1
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Roozbahani GM, Colosi PL, Oravecz A, Sorokina EM, Pfeifer W, Shokri S, Wei Y, Didier P, DeLuca M, Arya G, Tora L, Lakadamyali M, Poirier MG, Castro CE. Piggybacking functionalized DNA nanostructures into live-cell nuclei. SCIENCE ADVANCES 2024; 10:eadn9423. [PMID: 38968349 PMCID: PMC11225781 DOI: 10.1126/sciadv.adn9423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 06/03/2024] [Indexed: 07/07/2024]
Abstract
DNA origami nanostructures (DOs) are promising tools for applications including drug delivery, biosensing, detecting biomolecules, and probing chromatin substructures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing, visualizing, and controlling biomolecular processes within live cells. We present an approach to deliver DOs into live-cell nuclei. We show that these DOs do not undergo detectable structural degradation in cell culture media or cell extracts for 24 hours. To deliver DOs into the nuclei of human U2OS cells, we conjugated 30-nanometer DO nanorods with an antibody raised against a nuclear factor, specifically the largest subunit of RNA polymerase II (Pol II). We find that DOs remain structurally intact in cells for 24 hours, including inside the nucleus. We demonstrate that electroporated anti-Pol II antibody-conjugated DOs are piggybacked into nuclei and exhibit subdiffusive motion inside the nucleus. Our results establish interfacing DOs with a nuclear factor as an effective method to deliver nanodevices into live-cell nuclei.
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Affiliation(s)
- Golbarg M. Roozbahani
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - P. L. Colosi
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Attila Oravecz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch 67404, France
- Université de Strasbourg, Illkirch 67404, France
| | - Elena M. Sorokina
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wolfgang Pfeifer
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Siamak Shokri
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Yin Wei
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Pascal Didier
- Université de Strasbourg, Illkirch 67404, France
- Laboratoire de Biophotonique et Pharmacologie, Illkirch 67401, France
| | - Marcello DeLuca
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch 67404, France
- Université de Strasbourg, Illkirch 67404, France
| | - Melike Lakadamyali
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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2
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Ma C, Li S, Zeng Y, Lyu Y. DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications. BIOSENSORS 2024; 14:236. [PMID: 38785710 PMCID: PMC11117991 DOI: 10.3390/bios14050236] [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: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.
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Affiliation(s)
- Chunran Ma
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Shiquan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yuqi Zeng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (C.M.); (S.L.); (Y.Z.)
- Furong Laboratory, Changsha 410082, China
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3
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Teng T, Bernal‐Chanchavac J, Stephanopoulos N, Castro CE. Construction of Reconfigurable and Polymorphic DNA Origami Assemblies with Coiled-Coil Patches and Patterns. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307257. [PMID: 38459678 PMCID: PMC11132032 DOI: 10.1002/advs.202307257] [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: 10/13/2023] [Revised: 12/22/2023] [Indexed: 03/10/2024]
Abstract
DNA origami nanodevices achieve programmable structure and tunable mechanical and dynamic properties by leveraging the sequence-specific interactions of nucleic acids. Previous advances have also established DNA origami as a useful building block to make well-defined micron-scale structures through hierarchical self-assembly, but these efforts have largely leveraged the structural features of DNA origami. The tunable dynamic and mechanical properties also provide an opportunity to make assemblies with adaptive structures and properties. Here the integration of DNA origami hinge nanodevices and coiled-coil peptides are reported into hybrid reconfigurable assemblies. With the same dynamic device and peptide interaction, it is made multiple higher-order assemblies (i.e., polymorphic assembly) by organizing clusters of peptides into patches or arranging single peptides into patterns on the surfaces of DNA origami to control the relative orientation of devices. The coiled-coil interactions are used to construct circular and linear assemblies whose structure and mechanical properties can be modulated with DNA-based reconfiguration. Reconfiguration of linear assemblies leads to micron scale motions and ≈2.5-10-fold increase in bending stiffness. The results provide a foundation for stimulus-responsive hybrid assemblies that can adapt their structure and properties in response to nucleic acid, peptide, protein, or other triggers.
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Affiliation(s)
- Teng Teng
- Department of Mechanical and Aerospace EngineeringThe Ohio State UniversityColumbusOH43210USA
| | - Julio Bernal‐Chanchavac
- School of Molecular SciencesArizona State UniversityTempeAZ85287USA
- Center for Molecular Design and BiomimeticsThe Biodesign Institute, Arizona State UniversityTempeAZ85287USA
| | - Nicholas Stephanopoulos
- School of Molecular SciencesArizona State UniversityTempeAZ85287USA
- Center for Molecular Design and BiomimeticsThe Biodesign Institute, Arizona State UniversityTempeAZ85287USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace EngineeringThe Ohio State UniversityColumbusOH43210USA
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4
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Vallina NS, McRae EKS, Geary C, Andersen ES. An RNA origami robot that traps and releases a fluorescent aptamer. SCIENCE ADVANCES 2024; 10:eadk1250. [PMID: 38507482 PMCID: PMC10954211 DOI: 10.1126/sciadv.adk1250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
RNA nanotechnology aims to use RNA as a programmable material to create self-assembling nanodevices for application in medicine and synthetic biology. The main challenge is to develop advanced RNA robotic devices that both sense, compute, and actuate to obtain enhanced control over molecular processes. Here, we use the RNA origami method to prototype an RNA robotic device, named the "Traptamer," that mechanically traps the fluorescent aptamer, iSpinach. The Traptamer is shown to sense two RNA key strands, acts as a Boolean AND gate, and reversibly controls the fluorescence of the iSpinach aptamer. Cryo-electron microscopy of the closed Traptamer structure at 5.45-angstrom resolution reveals the mechanical mode of distortion of the iSpinach motif. Our study suggests a general approach to distorting RNA motifs and a path forward to build sophisticated RNA machines that through sensing, computing, and actuation modules can be used to precisely control RNA functionalities in cellular systems.
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Affiliation(s)
| | - Ewan K. S. McRae
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave, R10-117, Houston, TX 77030, USA
| | - Cody Geary
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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5
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Robbins A, Hildebolt H, Neuhoff M, Beshay P, Winter JO, Castro CE, Bundschuh R, Poirier MG. Cooperative control of a DNA origami force sensor. Sci Rep 2024; 14:4132. [PMID: 38374280 PMCID: PMC10876929 DOI: 10.1038/s41598-024-53841-3] [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: 06/26/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Biomolecular systems are dependent on a complex interplay of forces. Modern force spectroscopy techniques provide means of interrogating these forces, but they are not optimized for studies in constrained environments as they require attachment to micron-scale probes such as beads or cantilevers. Nanomechanical devices are a promising alternative, but this requires versatile designs that can be tuned to respond to a wide range of forces. We investigate the properties of a nanoscale force sensitive DNA origami device which is highly customizable in geometry, functionalization, and mechanical properties. The device, referred to as the NanoDyn, has a binary (open or closed) response to an applied force by undergoing a reversible structural transition. The transition force is tuned with minor alterations of 1 to 3 DNA oligonucleotides and spans tens of picoNewtons (pN). The DNA oligonucleotide design parameters also strongly influence the efficiency of resetting the initial state, with higher stability devices (≳10 pN) resetting more reliably during repeated force-loading cycles. Finally, we show the opening force is tunable in real time by adding a single DNA oligonucleotide. These results establish the potential of the NanoDyn as a versatile force sensor and provide fundamental insights into how design parameters modulate mechanical and dynamic properties.
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Affiliation(s)
- Ariel Robbins
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Hazen Hildebolt
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael Neuhoff
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Peter Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Jessica O Winter
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E Castro
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.
