acid molecules, showcasing extensive potential applications in biomedicine development. The carrier module and function module combination is crucial for probe design, where an improper combination can significantly impede the functionality of sensing platforms. This study explores the effect of various combinations on the sensing performance of nanodevices through simulations and experimental approaches. Variances in response velocities, sensitivities, and cell uptake efficiencies across different structures are observed. Factors such as the number of functional molecules loaded, loading positions, and intermodular distances affect the rigidity and stability of the nanostructure. The findings reveal that the structures with full loads and moderate distances between modules have the lowest potential energy. Based on these insights, a multisignal detection platform that offers optimal sensitivity and response speed is developed. This research offers valuable insights for designing FNAs-based probes and presents a streamlined method for the conceptualization and optimization of DNA nanodevices.
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Affiliation(s)
- Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yi-Lei Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yu-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Peng-Fei Shi
- College of Medicine, Linyi University, Linyi, 276005, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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16
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Beneduce C, Sciortino F, Šulc P, Russo J. Engineering Azeotropy to Optimize the Self-Assembly of Colloidal Mixtures. ACS NANO 2023; 17:24841-24853. [PMID: 38048489 PMCID: PMC10753881 DOI: 10.1021/acsnano.3c05569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 12/06/2023]
Abstract
The goal of inverse self-assembly is to design interparticle interactions capable of assembling the units into a desired target structure. The effective assembly of complex structures often requires the use of multiple components, each new component increasing the thermodynamic degrees of freedom and, hence, the complexity of the self-assembly pathway. In this work we explore the possibility to use azeotropy, i.e., a special thermodynamic condition where the system behaves effectively as a one-component system, as a way to control the self-assembly of an arbitrary number of components. Exploiting the mass-balance equations, we show how to select patchy particle systems that exhibit azeotropic points along the desired self-assembly pathway. As an example we map the phase diagram of a binary mixture that, by design, fully assembles into cubic (and only cubic) diamond crystal via an azeotropic point. The ability to explicitly include azeotropic points in artificial designs reveals effective pathways for the self-assembly of complex structures.
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Affiliation(s)
- Camilla Beneduce
- Dipartimento
di Fisica, Sapienza Università di
Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Francesco Sciortino
- Dipartimento
di Fisica, Sapienza Università di
Roma, P.le Aldo Moro 5, 00185 Rome, Italy
| | - 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, United States
- School
of Natural Sciences, Department of Bioscience, TU Munich, Am Coulombwall
4a, 85748, Garching, Germany
| | - John Russo
- Dipartimento
di Fisica, Sapienza Università di
Roma, P.le Aldo Moro 5, 00185 Rome, Italy
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17
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Zhang L, Zhao H, Yang H, Su X. Coarse-grained model simulation-guided localized DNA signal amplification probe for miRNA detection. Biosens Bioelectron 2023; 239:115622. [PMID: 37611449 DOI: 10.1016/j.bios.2023.115622] [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: 05/29/2023] [Revised: 08/03/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
DNA-based enzyme-free signal amplification strategies are widely employed to detect biomarkers in low abundance. To enhance signal amplification, localized DNA reaction units which increases molecular collision probability is commonly utilized. However, the current understanding of the structure-function relationships in localized DNA signal amplification probes is limited, leading to unsatisfied performance. In this study, we introduced a coarse-grained molecular model to simulate the dynamic behavior of two DNA reaction units within a DNA enzyme-free signal amplification circuit called Localized Catalytic Hairpin Assembly (LCHA). We investigated the impact of localized distance and flexibility on reaction performance. The most efficient LCHA probe guided by simulation exhibits sensitivity 28 times greater that of free CHA, with a detection limit of miR-21 reaching 16 pM, while the least effective LCHA probe demonstrated a modest improvement of only 7 times. We successfully employed the optimized probe to differentiate cancer cells from normal cells based on their miR-21 expression levels, showcasing its quantification ability. By elucidating the mechanistic insights and structure-function relationship in our work, we aim to contribute valuable information that can save users' time and reduce costs when designing localized DNA probes. With a comprehensive understanding of how the localization affects probe performance, researchers can now make more informed and efficient decisions during the design process. This work would find broad applications of DNA nanotechnology in biosensing, biocomputing, and bionic robots.