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6
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Roozbahani GM, Colosi P, Oravecz A, Sorokina EM, Pfeifer W, Shokri S, Wei Y, Didier P, DeLuca M, Arya G, Tora L, Lakadamyali M, Poirier MG, Castro CE. Piggybacking functionalized DNA nanostructures into live cell nuclei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.30.573746. [PMID: 38260628 PMCID: PMC10802371 DOI: 10.1101/2023.12.30.573746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
DNA origami (DO) are promising tools for in vitro or in vivo applications including drug delivery; biosensing, detecting biomolecules; and probing chromatin sub-structures. Targeting these nanodevices to mammalian cell nuclei could provide impactful approaches for probing visualizing and controlling important biological processes in live cells. Here we present an approach to deliver DO strucures into live cell nuclei. We show that labelled DOs do not undergo detectable structural degradation in cell culture media or human cell extracts for 24 hr. To deliver DO platforms into the nuclei of human U2OS cells, we conjugated 30 nm long DO nanorods with an antibody raised against the largest subunit of RNA Polymerase II (Pol II), a key enzyme involved in gene transcription. We find that DOs remain structurally intact in cells for 24hr, including within the nucleus. Using fluorescence microscopy we demonstrate that the electroporated anti-Pol II antibody conjugated DOs are efficiently piggybacked into nuclei and exihibit sub-diffusive motion inside the nucleus. Our results reveal that functionalizing DOs with an antibody raised against a nuclear factor is a highly effective method for the delivery of nanodevices into live cell nuclei.
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Affiliation(s)
- Golbarg M. Roozbahani
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Patricia Colosi
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Attila Oravecz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, 67404, France
- Université de Strasbourg, Illkirch, 67404, France
| | - Elena M. Sorokina
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wolfgang Pfeifer
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Siamak Shokri
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Yin Wei
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Pascal Didier
- Université de Strasbourg, Illkirch, 67404, France
- Laboratoire de Biophotonique et Pharmacologie, Illkirch, 67401, France
| | - Marcello DeLuca
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, 27708, United States
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67404, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67404, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, 67404, France
- Université de Strasbourg, Illkirch, 67404, France
| | - Melike Lakadamyali
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael G. Poirier
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
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7
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Mentis AFA, Papavassiliou KA, Papavassiliou AG. DNA origami: a tool to evaluate and harness transcription factors. J Mol Med (Berl) 2023; 101:1493-1498. [PMID: 37813986 DOI: 10.1007/s00109-023-02380-x] [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: 08/10/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023]
Abstract
Alongside other players, such as CpG methylation and the "histone code," transcription factors (TFs) represent a key feature of gene regulation. TFs are implicated in critical cellular processes, ranging from cell death, growth, and differentiation, up to intranuclear signaling of steroid and other hormones, physical entities, and hypoxia regulation. Notwithstanding an extensive body of research in this field, several questions and therapeutic options remain unanswered and unexplored, respectively. Of note, many of these TFs represent therapeutic targets, which are either difficult to be pharmacologically tackled or are still not drugged via traditional approaches, such as small-molecule inhibition. Upon providing a brief overview of TFs, we focus herein on how synthetic biology/medicine could assist in their study as well as their therapeutic targeting. Specifically, we contend that DNA origami, i.e., a novel synthetic DNA nanotechnological approach, represents an excellent synthetic biology/medicine tool to accomplish the above goals, since it can harness several vital characteristics of DNA: DNA polymerization, DNA complementarity, DNA "programmability," and DNA "editability." In doing so, DNA origami can be applied to study TF dynamics during DNA transcription, to elucidate xeno-nucleic acids with distinct scaffolds and unconventional base pairs, and to use TFs as competitors of oncogene-engaged promoters. Overall, because of their potential for high-throughput design and their favorable pharmacodynamic and pharmacokinetic properties, DNA origami can be a novel armory for TF-related drug design. Last, we discuss future trends in the field, such as RNA origami and innovative DNA origami-based therapeutic delivery approaches.
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Affiliation(s)
| | - Kostas A Papavassiliou
- First University Department of Respiratory Medicine, Sotiria' Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece.
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8
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Wang Y, Jin X, Castro C. Accelerating the characterization of dynamic DNA origami devices with deep neural networks. Sci Rep 2023; 13:15196. [PMID: 37709771 PMCID: PMC10502017 DOI: 10.1038/s41598-023-41459-w] [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: 05/12/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023] Open
Abstract
Mechanical characterization of dynamic DNA nanodevices is essential to facilitate their use in applications like molecular diagnostics, force sensing, and nanorobotics that rely on device reconfiguration and interactions with other materials. A common approach to evaluate the mechanical properties of dynamic DNA nanodevices is by quantifying conformational distributions, where the magnitude of fluctuations correlates to the stiffness. This is generally carried out through manual measurement from experimental images, which is a tedious process and a critical bottleneck in the characterization pipeline. While many tools support the analysis of static molecular structures, there is a need for tools to facilitate the rapid characterization of dynamic DNA devices that undergo large conformational fluctuations. Here, we develop a data processing pipeline based on Deep Neural Networks (DNNs) to address this problem. The YOLOv5 and Resnet50 network architecture were used for the two key subtasks: particle detection and pose (i.e. conformation) estimation. We demonstrate effective network performance (F1 score 0.85 in particle detection) and good agreement with experimental distributions with limited user input and small training sets (~ 5 to 10 images). We also demonstrate this pipeline can be applied to multiple nanodevices, providing a robust approach for the rapid characterization of dynamic DNA devices.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA.
| | - Xin Jin
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA.
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9
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Robbins A, Hildebolt H, Neuhoff M, Beshay P, Winter JO, Castro CE, Bundschuh R, Poirier MG. Cooperative control of a DNA origami force sensor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546608. [PMID: 37425797 PMCID: PMC10327127 DOI: 10.1101/2023.06.26.546608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Most biomolecular systems are dependent on a complex interplay of forces. Modern force spectroscopy techniques provide means of interrogating these forces. These techniques, however, are not optimized for studies in constrained or crowded environments as they typically require micron-scale beads in the case of magnetic or optical tweezers, or direct attachment to a cantilever in the case of atomic force microscopy. We implement a nanoscale force-sensing device using a DNA origami which is highly customizable in geometry, functionalization, and mechanical properties. The device, referred to as the NanoDyn, functions as a binary (open or closed) force sensor that undergoes a structural transition under an external force. The transition force is tuned with minor alterations of 1 to 3 DNA oligonucleotides and spans tens of picoNewtons (pN). This actuation of the NanoDyn is reversible and the design parameters strongly influence the efficiency of resetting the initial state, with higher stability devices (≳10 pN) resetting more reliably during repeated force-loading cycles. Finally, we show that the opening force can be adjusted in real time by the addition of a single DNA oligonucleotide. These results establish the NanoDyn as a versatile force sensor and provide fundamental insights into how design parameters modulate mechanical and dynamic properties.
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Affiliation(s)
- Ariel Robbins
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Hazen Hildebolt
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Michael Neuhoff
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Peter Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jessica O. Winter
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E. Castro
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G. Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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10
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Mills A, Aissaoui N, Finkel J, Elezgaray J, Bellot G. Mechanical DNA Origami to Investigate Biological Systems. Adv Biol (Weinh) 2023; 7:e2200224. [PMID: 36509679 DOI: 10.1002/adbi.202200224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to self-assemble DNA nanodevices with programmed structural dynamics that can sense and respond to the local environment can enable transformative applications in fields including mechanobiology and nanomedicine. The responsive function of biomolecules is often driven by alterations in conformational distributions mediated by highly sensitive interactions with the local environment. In this review, the current state-of-the-art in constructing complex DNA geometries with dynamic and mechanical properties to enable a molecular scale force measurement is first summarized. Next, an overview of engineering modular DNA devices that interact with cell surfaces is highlighted detailing examples of mechanosensitive proteins and the force-induced dynamic molecular interaction on the downstream biochemical signaling. Finally, the challenges and an outlook on this promising class of DNA devices acting as nanomachines to operate at a low piconewton range suitable for a majority of biological effects or as hybrid materials to achieve higher tension exertion required for other biological investigations, are discussed.
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Affiliation(s)
- Allan Mills
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Nesrine Aissaoui
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, Paris, 75006, France
| | - Julie Finkel
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
| | - Juan Elezgaray
- CRPP, CNRS, UMR 5031, Université de Bordeaux, Pessac, 33600, France
| | - Gaëtan Bellot
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, 34090, France
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11
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Natarajan AK, Ryssy J, Kuzyk A. A DNA origami-based device for investigating DNA bending proteins by transmission electron microscopy. NANOSCALE 2023; 15:3212-3218. [PMID: 36722916 DOI: 10.1039/d2nr05366g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The DNA origami technique offers precise positioning of nanoscale objects with high accuracy. This has facilitated the development of DNA origami-based functional nanomechanical devices that enable the investigation of DNA-protein interactions at the single particle level. Herein, we used the DNA origami technique to fabricate a nanoscale device for studying DNA bending proteins. For a proof of concept, we used TATA-box binding protein (TBP) to evaluate our approach. Upon binding to the TATA box, TBP causes a bend to DNA of ∼90°. Our device translates this bending into an angular change that is readily observable with a conventional transmission electron microscope (TEM). Furthermore, we investigated the roles of transcription factor II A (TF(II)A) and transcription factor II B (TF(II)B). Our results indicate that TF(II)A introduces additional bending, whereas TF(II)B does not significantly alter the TBP-DNA structure. Our approach can be readily adopted to a wide range of DNA-bending proteins and will aid the development of DNA-origami-based devices tailored for the investigation of DNA-protein interactions.
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Affiliation(s)
- Ashwin Karthick Natarajan
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
| | - Joonas Ryssy
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, Aalto University, School of Science, P.O. Box 12200, FI-00076 Aalto, Finland.
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12
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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13
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Haydell M, Ma Y. DNA Origami: Recent Progress and Applications. Methods Mol Biol 2023; 2639:3-19. [PMID: 37166708 DOI: 10.1007/978-1-0716-3028-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This chapter explores the basic concept of DNA origami and its various types. By showing the progress made in structural DNA nanotechnology during the last 15 years, the chapter draws attention to the capability of DNA origami to construct complex structures in both 2D and 3D level. As well as looking at a few examples of dynamic DNA nanostructures, the chapter also explores the possible applications of DNA origami in different fields, such as biological computing, nanorobotics, and DNA walkers.
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Affiliation(s)
- Michael Haydell
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Yinzhou Ma
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing, China.
- Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, Beijing, China.
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14
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Shahhosseini M, Beshay PE, Akbari E, Roki N, Lucas CR, Avendano A, Song JW, Castro CE. Multiplexed Detection of Molecular Interactions with DNA Origami Engineered Cells in 3D Collagen Matrices. ACS APPLIED MATERIALS & INTERFACES 2022; 14:55307-55319. [PMID: 36509424 PMCID: PMC9785045 DOI: 10.1021/acsami.2c07971] [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: 05/12/2022] [Accepted: 09/29/2022] [Indexed: 06/17/2023]
Abstract
The interactions of cells with signaling molecules present in their local microenvironment maintain cell proliferation, differentiation, and spatial organization and mediate progression of diseases such as metabolic disorders and cancer. Real-time monitoring of the interactions between cells and their extracellular ligands in a three-dimensional (3D) microenvironment can inform detection and understanding of cell processes and the development of effective therapeutic agents. DNA origami technology allows for the design and fabrication of biocompatible and 3D functional nanodevices via molecular self-assembly for various applications including molecular sensing. Here, we report a robust method to monitor live cell interactions with molecules in their surrounding environment in a 3D tissue model using a microfluidic device. We used a DNA origami cell sensing platform (CSP) to detect two specific nucleic acid sequences on the membrane of B cells and dendritic cells. We further demonstrated real-time detection of biomolecules with the DNA sensing platform on the surface of dendritic cells in a 3D microfluidic tissue model. Our results establish the integration of live cells with membranes engineered with DNA nanodevices into microfluidic chips as a highly capable biosensor approach to investigate subcellular interactions in physiologically relevant 3D environments under controlled biomolecular transport.
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Affiliation(s)
- Melika Shahhosseini
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
| | - Peter E. Beshay
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
| | - Ehsan Akbari
- Biophysics
Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Niksa Roki
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
- Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210 United States
| | - Christopher R. Lucas
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
- Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210 United States
| | - Alex Avendano
- Department
of Biomedical Engineering, The Ohio State
University, Columbus, Ohio 43210, United States
| | - Jonathan W. Song
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
- Comprehensive
Cancer Center, The Ohio State University, Columbus, Ohio 43210 United States
| | - Carlos E. Castro
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, 201 West 19th Avenue, Columbus, Ohio 43210, United States
- Biophysics
Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
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15
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Mao X, Liu M, Li Q, Fan C, Zuo X. DNA-Based Molecular Machines. JACS AU 2022; 2:2381-2399. [PMID: 36465542 PMCID: PMC9709946 DOI: 10.1021/jacsau.2c00292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 05/17/2023]
Abstract
Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.
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Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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16
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HIV-1 Preintegration Complex Preferentially Integrates the Viral DNA into Nucleosomes Containing Trimethylated Histone 3-Lysine 36 Modification and Flanking Linker DNA. J Virol 2022; 96:e0101122. [PMID: 36094316 PMCID: PMC9517705 DOI: 10.1128/jvi.01011-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
HIV-1 DNA is preferentially integrated into chromosomal hot spots by the preintegration complex (PIC). To understand the mechanism, we measured the DNA integration activity of PICs-extracted from infected cells-and intasomes, biochemically assembled PIC substructures using a number of relevant target substrates. We observed that PIC-mediated integration into human chromatin is preferred compared to genomic DNA. Surprisingly, nucleosomes lacking histone modifications were not preferred integration compared to the analogous naked DNA. Nucleosomes containing the trimethylated histone 3 lysine 36 (H3K36me3), an epigenetic mark linked to active transcription, significantly stimulated integration, but the levels remained lower than the naked DNA. Notably, H3K36me3-modified nucleosomes with linker DNA optimally supported integration mediated by the PIC but not by the intasome. Interestingly, optimal intasome-mediated integration required the cellular cofactor LEDGF. Unexpectedly, LEDGF minimally affected PIC-mediated integration into naked DNA but blocked integration into nucleosomes. The block for the PIC-mediated integration was significantly relieved by H3K36me3 modification. Mapping the integration sites in the preferred substrates revealed that specific features of the nucleosome-bound DNA are preferred for integration, whereas integration into naked DNA was random. Finally, biochemical and genetic studies demonstrate that DNA condensation by the H1 protein dramatically reduces integration, providing further evidence that features inherent to the open chromatin are preferred for HIV-1 integration. Collectively, these results identify the optimal target substrate for HIV-1 integration, report a mechanistic link between H3K36me3 and integration preference, and importantly, reveal distinct mechanisms utilized by the PIC for integration compared to the intasomes. IMPORTANCE HIV-1 infection is dependent on integration of the viral DNA into the host chromosomes. The preintegration complex (PIC) containing the viral DNA, the virally encoded integrase (IN) enzyme, and other viral/host factors carries out HIV-1 integration. HIV-1 integration is not dependent on the target DNA sequence, and yet the viral DNA is selectively inserted into specific "hot spots" of human chromosomes. A growing body of literature indicates that structural features of the human chromatin are important for integration targeting. However, the mechanisms that guide the PIC and enable insertion of the PIC-associated viral DNA into specific hot spots of the human chromosomes are not fully understood. In this study, we describe a biochemical mechanism for the preference of the HIV-1 DNA integration into open chromatin. Furthermore, our study defines a direct role for the histone epigenetic mark H3K36me3 in HIV-1 integration preference and identify an optimal substrate for HIV-1 PIC-mediated viral DNA integration.