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Affiliation(s)
- Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Hongyang Zhao
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huixiao Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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18
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Luo X, Saliba D, Yang T, Gentile S, Mori K, Islas P, Das T, Bagheri N, Porchetta A, Guarne A, Cosa G, Sleiman HF. Minimalist Design of Wireframe DNA Nanotubes: Tunable Geometry, Size, Chirality, and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309869. [PMID: 37610293 DOI: 10.1002/anie.202309869] [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: 07/11/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/24/2023]
Abstract
DNA nanotubes (NTs) have attracted extensive interest as artificial cytoskeletons for biomedical, synthetic biology, and materials applications. Here, we report the modular design and assembly of a minimalist yet robust DNA wireframe nanotube with tunable cross-sectional geometry, cavity size, chirality, and length, while using only four DNA strands. We introduce an h-motif structure incorporating double-crossover (DX) tile-like DNA edges to achieve structural rigidity and provide efficient self-assembly of h-motif-based DNA nanotube (H-NT) units, thus producing programmable, micrometer-long nanotubes. We demonstrate control of the H-NT nanotube length via short DNA modulators. Finally, we use an enzyme, RNase H, to take these structures out of equilibrium and trigger nanotube assembly at a physiologically relevant temperature, underlining future cellular applications. The minimalist H-NTs can assemble at near-physiological salt conditions and will serve as an easily synthesized, DNA-economical modular template for biosensors, plasmonics, or other functional materials and as cost-efficient drug-delivery vehicles for biomedical applications.
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Affiliation(s)
- Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Daniel Saliba
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Tianxiao Yang
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal QC, Canada
| | - Serena Gentile
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | - Keita Mori
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Patricia Islas
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Trishalina Das
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Neda Bagheri
- Department of Chemistry, University of Rome Tor Vergata, Rome, Italy
| | | | - Alba Guarne
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal QC, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal QC, H3A 0B8, Canada
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19
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Karna D, Mano E, Ji J, Kawamata I, Suzuki Y, Mao H. Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies. Nat Commun 2023; 14:6459. [PMID: 37833326 PMCID: PMC10575982 DOI: 10.1038/s41467-023-41604-z] [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: 01/20/2023] [Accepted: 09/06/2023] [Indexed: 10/15/2023] Open
Abstract
The intrinsic complexity of many mesoscale (10-100 nm) cellular machineries makes it challenging to elucidate their topological arrangement and transition dynamics. Here, we exploit DNA origami nanospring as a model system to demonstrate that tens of piconewton linear force can modulate higher-order conformation dynamics of mesoscale molecular assemblies. By switching between two chemical structures (i.e., duplex and tetraplex DNA) in the junctions of adjacent origami modules, the corresponding stretching or compressing chemo-mechanical stress reversibly flips the backbone orientations of the DNA nanosprings. Both coarse-grained molecular dynamics simulations and atomic force microscopy measurements reveal that such a backbone conformational switch does not alter the right-handed chirality of the nanospring helix. This result suggests that mesoscale helical handedness may be governed by the torque, rather than the achiral orientation, of nanospring backbones. It offers a topology-based caging/uncaging concept to present chemicals in response to environmental cues in solution.
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Affiliation(s)
- Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Eriko Mano
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Jiahao Ji
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Ibuki Kawamata
- Department of Robotics, Graduate School of Engineering, Tohoku University, 6-6-01 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8579, Japan.
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8578, Japan.
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, 1577 Kurimamachiya-Cho, Tsu, 514-8507, Japan.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA.