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17
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Kaufhold WT, Pfeifer W, Castro CE, Di Michele L. Probing the Mechanical Properties of DNA Nanostructures with Metadynamics. ACS NANO 2022; 16:8784-8797. [PMID: 35580231 PMCID: PMC9245350 DOI: 10.1021/acsnano.1c08999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, the convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecular conformational distributions by flattening free energy landscapes. Here we leveraged this approach to sample the free energy landscapes of DNA nanostructures whose unbiased dynamics are nonergodic, including bistable Holliday junctions and part of a bistable DNA origami structure. Taking a DNA origami-compliant joint as a case study, we further demonstrate that metadynamics can predict the mechanical response of a full DNA origami device to an applied force, showing good agreement with experiments. Our results exemplify the efficient computation of free energy landscapes and force response in DNA nanodevices, which could be applied for rapid feedback in iterative design workflows and generally facilitate the integration of simulation and experiments. Metadynamics will be particularly useful to guide the design of dynamic devices for nanorobotics, biosensing, or nanomanufacturing applications.
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Affiliation(s)
- Will T. Kaufhold
- Department
of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
- Department
of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Wolfgang Pfeifer
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Carlos E. Castro
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Lorenzo Di Michele
- Department
of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
- Department
of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
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18
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Kaufhold WT, Pfeifer W, Castro CE, Di Michele L. Probing the Mechanical Properties of DNA Nanostructures with Metadynamics. ACS NANO 2022; 16:8784-8797. [PMID: 35580231 DOI: 10.48550/arxiv.2110.01477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, the convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecular conformational distributions by flattening free energy landscapes. Here we leveraged this approach to sample the free energy landscapes of DNA nanostructures whose unbiased dynamics are nonergodic, including bistable Holliday junctions and part of a bistable DNA origami structure. Taking a DNA origami-compliant joint as a case study, we further demonstrate that metadynamics can predict the mechanical response of a full DNA origami device to an applied force, showing good agreement with experiments. Our results exemplify the efficient computation of free energy landscapes and force response in DNA nanodevices, which could be applied for rapid feedback in iterative design workflows and generally facilitate the integration of simulation and experiments. Metadynamics will be particularly useful to guide the design of dynamic devices for nanorobotics, biosensing, or nanomanufacturing applications.
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Affiliation(s)
- Will T Kaufhold
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
- Department of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Wolfgang Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Lorenzo Di Michele
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
- Department of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
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19
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The Free-Energy Landscape of a Mechanically Bistable DNA Origami. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12125875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Molecular simulations using coarse-grained models allow the structure, dynamics and mechanics of DNA origamis to be comprehensively characterized. Here, we focus on the free-energy landscape of a jointed DNA origami that has been designed to exhibit two mechanically stable states and for which a bistable landscape has been inferred from ensembles of structures visualized by electron microscopy. Surprisingly, simulations using the oxDNA model predict that the defect-free origami has a single free-energy minimum. The expected second state is not stable because the hinge joints do not simply allow free angular motion but instead lead to increasing free-energetic penalties as the joint angles relevant to the second state are approached. This raises interesting questions about the cause of this difference between simulations and experiment, such as how assembly defects might affect the ensemble of structures observed experimentally.
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20
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Darcy M, Crocker K, Wang Y, Le JV, Mohammadiroozbahani G, Abdelhamid MAS, Craggs TD, Castro CE, Bundschuh R, Poirier MG. High-Force Application by a Nanoscale DNA Force Spectrometer. ACS NANO 2022; 16:5682-5695. [PMID: 35385658 PMCID: PMC9048690 DOI: 10.1021/acsnano.1c10698] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/28/2022] [Indexed: 05/06/2023]
Abstract
The ability to apply and measure high forces (>10 pN) on the nanometer scale is critical to the development of nanomedicine, molecular robotics, and the understanding of biological processes such as chromatin condensation, membrane deformation, and viral packaging. Established force spectroscopy techniques including optical traps, magnetic tweezers, and atomic force microscopy rely on micron-sized or larger handles to apply forces, limiting their applications within constrained geometries including cellular environments and nanofluidic devices. A promising alternative to these approaches is DNA-based molecular calipers. However, this approach is currently limited to forces on the scale of a few piconewtons. To study the force application capabilities of DNA devices, we implemented DNA origami nanocalipers with tunable mechanical properties in a geometry that allows application of force to rupture a DNA duplex. We integrated static and dynamic single-molecule characterization methods and statistical mechanical modeling to quantify the device properties including force output and dynamic range. We found that the thermally driven dynamics of the device are capable of applying forces of at least 20 piconewtons with a nanometer-scale dynamic range. These characteristics could eventually be used to study other biomolecular processes such as protein unfolding or to control high-affinity interactions in nanomechanical devices or molecular robots.
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Affiliation(s)
- Michael Darcy
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kyle Crocker
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yuchen Wang
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jenny V. Le
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Golbarg Mohammadiroozbahani
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | | | - Timothy D. Craggs
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K.
| | - Carlos E. Castro
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ralf Bundschuh
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael G. Poirier
- Department
of Physics, Department of Mechanical and Aerospace Engineering, Biophysics Graduate
Program, Department of Chemistry and Biochemistry, and Division of Hematology, Department
of Internal Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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21
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Molecular sensors for detection of tumor-stroma crosstalk. Adv Cancer Res 2022; 154:47-91. [PMID: 35459472 DOI: 10.1016/bs.acr.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In most solid tumors, malignant cells coexist with non-cancerous host tissue comprised of a variety of extracellular matrix components and cell types, notably fibroblasts, immune cells, and endothelial cells. It is becoming increasingly evident that the non-cancerous host tissue, often referred to as the tumor stroma or the tumor microenvironment, wields tremendous influence in the proliferation, survival, and metastatic ability of cancer cells. The tumor stroma has an active biological role in the transmission of signals, such as growth factors and chemokines that activate oncogenic signaling pathways by autocrine and paracrine mechanisms. Moreover, the constituents of the stroma define the mechanical properties and the physical features of solid tumors, which influence cancer progression and response to therapy. Inspired by the emerging importance of tumor-stroma crosstalk and oncogenic physical forces, numerous biosensors, or advanced imaging and analysis techniques have been developed and applied to investigate complex and challenging questions in cancer research. These techniques facilitate measurements and biological readouts at scales ranging from subcellular to tissue-level with unprecedented level of spatial and temporal precision. Here we examine the application of biosensor technology for studying the complex and dynamic multiscale interactions of the tumor-host system.
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22
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Abstract
Cellular processes and functions can be regulated by mechanical forces. Nanodevices that can measure and manipulate these forces are critical tools in chemical and cellular biology. Synthetic DNA oligonucleotides have been used to develop a wide range of powerful nanodevices due to their programmable nature and precise and predictable self-assembly. In recent years, various types of DNA-based mechanical nanodevices have been engineered for studying molecular-level forces. With the help of these nanodevices, our understanding of cellular responses to physical forces has been significantly advanced. In this article, we have reviewed some recent developments in DNA-based mechanical sensors and regulators for application in the characterization of cellular biomechanics and the manipulation of cellular morphology, motion and other functions. The design principles discussed in this article can be further used to inspire other types of powerful DNA-based mechanical nanodevices.
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Affiliation(s)
- Qian Tian
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Puspam Keshri
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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23
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Zhang X, Pan L, Guo R, Zhang Y, Li F, Li M, Li J, Shi J, Qu F, Zuo X, Mao X. DNA origami nanocalipers for pH sensing at the nanoscale. Chem Commun (Camb) 2022; 58:3673-3676. [PMID: 35225310 DOI: 10.1039/d1cc06701j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A DNA origami nanocaliper is employed as a shape-resolved nanomechanical device, with pH-responsive triplex DNA integrated into the two arms. The shape transition of the nanocaliper results in a subtle difference depending on the local pH that is visible via TEM imaging, demonstrating the potential of these nanocalipers to act as a universal platform for pH sensing at the nanoscale.
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Affiliation(s)
- Xinyue Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Li Pan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ruiyan Guo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Yueyue Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Fan Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Fengli Qu
- College of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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24
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Lin-Shiao E, Pfeifer WG, Shy BR, Saffari Doost M, Chen E, Vykunta VS, Hamilton JR, Stahl EC, Lopez DM, Sandoval Espinoza CR, Deyanov AE, Lew RJ, Poirer MG, Marson A, Castro CE, Doudna JA. CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells. Nucleic Acids Res 2022; 50:1256-1268. [PMID: 35104875 PMCID: PMC8860605 DOI: 10.1093/nar/gkac049] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/13/2022] [Accepted: 01/30/2022] [Indexed: 12/22/2022] Open
Abstract
DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.
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Affiliation(s)
- Enrique Lin-Shiao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - 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
| | - Brian R Shy
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mohammad Saffari Doost
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Evelyn Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vivasvan S Vykunta
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Jennifer R Hamilton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth C Stahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Diana M Lopez
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Cindy R Sandoval Espinoza
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexander E Deyanov
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel J Lew
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Michael G Poirer
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Alexander Marson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley 94720, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone Institutes, University of California, San Francisco, San Francisco, CA, 94158, USA
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25
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Beshay PE, Cortes-Medina MG, Menyhert MM, Song JW. The biophysics of cancer: emerging insights from micro- and nanoscale tools. ADVANCED NANOBIOMED RESEARCH 2022; 2:2100056. [PMID: 35156093 PMCID: PMC8827905 DOI: 10.1002/anbr.202100056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cancer is a complex and dynamic disease that is aberrant both biologically and physically. There is growing appreciation that physical abnormalities with both cancer cells and their microenvironment that span multiple length scales are important drivers for cancer growth and metastasis. The scope of this review is to highlight the key advancements in micro- and nano-scale tools for delineating the cause and consequences of the aberrant physical properties of tumors. We focus our review on three important physical aspects of cancer: 1) solid mechanical properties, 2) fluid mechanical properties, and 3) mechanical alterations to cancer cells. Beyond posing physical barriers to the delivery of cancer therapeutics, these properties are also known to influence numerous biological processes, including cancer cell invasion and migration leading to metastasis, and response and resistance to therapy. We comment on how micro- and nanoscale tools have transformed our fundamental understanding of the physical dynamics of cancer progression and their potential for bridging towards future applications at the interface of oncology and physical sciences.
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Affiliation(s)
- Peter E. Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210
| | | | - Miles M. Menyhert
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210
| | - Jonathan W. Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210,The Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210
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26
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Xu Z, Huang Y, Yin H, Zhu X, Tian Y, Min Q. DNA origami-based protein manipulation systems: From function regulation to biological application. Chembiochem 2021; 23:e202100597. [PMID: 34958167 DOI: 10.1002/cbic.202100597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/18/2021] [Indexed: 11/07/2022]
Abstract
Proteins directly participate in tremendous physiological processes and mediate a variety of cellular functions. However, precise manipulation of proteins with predefined relative position and stoichiometry for understanding protein-protein interactions and guiding cellular behaviors are still challenging. With superior programmability of DNA molecules, DNA origami technology is able to construct arbitrary nanostructures that can accurately control the arrangement of proteins with various functionalities to solve these problems. Herein, starting from the classification of DNA origami nanostructures and the category of assembled proteins, we summarize the existing DNA origami-based protein manipulation systems (PMSs), review the advances on the regulation of their functions, and discuss their applications in cellular behavior modulation and disease therapy. Moreover, the limitations and potential directions of DNA origami-based PMSs are also presented, which may offer guidance for rational construction and ingenious application.
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Affiliation(s)
- Ziqi Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Yide Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Xurong Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
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27
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Wang Y, Le JV, Crocker K, Darcy MA, Halley PD, Zhao D, Andrioff N, Croy C, Poirier MG, Bundschuh R, Castro CE. A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules. Nucleic Acids Res 2021; 49:8987-8999. [PMID: 34358322 PMCID: PMC8421221 DOI: 10.1093/nar/gkab656] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/30/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
Single molecule force spectroscopy is a powerful approach to probe the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. However, common approaches to apply forces to biomolecules require expensive and cumbersome equipment and relatively large probes such as beads or cantilevers, which limits their use for many environments and makes integrating with other methods challenging. Furthermore, existing methods have key limitations such as an inability to apply compressive forces on single molecules. We report a nanoscale DNA force spectrometer (nDFS), which is based on a DNA origami hinge with tunable mechanical and dynamic properties. The angular free energy landscape of the nDFS can be engineered across a wide range through substitution of less than 5% of the strand components. We further incorporate a removable strut that enables reversible toggling of the nDFS between open and closed states to allow for actuated application of tensile and compressive forces. We demonstrate the ability to apply compressive forces by inducing a large bend in a 249bp DNA molecule, and tensile forces by inducing DNA unwrapping of a nucleosome sample. These results establish a versatile tool for force spectroscopy and robust methods for designing nanoscale mechanical devices with tunable force application.
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Affiliation(s)
- Yuchen Wang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jenny V Le
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Michael A Darcy
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick D Halley
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Dengke Zhao
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Nick Andrioff
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Cassie Croy
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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28
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Huang CM, Kucinic A, Johnson JA, Su HJ, Castro CE. Integrated computer-aided engineering and design for DNA assemblies. NATURE MATERIALS 2021; 20:1264-1271. [PMID: 33875848 DOI: 10.1038/s41563-021-00978-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 03/04/2021] [Indexed: 05/15/2023]
Abstract
Recently, DNA has been used to make nanodevices for a myriad of applications across fields including medicine, nanomanufacturing, synthetic biology, biosensing and biophysics. However, current DNA nanodevices rely primarily on geometric design, and it remains challenging to rationally design functional properties such as force-response or actuation behaviour. Here we report an iterative design pipeline for DNA assemblies that integrates computer-aided engineering based on coarse-grained molecular dynamics with a versatile computer-aided design approach that combines top-down automation with bottom-up control over geometry. This intuitive framework allows for rapid construction of large, multicomponent assemblies from three-dimensional models with finer control over the geometrical, mechanical and dynamical properties of the DNA structures in an automated manner. This approach expands the scope of structural complexity and enhances mechanical and dynamic design of DNA assemblies.
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Affiliation(s)
- Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA
| | - Anjelica Kucinic
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Joshua A Johnson
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Hai-Jun Su
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA.
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA.
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA.