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20
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Siti W, Too HL, Anderson T, Liu XR, Loh IY, Wang Z. Autonomous DNA molecular motor tailor-designed to navigate DNA origami surface for fast complex motion and advanced nanorobotics. SCIENCE ADVANCES 2023; 9:eadi8444. [PMID: 37738343 PMCID: PMC10516491 DOI: 10.1126/sciadv.adi8444] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/23/2023] [Indexed: 09/24/2023]
Abstract
Nanorobots powered by designed DNA molecular motors on DNA origami platforms are vigorously pursued but still short of fully autonomous and sustainable operation, as the reported systems rely on manually operated or autonomous but bridge-burning molecular motors. Expanding DNA nanorobotics requires origami-based autonomous non-bridge-burning motors, but such advanced artificial molecular motors are rare, and their integration with DNA origami remains a challenge. Here, we report an autonomous non-bridge-burning DNA motor tailor-designed for a triangle DNA origami substrate. This is a translational bipedal molecular motor but demonstrates effective translocation on both straight and curved segments of a self-closed circular track on the origami, including sharp ~90° turns by a single hand-over-hand step. The motor is highly directional and attains a record-high speed among the autonomous artificial molecular motors reported to date. The resultant DNA motor-origami system, with its complex translational-rotational motion and big nanorobotic capacity, potentially offers a self-contained "seed" nanorobotic platform to automate or scale up many applications.
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Affiliation(s)
- Winna Siti
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Hon Lin Too
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Integrated Science and Engineering Programme, NUS Graduate School, Singapore 119077, Singapore
| | - Tommy Anderson
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Xiao Rui Liu
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Iong Ying Loh
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
| | - Zhisong Wang
- Department of Physics, National University of Singapore, Singapore 117542, Singapore
- Integrated Science and Engineering Programme, NUS Graduate School, Singapore 119077, Singapore
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21
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Xu Y, Zheng R, Prasad A, Liu M, Wan Z, Zhou X, Porter RM, Sample M, Poppleton E, Procyk J, Liu H, Li Y, Wang S, Yan H, Sulc P, Stephanopoulos N. High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558353. [PMID: 37790307 PMCID: PMC10542138 DOI: 10.1101/2023.09.18.558353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Multivalency enables nanostructures to bind molecular targets with high affinity. Although antibodies can be generated against a wide range of antigens, their shape and size cannot be tuned to match a given target. DNA nanotechnology provides an attractive approach for designing customized multivalent scaffolds due to the addressability and programmability of the nanostructure shape and size. Here, we design a nanoscale synthetic antibody ("nano-synbody") based on a three-helix bundle DNA nanostructure with one, two, or three identical arms terminating in a mini-binder protein that targets the SARS-CoV-2 spike protein. The nano-synbody was designed to match the valence and distance between the three receptor binding domains (RBDs) in the spike trimer, in order to enhance affinity. The protein-DNA nano-synbody shows tight binding to the wild-type, Delta, and several Omicron variants of the SARS-CoV-2 spike trimer, with affinity increasing as the number of arms increases from one to three. The effectiveness of the nano-synbody was also verified using a pseudovirus neutralization assay, with the three-arm nanostructure inhibiting two Omicron variants against which the structures with only one or two arms are ineffective. The structure of the three-arm nano-synbody bound to the Omicron variant spike trimer was solved by negative-stain transmission electron microscopy reconstruction, and shows the protein-DNA nanostructure with all three arms attached to the RBD domains, confirming the intended trivalent attachment. The ability to tune the size and shape of the nano-synbody, as well as its potential ability to attach two or more different binding ligands, will enable the high-affinity targeting of a range of proteins not possible with traditional antibodies.
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22
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Liu XR, Loh IY, Siti W, Too HL, Anderson T, Wang Z. A light-operated integrated DNA walker-origami system beyond bridge burning. NANOSCALE HORIZONS 2023; 8:827-841. [PMID: 37038716 DOI: 10.1039/d2nh00565d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Integrating rationally designed DNA molecular walkers and DNA origami platforms is a promising route towards advanced nano-robotics of diverse functions. Unleashing the full potential in this direction requires DNA walker-origami systems beyond the present simplistic bridge-burning designs for automated repeatable operation and scalable nano-robotic functions. Here we report such a DNA walker-origami system integrating an advanced light-powered DNA bipedal walker and a ∼170 nm-long rod-like DNA origami platform. This light-powered walker is fully qualified as a genuine translational molecular motor, and relies entirely on pure mechanical effects that are complicated by the origami surface but must be preserved for the walker's proper operation. This is made possible by tailor-designing the origami for optimal match with the walker to best preserve its core mechanics. A new fluorescence method is combined with site-controlled motility experiments to yield distinct and reliable signals for the walker's self-directed and processive motion despite origami-complicated fluorophore emission. The resultant integrated DNA walker-origami system provides a 'seed' system for future development of advanced light-powered DNA nano-robots (e.g., for scalable walker-automated chemical synthesis), and also truly bio-mimicking nano-muscles powered by genuine artificial translational molecular motors.
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Affiliation(s)
- Xiao Rui Liu
- Department of Physics, National University of Singapore, 117542, Singapore.
| | - Iong Ying Loh
- Department of Physics, National University of Singapore, 117542, Singapore.
| | - Winna Siti
- Department of Physics, National University of Singapore, 117542, Singapore.
| | - Hon Lin Too
- Department of Physics, National University of Singapore, 117542, Singapore.
- Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, 117542, Singapore
| | - Tommy Anderson
- Department of Physics, National University of Singapore, 117542, Singapore.
| | - Zhisong Wang
- Department of Physics, National University of Singapore, 117542, Singapore.
- Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, 117542, Singapore
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23
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Cervantes-Salguero K, Gutiérrez Fosado YA, Megone W, Gautrot JE, Palma M. Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization. Molecules 2023; 28:molecules28093686. [PMID: 37175096 PMCID: PMC10180480 DOI: 10.3390/molecules28093686] [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: 03/03/2023] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
DNA is programmed to hierarchically self-assemble into superstructures spanning from nanometer to micrometer scales. Here, we demonstrate DNA nanosheets assembled out of a rationally designed flexible DNA unit (F-unit), whose shape resembles a Feynman diagram. F-units were designed to self-assemble in two dimensions and to display a high DNA density of hydrophobic moieties. oxDNA simulations confirmed the planarity of the F-unit. DNA nanosheets with a thickness of a single DNA duplex layer and with large coverage (at least 30 μm × 30 μm) were assembled from the liquid phase at the solid/liquid interface, as unambiguously evidenced by atomic force microscopy imaging. Interestingly, single-layer nanodiscs formed in solution at low DNA concentrations. DNA nanosheet superstructures were further assembled at liquid/liquid interfaces, as demonstrated by the fluorescence of a double-stranded DNA intercalator. Moreover, the interfacial mechanical properties of the nanosheet superstructures were measured as a response to temperature changes, demonstrating the control of interfacial shear mechanics based on DNA nanostructure engineering. The rational design of the F-unit, along with the presented results, provide an avenue toward the controlled assembly of reconfigurable/responsive nanosheets and membranes at liquid/liquid interfaces, to be potentially used in the characterization of biomechanical processes and materials transport.
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Affiliation(s)
- Keitel Cervantes-Salguero
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - William Megone
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Julien E Gautrot
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Matteo Palma
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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24
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Lolaico M, Blokhuizen S, Shen B, Wang Y, Högberg B. Computer-Aided Design of A-Trail Routed Wireframe DNA Nanostructures with Square Lattice Edges. ACS NANO 2023; 17:6565-6574. [PMID: 36951760 PMCID: PMC10100577 DOI: 10.1021/acsnano.2c11982] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
In recent years, interest in wireframe DNA origami has increased, with different designs, software, and applications emerging at a fast pace. It is now possible to design a wide variety of shapes by starting with a 2D or 3D mesh and using different scaffold routing strategies. The design choices of the edges in wireframe structures can be important in some applications and have already been shown to influence the interactions between nanostructures and cells. In this work, we increase the alternatives for the design of A-trail routed wireframe DNA structures by using four-helix bundles (4HB). Our approach is based on the incorporation of additional helices to the edges of the wireframe structure to create a 4HB on a square lattice. We first developed the software for the design of these structures, followed by a demonstration of the successful design and folding of a library of structures, and then, finally, we investigated the higher mechanical rigidity of the reinforced structures. In addition, the routing of the scaffold allows us to easily incorporate these reinforced edges together with more flexible, single helix edges, thereby allowing the user to customize the desired stiffness of the structure. We demonstrated the successful folding of this type of hybrid structure and the different stiffnesses of the different parts of the nanostructures using a combination of computational and experimental techniques.