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29
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Crocker K, Johnson J, Pfeifer W, Castro C, Bundschuh R. A quantitative model for a nanoscale switch accurately predicts thermal actuation behavior. NANOSCALE 2021; 13:13746-13757. [PMID: 34477649 DOI: 10.1039/d1nr02873a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Manipulation of temperature can be used to actuate DNA origami nano-hinges containing gold nanoparticles. We develop a physical model of this system that uses partition function analysis of the interaction between the nano-hinge and nanoparticle to predict the probability that the nano-hinge is open at a given temperature. The model agrees well with experimental data and predicts experimental conditions that allow the actuation temperature of the nano-hinge to be tuned over a range of temperatures from 30 °C to 45 °C. Additionally, the model identifies microscopic interactions that are important to the macroscopic behavior of the system, revealing surprising features of the system. This combination of physical insight and predictive potential is likely to inform future designs that integrate nanoparticles into dynamic DNA origami structures or use strand binding interactions to control dynamic DNA origami behavior. Furthermore, our modeling approach could be expanded to consider the incorporation, stability, and actuation of other types of functional elements or actuation mechanisms integrated into nucleic acid devices.
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Affiliation(s)
- Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA.
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30
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Beltrán SM, Slepian MJ, Taylor RE. Extending the Capabilities of Molecular Force Sensors via DNA Nanotechnology. Crit Rev Biomed Eng 2021; 48:1-16. [PMID: 32749116 DOI: 10.1615/critrevbiomedeng.2020033450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
At the nanoscale, pushing, pulling, and shearing forces drive biochemical processes in development and remodeling as well as in wound healing and disease progression. Research in the field of mechanobiology investigates not only how these loads affect biochemical signaling pathways but also how signaling pathways respond to local loading by triggering mechanical changes such as regional stiffening of a tissue. This feedback between mechanical and biochemical signaling is increasingly recognized as fundamental in embryonic development, tissue morphogenesis, cell signaling, and disease pathogenesis. Historically, the interdisciplinary field of mechanobiology has been driven by the development of technologies for measuring and manipulating cellular and molecular forces, with each new tool enabling vast new lines of inquiry. In this review, we discuss recent advances in the manufacturing and capabilities of molecular-scale force and strain sensors. We also demonstrate how DNA nanotechnology has been critical to the enhancement of existing techniques and to the development of unique capabilities for future mechanosensor assembly. DNA is a responsive and programmable building material for sensor fabrication. It enables the systematic interrogation of molecular biomechanics with forces at the 1- to 200-pN scale that are needed to elucidate the fundamental means by which cells and proteins transduce mechanical signals.
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Affiliation(s)
- Susana M Beltrán
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Marvin J Slepian
- Department of Medicine and Sarver Heart Center, University of Arizona, Tucson; Department of Biomedical Engineering, University of Arizona, Tucson; Department of Materials Science and Engineering, University of Arizona, Tucson
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
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31
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Kong G, Xiong M, Liu L, Hu L, Meng HM, Ke G, Zhang XB, Tan W. DNA origami-based protein networks: from basic construction to emerging applications. Chem Soc Rev 2021; 50:1846-1873. [PMID: 33306073 DOI: 10.1039/d0cs00255k] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.
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Affiliation(s)
- Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Ling Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Hong-Min Meng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
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32
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DNA Nanodevices as Mechanical Probes of Protein Structure and Function. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA nanotechnology has reported a wide range of structurally tunable scaffolds with precise control over their size, shape and mechanical properties. One promising application of these nanodevices is as probes for protein function or determination of protein structure. In this perspective we cover several recent examples in this field, including determining the effect of ligand spacing and multivalency on cell activation, applying forces at the nanoscale, and helping to solve protein structure by cryo-EM. We also highlight some future directions in the chemistry necessary for integrating proteins with DNA nanoscaffolds, as well as opportunities for computational modeling of hybrid protein-DNA nanomaterials.
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33
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Abstract
DNA origami enables the bottom-up construction of chemically addressable, nanoscale objects with user-defined shapes and tailored functionalities. As such, not only can DNA origami objects be used to improve existing experimental methods in biophysics, but they also open up completely new avenues of exploration. In this review, we discuss basic biophysical concepts that are relevant for prospective DNA origami users. We summarize biochemical strategies for interfacing DNA origami with biomolecules of interest. We describe various applications of DNA origami, emphasizing the added value or new biophysical insights that can be generated: rulers and positioning devices, force measurement and force application devices, alignment supports for structural analysis for biomolecules in cryogenic electron microscopy and nuclear magnetic resonance, probes for manipulating and interacting with lipid membranes, and programmable nanopores. We conclude with some thoughts on so-far little explored opportunities for using DNA origami in more complex environments such as the cell or even organisms.
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Affiliation(s)
- Wouter Engelen
- Physik Department, Technische Universität München, 85748 Garching bei München, Germany;
| | - Hendrik Dietz
- Physik Department, Technische Universität München, 85748 Garching bei München, Germany;
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34
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Xu X, Han D. DNA-Guided Programmable Protein Assemblies for Biomedical Applications. Chempluschem 2021; 86:284-290. [PMID: 33605561 DOI: 10.1002/cplu.202100001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/13/2021] [Indexed: 12/22/2022]
Abstract
While the protein assemblies have been found widely existing and playing significant roles in biological systems, their imitation and re-construction is further boosting more applications in biomedical research, such as enzymatic reaction regulation, sensing, and biomedicine. DNA nanotechnology provides a programmable strategy for the fabrication of nanostructures with unprecedented accuracy on the nanoscale. By linking the DNA nanotechnology with proteins of different functions, the precise construction of DNA-guided protein assemblies can be achieved for various biomedical applications. This minireview summarizes the recent advances in the programmable protein assemblies on DNA nanoplatforms and discusses the outlook of DNA-guided protein assemblies in the biomedical research.
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Affiliation(s)
- Xuemei Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Da Han
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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35
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36
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Feng Y, Hashiya F, Hidaka K, Sugiyama H, Endo M. Direct Observation of Dynamic Interactions between Orientation-Controlled Nucleosomes in a DNA Origami Frame. Chemistry 2020; 26:15282-15289. [PMID: 32830347 DOI: 10.1002/chem.202003071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/30/2020] [Indexed: 11/12/2022]
Abstract
The nucleosome is one of the most fundamental units involved in gene expression and consequent cell development, differentiation, and expression of cell functions. We report here a method to place reconstituted nucleosomes into a DNA origami frame for direct observation using high-speed atomic-force microscopy (HS-AFM). By using this method, multiple nucleosomes can be incorporated into a DNA origami frame and real-time movement of nucleosomes can be visualized. The arrangement and conformation of nucleosomes and the distance between two nucleosomes can be designed and controlled. In addition, four nucleosomes can be placed in a DNA frame. Multiple nucleosomes were well accessible in each conformation. Dynamic movement of the individual nucleosomes were precisely monitored in the DNA frame, and their assembly and interaction were directly observed. Neither mica surface modification nor chemical fixation of nucleosomes is used in this method, meaning that the DNA frame not only holds nucleosomes, but also retains their natural state. This method offers a promising platform for investigating nucleosome interactions and for studying chromatin structure.
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Affiliation(s)
- Yihong Feng
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Fumitaka Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,present address: Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, 606-8501, Japan
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37
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Chhabra H, Mishra G, Cao Y, Prešern D, Skoruppa E, Tortora MMC, Doye JPK. Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures. J Chem Theory Comput 2020; 16:7748-7763. [PMID: 33164531 DOI: 10.1021/acs.jctc.0c00661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To study the elastic properties of rodlike DNA nanostructures, we perform long simulations of these structures using the oxDNA coarse-grained model. By analyzing the fluctuations in these trajectories, we obtain estimates of the bend and twist persistence lengths and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a wormlike chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase nonlinearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths that we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origamis have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.