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Affiliation(s)
- Marco Lolaico
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Sebbe Blokhuizen
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Boxuan Shen
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University School of Chemical Engineering, P.O. Box 16100, 00076 Aalto, Finland
| | - Yang Wang
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Björn Högberg
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
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25
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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: 11] [Impact Index Per Article: 11.0] [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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26
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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27
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Morzy D, Tekin C, Caroprese V, Rubio-Sánchez R, Di Michele L, Bastings MMC. Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes. NANOSCALE 2023; 15:2849-2859. [PMID: 36688792 PMCID: PMC9909679 DOI: 10.1039/d2nr05368c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/16/2023] [Indexed: 05/27/2023]
Abstract
Nucleic acids and lipids function in close proximity in biological processes, as well as in nanoengineered constructs for therapeutic applications. As both molecules carry a rich charge profile, and frequently coexist in complex ionic solutions, the electrostatics surely play a pivotal role in interactions between them. Here we discuss how each component of a DNA/ion/lipid system determines its electrostatic attachment. We examine membrane binding of a library of DNA molecules varying from nanoengineered DNA origami through plasmids to short DNA domains, demonstrating the interplay between the molecular structure of the nucleic acid and the phase of lipid bilayers. Furthermore, the magnitude of DNA/lipid interactions is tuned by varying the concentration of magnesium ions in the physiologically relevant range. Notably, we observe that the structural and mechanical properties of DNA are critical in determining its attachment to lipid bilayers and demonstrate that binding is correlated positively with the size, and negatively with the flexibility of the nucleic acid. The findings are utilized in a proof-of-concept comparison of membrane interactions of two DNA origami designs - potential nanotherapeutic platforms - showing how the results can have a direct impact on the choice of DNA geometry for biotechnological applications.
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Affiliation(s)
- Diana Morzy
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
| | - Cem Tekin
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
| | - Vincenzo Caroprese
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
| | - Roger Rubio-Sánchez
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Maartje M C Bastings
- Programmable Biomaterials Laboratory, Institute of Materials, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland.
- Interfaculty Bioengineering Institute, School of Engineering, Ecole Polytechnique Fédérale Lausanne, Lausanne, 1015, Switzerland
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28
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Moussa S, Kilgour M, Jans C, Hernandez-Garcia A, Cuperlovic-Culf M, Bengio Y, Simine L. Diversifying Design of Nucleic Acid Aptamers Using Unsupervised Machine Learning. J Phys Chem B 2023; 127:62-68. [PMID: 36574492 DOI: 10.1021/acs.jpcb.2c05660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Inverse design of short single-stranded RNA and DNA sequences (aptamers) is the task of finding sequences that satisfy a set of desired criteria. Relevant criteria may be, for example, the presence of specific folding motifs, binding to molecular ligands, sensing properties, and so on. Most practical approaches to aptamer design identify a small set of promising candidate sequences using high-throughput experiments (e.g., SELEX) and then optimize performance by introducing only minor modifications to the empirically found candidates. Sequences that possess the desired properties but differ drastically in chemical composition will add diversity to the search space and facilitate the discovery of useful nucleic acid aptamers. Systematic diversification protocols are needed. Here we propose to use an unsupervised machine learning model known as the Potts model to discover new, useful sequences with controllable sequence diversity. We start by training a Potts model using the maximum entropy principle on a small set of empirically identified sequences unified by a common feature. To generate new candidate sequences with a controllable degree of diversity, we take advantage of the model's spectral feature: an "energy" bandgap separating sequences that are similar to the training set from those that are distinct. By controlling the Potts energy range that is sampled, we generate sequences that are distinct from the training set yet still likely to have the encoded features. To demonstrate performance, we apply our approach to design diverse pools of sequences with specified secondary structure motifs in 30-mer RNA and DNA aptamers.
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Affiliation(s)
- Siba Moussa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QuebecH3A 0B8, Canada
| | - Michael Kilgour
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QuebecH3A 0B8, Canada
| | - Clara Jans
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QuebecH3A 0B8, Canada
| | - Alex Hernandez-Garcia
- Montreal Institute for Learning Algorithms, 6666 St. Urbain, #200, Montreal, QuebecH2S 3H1, Canada
| | - Miroslava Cuperlovic-Culf
- Digital Technologies Research Centre, National Research Council of Canada, 1200 Montreal Road, Ottawa, OntarioK1A 0R6, Canada
| | - Yoshua Bengio
- Montreal Institute for Learning Algorithms, 6666 St. Urbain, #200, Montreal, QuebecH2S 3H1, Canada
| | - Lena Simine
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QuebecH3A 0B8, Canada
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29
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Fu D, Pradeep Narayanan R, Prasad A, Zhang F, Williams D, Schreck JS, Yan H, Reif J. Automated design of 3D DNA origami with non-rasterized 2D curvature. SCIENCE ADVANCES 2022; 8:eade4455. [PMID: 36563147 PMCID: PMC9788767 DOI: 10.1126/sciadv.ade4455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Improving the precision and function of encapsulating three-dimensional (3D) DNA nanostructures via curved geometries could have transformative impacts on areas such as molecular transport, drug delivery, and nanofabrication. However, the addition of non-rasterized curvature escalates design complexity without algorithmic regularity, and these challenges have limited the ad hoc development and usage of previously unknown shapes. In this work, we develop and automate the application of a set of previously unknown design principles that now includes a multilayer design for closed and curved DNA nanostructures to resolve past obstacles in shape selection, yield, mechanical rigidity, and accessibility. We design, analyze, and experimentally demonstrate a set of diverse 3D curved nanoarchitectures, showing planar asymmetry and examining partial multilayer designs. Our automated design tool implements a combined algorithmic and numerical approximation strategy for scaffold routing and crossover placement, which may enable wider applications of general DNA nanostructure design for nonregular or oblique shapes.
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Affiliation(s)
- Daniel Fu
- Department of Computer Science, Duke University, Durham, NC, USA
| | - Raghu Pradeep Narayanan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Abhay Prasad
- School of Molecular Sciences and Center for Molecular Design and Biomimetics at Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ, USA
| | - Dewight Williams
- Erying Materials Center, Office of Knowledge Enterprise Development, Arizona State University, Tempe, AZ, USA
| | - John S. Schreck
- National Center for Atmospheric Research (NCAR), Computational and Information Systems Laboratory, Boulder, CO, USA
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics at Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - John Reif
- Department of Computer Science, Duke University, Durham, NC, USA
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30
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Li L, Liu S, Zhang C, Guo Z, Shao S, Deng X, Liu Q. Recent Advances in DNA-Based Cell Surface Engineering for Biological Applications. Chemistry 2022; 28:e202202070. [PMID: 35977912 DOI: 10.1002/chem.202202070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Indexed: 12/14/2022]
Abstract
Due to its excellent programmability and biocompatibility, DNA molecule has unique advantages in cell surface engineering. Recent progresses provide a reliable and feasible way to engineer cell surfaces with diverse DNA molecules and DNA nanostructures. The abundant form of DNA nanostructures has greatly expanded the toolbox of DNA-based cell surface engineering and gave rise to a variety of novel and fascinating applications. In this review, we summarize recent advances in DNA-based cell surface engineering and its biological applications. We first introduce some widely used methods of immobilizing DNA molecules on cell surfaces and their application features. Then we discuss the approaches of employing DNA nanostructures and dynamic DNA nanotechnology as elements for creating functional cell surfaces. Finally, we review the extensive biological applications of DNA-based cell surface engineering and discuss the challenges and prospects of DNA-based cell surface engineering.
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Affiliation(s)
- Lexun Li
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Shuang Liu
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Chunjuan Zhang
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Zhenzhen Guo
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Shuxuan Shao
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Xiaodan Deng
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
| | - Qiaoling Liu
- Molecular Science and Biomedicine Laboratory (MBL) State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Biology, Hunan University Changsha, Hunan, 410082, People's Republic of China
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