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Affiliation(s)
- Hemani Chhabra
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Garima Mishra
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Yijing Cao
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Domen Prešern
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Maxime M C Tortora
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.,Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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38
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Maffeo C, Aksimentiev A. MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems. Nucleic Acids Res 2020; 48:5135-5146. [PMID: 32232413 PMCID: PMC7229838 DOI: 10.1093/nar/gkaa200] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/06/2020] [Accepted: 03/17/2020] [Indexed: 12/25/2022] Open
Abstract
Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e. wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.
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Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, IL 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, Urbana, IL 61801, USA
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39
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Abstract
Over the past decade, DNA nanotechnology has spawned a broad variety of functional nanostructures tailored toward the enabled state at which applications are coming increasingly in view. One of the branches of these applications is in synthetic biology, where the intrinsic programmability of the DNA nanostructures may pave the way for smart task-specific molecular robotics. In brief, the synthesis of the user-defined artificial DNA nano-objects is based on employing DNA molecules with custom lengths and sequences as building materials that predictably assemble together by obeying Watson-Crick base pairing rules. The general workflow of creating DNA nanoshapes is getting more and more straightforward, and some objects can be designed automatically from the top down. The versatile DNA nano-objects can serve as synthetic tools at the interface with biology, for example, in therapeutics and diagnostics as dynamic logic-gated nanopills, light-, pH-, and thermally driven devices. Such diverse apparatuses can also serve as optical polarizers, sensors and capsules, autonomous cargo-sorting robots, rotary machines, precision measurement tools, as well as electric and magnetic-field directed robotic arms. In this review, we summarize the recent progress in robotic DNA nanostructures, mechanics, and their various implementations.
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Affiliation(s)
- Sami Nummelin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Boxuan Shen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Petteri Piskunen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Qing Liu
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
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40
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41
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Rosier BJHM, Markvoort AJ, Gumí Audenis B, Roodhuizen JAL, den Hamer A, Brunsveld L, de Greef TFA. Proximity-induced caspase-9 activation on a DNA origami-based synthetic apoptosome. Nat Catal 2020; 3:295-306. [PMID: 32190819 PMCID: PMC7080557 DOI: 10.1038/s41929-019-0403-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Living cells regulate key cellular processes by spatial organisation of catalytically active proteins in higher-order signalling complexes. These act as organising centres to facilitate proximity-induced activation and inhibition of multiple intrinsically weakly associating signalling components, which makes elucidation of the underlying protein-protein interactions challenging. Here we show that DNA origami nanostructures provide a programmable molecular platform for the systematic analysis of signalling proteins by engineering a synthetic DNA origami-based version of the apoptosome, a multi-protein complex that regulates apoptosis by co-localizing multiple caspase-9 monomers. Tethering of both wildtype and inactive caspase-9 variants to a DNA origami platform demonstrates that enzymatic activity is induced by proximity-driven dimerization with half-of-sites reactivity, and additionally, reveals a multivalent activity enhancement in oligomers of three and four enzymes. Our results offer fundamental insights in caspase-9 activity regulation and demonstrate that DNA origami-based protein assembly platforms have the potential to inform the function of other multi-enzyme complexes involved in inflammation, innate immunity and cell death.
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Affiliation(s)
- Bas J H M Rosier
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Albert J Markvoort
- Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands
| | - Berta Gumí Audenis
- Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Laboratory of Self-Organising Soft Matter and Laboratory of Macromolecular and Organic Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, The Netherlands
| | - Job A L Roodhuizen
- Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands
| | - Anniek den Hamer
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.,Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, The Netherlands.,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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42
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Ensembles of Breathing Nucleosomes: A Computational Study. Biophys J 2019; 118:2297-2308. [PMID: 31882248 DOI: 10.1016/j.bpj.2019.11.3395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/13/2022] Open
Abstract
About three-fourths of the human DNA molecules are wrapped into nucleosomes, protein spools with DNA. Nucleosomes are highly dynamic, transiently exposing their DNA through spontaneous unspooling. Recent experiments allowed to observe the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matching between the solvent and the protein core. In this study, we calculate such an ensemble through a Monte Carlo simulation of a coarse-grained nucleosome model with sequence-dependent DNA mechanics. Our analysis gives detailed insights into the sequence dependence of nucleosome breathing observed in the experiment and allows us to determine the adsorption energy of the DNA bound to the protein core as a function of the ionic strength. Moreover, we predict the breathing behavior of other potentially interesting sequences and compare the findings to earlier related experiments.
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43
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Johnson JA, Dehankar A, Winter JO, Castro CE. Reciprocal Control of Hierarchical DNA Origami-Nanoparticle Assemblies. NANO LETTERS 2019; 19:8469-8475. [PMID: 31664841 DOI: 10.1021/acs.nanolett.9b02786] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA origami mechanisms offer promising tools for precision nanomanipulation of molecules or nanomaterials. Recent advances have extended the function of individual DNA origami devices to material scales via hierarchical assemblies. However, achieving rapid and precise control of large conformational changes in hierarchical assemblies remains a critical challenge. Here, we demonstrate a method for controlling DNA origami-nanoparticle assemblies through a multiscale approach, in which nanoparticles impart control on the conformation of individual DNA origami mechanisms, whereas DNA origami assemblies control the conformation of nanoparticle arrays. Specifically, we show that the angular distributions of DNA origami hinge mechanisms are tunable as a function of nanoparticle size and distance from the hinge vertex. We selectively adjust the affinity of nanoparticle binding sites, resulting in hinge actuation via DNA melting without releasing the nanoparticle, thereby enabling rapid and reversible temperature-based actuation. Finally, we demonstrate this rapid actuation in DNA origami-nanoparticle arrays of length scales extending over a micron. These results provide guiding principles toward the design of dynamic, DNA-origami hierarchical materials capable of storing and releasing mechanical energy.
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44
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Molecular scaffolds: when DNA becomes the hardware for single-molecule investigations. Curr Opin Chem Biol 2019; 53:192-203. [DOI: 10.1016/j.cbpa.2019.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/21/2019] [Accepted: 09/24/2019] [Indexed: 01/14/2023]
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45
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Zhao D, Le JV, Darcy MA, Crocker K, Poirier MG, Castro C, Bundschuh R. Quantitative Modeling of Nucleosome Unwrapping from Both Ends. Biophys J 2019; 117:2204-2216. [PMID: 31732143 DOI: 10.1016/j.bpj.2019.09.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/05/2019] [Accepted: 09/27/2019] [Indexed: 01/08/2023] Open
Abstract
In eukaryotic cells, DNA is packaged into chromatin where nucleosomes are the basic packaging unit. Important cellular processes including gene expression, DNA replication, and DNA repair require nucleosomal DNA to be unwrapped so that functional proteins can access their target sites, which otherwise are sterically occluded. A key question in this process is what the unwrapped conformations individual nucleosomes adopt within chromatin are. Here, we develop a concurrent nucleosome unwrapping model to address this question. We hypothesize that for a given end-to-end distance of the nucleosomal DNA, the nucleosomal DNA stochastically unwraps from the histone core from both ends independently and that this combination of unwrapping from both sides results in a significant increase in the average distance between the DNA extending from both sides of the nucleosomes. We test our model on recently published experiments using a DNA origami nanocaliper that quantifies nucleosome unwrapping and achieve good agreement between experiment and model prediction. We then investigate the DNA origami caliper distribution when attached to a hexasome (a nucleosome lacking an H2A/H2B dimer). A significant shift in the caliper angle distribution caused by the asymmetric structural features of the hexasome seen experimentally is consistent with the model. Our modeling approach may be more broadly useful to the interpretation of other studies of nucleosome dynamics, chromatin dynamics, and regulatory processes involving nucleosome unwrapping, as well as more generally to optimization of future DNA origami designs to probe mechanical properties of biomolecules.
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Affiliation(s)
- Dengke Zhao
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Jenny V Le
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Michael A Darcy
- Department of Physics, The Ohio State University, Columbus, Ohio
| | - Kyle Crocker
- Department of Physics, The Ohio State University, Columbus, Ohio
| | - Michael G Poirier
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Department of Physics, The Ohio State University, Columbus, Ohio; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Carlos Castro
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio
| | - Ralf Bundschuh
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Department of Physics, The Ohio State University, Columbus, Ohio; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio; Center for RNA Biology, The Ohio State University, Columbus, Ohio.
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46
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Zhou K, Dong J, Zhou Y, Dong J, Wang M, Wang Q. Toward Precise Manipulation of DNA-Protein Hybrid Nanoarchitectures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1804044. [PMID: 30645016 DOI: 10.1002/smll.201804044] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Nucleic acids and proteins are the two primary building materials of living organisms. Over the past decade, artificial DNA-protein hybrid structures have been pursued for a wide range of applications. DNA nanotechnology, in particular, has dramatically expanded nanoscale molecule engineering and contributed to the spatial arrangement of protein components. Strategies for designing site-specific coupling of DNA oligomers to proteins are needed in order to allow for precise control over stoichiometry and position. Efforts have also been focused on coassembly of protein-DNA complexes by engineering their fundamental molecular recognition interactions. This Concept focuses on the precise manipulation of DNA-protein nanoarchitectures. Particular attention is paid to site-selectivity within DNA-protein conjugates, regulation of protein orientation using DNA scaffolds, and coassembly principles upon unique structural motifs. Current challenges and future directions are also discussed in the design and application of DNA-protein nanoarchitectures.
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Affiliation(s)
- Kun Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Jinchen Dong
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Meng Wang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China
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47
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Wamhoff EC, Banal JL, Bricker WP, Shepherd TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming Structured DNA Assemblies to Probe Biophysical Processes. Annu Rev Biophys 2019; 48:395-419. [PMID: 31084582 PMCID: PMC7035826 DOI: 10.1146/annurev-biophys-052118-115259] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Rémi Veneziano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew B Stone
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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48
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Mathur D, Medintz IL. The Growing Development of DNA Nanostructures for Potential Healthcare-Related Applications. Adv Healthc Mater 2019; 8:e1801546. [PMID: 30843670 PMCID: PMC9285959 DOI: 10.1002/adhm.201801546] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/17/2019] [Indexed: 12/21/2022]
Abstract
DNA self-assembly has proven to be a highly versatile tool for engineering complex and dynamic biocompatible nanostructures from the bottom up with a wide range of potential bioapplications currently being pursued. Primary among these is healthcare, with the goal of developing diagnostic, imaging, and drug delivery devices along with combinatorial theranostic devices. The path to understanding a role for DNA nanotechnology in biomedical sciences is being approached carefully and systematically, starting from analyzing the stability and immune-stimulatory properties of DNA nanostructures in physiological conditions, to estimating their accessibility and application inside cellular and model animal systems. Much remains to be uncovered but the field continues to show promising results toward developing useful biomedical devices. This review discusses some aspects of DNA nanotechnology that makes it a favorable ingredient for creating nanoscale research and biomedical devices and looks at experiments undertaken to determine its stability in vivo. This is presented in conjugation with examples of state-of-the-art developments in biomolecular sensing, imaging, and drug delivery. Finally, some of the major challenges that warrant the attention of the scientific community are highlighted, in order to advance the field into clinically relevant applications.
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Affiliation(s)
- Divita Mathur
- Center for Bio/Molecular Science and Engineering U.S. Naval Research Laboratory Code 6910 Washington DC 20375 USA
- College of Science George Mason University Fairfax VA 22030 USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering U.S. Naval Research Laboratory Code 6907 Washington DC 20375 USA
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49
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Directing curli polymerization with DNA origami nucleators. Nat Commun 2019; 10:1395. [PMID: 30918257 PMCID: PMC6437208 DOI: 10.1038/s41467-019-09369-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 03/07/2019] [Indexed: 01/16/2023] Open
Abstract
The physiological or pathological formation of fibrils often relies on molecular-scale nucleators that finely control the kinetics and structural features. However, mechanistic understanding of how protein nucleators mediate fibril formation in cells remains elusive. Here, we develop a CsgB-decorated DNA origami (CB-origami) to mimic protein nucleators in Escherichia coli biofilm that direct curli polymerization. We show that CB-origami directs curli subunit CsgA monomers to form oligomers and then accelerates fibril formation by increasing the proliferation rate of primary pathways. Fibrils grow either out from (departure mode) or towards the nucleators (arrival mode), implying two distinct roles of CsgB: as nucleation sites and as trap sites to capture growing nanofibrils in vicinity. Curli polymerization follows typical stop-and-go dynamics but exhibits a higher instantaneous elongation rate compared with independent fibril growth. This origami nucleator thus provides an in vitro platform for mechanistically probing molecular nucleation and controlling directional fibril polymerization for bionanotechnology.
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50
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Stelson AC, Liu M, Little CAE, Long CJ, Orloff ND, Stephanopoulos N, Booth JC. Label-free detection of conformational changes in switchable DNA nanostructures with microwave microfluidics. Nat Commun 2019; 10:1174. [PMID: 30862776 PMCID: PMC6414672 DOI: 10.1038/s41467-019-09017-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 02/11/2019] [Indexed: 01/23/2023] Open
Abstract
Detection of conformational changes in biomolecular assemblies provides critical information into biological and self-assembly processes. State-of-the-art in situ biomolecular conformation detection techniques rely on fluorescent labels or protein-specific binding agents to signal conformational changes. Here, we present an on-chip, label-free technique to detect conformational changes in a DNA nanomechanical tweezer structure with microwave microfluidics. We measure the electromagnetic properties of suspended DNA tweezer solutions from 50 kHz to 110 GHz and directly detect two distinct conformations of the structures. We develop a physical model to describe the electrical properties of the tweezers, and correlate model parameters to conformational changes. The strongest indicator for conformational changes in DNA tweezers are the ionic conductivity, while shifts in the magnitude of the cooperative water relaxation indicate the addition of fuel strands used to open the tweezer. Microwave microfluidic detection of conformational changes is a generalizable, non-destructive technique, making it attractive for high-throughput measurements. Methods to study conformational changes in biomolecules are limited in resolution and require labelling or other modifications of target analytes. Here the authors present a label-free, microwave microfluidic approach to detect conformational changes of DNA nanostructures based on ionic conductivity.
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Affiliation(s)
- Angela C Stelson
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA
| | - Minghui Liu
- School of Molecular Sciences, Arizona State University, 551 E University Dr, Tempe, AZ, 85281, USA.,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 727 E. Tyler St., Tempe, AZ, 85281, USA
| | - Charles A E Little
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA
| | - Christian J Long
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA
| | - Nathan D Orloff
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, 551 E University Dr, Tempe, AZ, 85281, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 727 E. Tyler St., Tempe, AZ, 85281, USA.
| | - James C Booth
- National Institute of Standards and Technology, Radio Frequency Electronics Group, Boulder CO 325 Broadway St, Boulder, CO, 80305, USA.
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