1
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Kou B, Wang Z, Mousavi S, Wang P, Ke Y. Dynamic Gold Nanostructures Based on DNA Self Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308862. [PMID: 38143287 DOI: 10.1002/smll.202308862] [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: 10/04/2023] [Revised: 12/10/2023] [Indexed: 12/26/2023]
Abstract
The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.
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Affiliation(s)
- Bo Kou
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Zhichao Wang
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Shikufa Mousavi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
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2
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Daly ML, Nishi K, Klawa SJ, Hinton KY, Gao Y, Freeman R. Designer peptide-DNA cytoskeletons regulate the function of synthetic cells. Nat Chem 2024:10.1038/s41557-024-01509-w. [PMID: 38654104 DOI: 10.1038/s41557-024-01509-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/15/2024] [Indexed: 04/25/2024]
Abstract
The bottom-up engineering of artificial cells requires a reconfigurable cytoskeleton that can organize at distinct locations and dynamically modulate its structural and mechanical properties. Here, inspired by the vast array of actin-binding proteins and their ability to reversibly crosslink or bundle filaments, we have designed a library of peptide-DNA crosslinkers varying in length, valency and geometry. Peptide filaments conjoint through DNA hybridization give rise to tactoid-shaped bundles with tunable aspect ratios and mechanics. When confined in cell-sized water-in-oil droplets, the DNA crosslinker design guides the localization of cytoskeletal structures at the cortex or within the lumen of the synthetic cells. The tunable spatial arrangement regulates the passive diffusion of payloads within the droplets and complementary DNA handles allow for the reversible recruitment and release of payloads on and off the cytoskeleton. Heat-induced reconfiguration of peptide-DNA architectures triggers shape deformations of droplets, regulated by DNA melting temperatures. Altogether, the modular design of peptide-DNA architectures is a powerful strategy towards the bottom-up assembly of synthetic cells.
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Affiliation(s)
- Margaret L Daly
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kengo Nishi
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kameryn Y Hinton
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuan Gao
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA.
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3
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Lu X, Zhang D, Chen X, Yao C, Li Z. Interfacial Profiling of MicroRNAs at Patterned Nanogaps for an Integrated Microfluidic-SERS Liquid Biopsy. Anal Chem 2023; 95:16049-16053. [PMID: 37781972 DOI: 10.1021/acs.analchem.3c02945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
A versatile microfluidic-SERS barcoding system is developed for sensitive and multiplexed imaging of circulating microRNAs through interfacial probing of encoded nanorod aggregates at diverse patterned nanogaps. The use of a single-layer, vertically oriented nanorod array creates a plasmonic coupling-based electromagnetic field with enormously enhanced Raman outputs. The introduction of the herringbone micromixer with circulated microflow sampling accelerates the hybridization and capture of nanorod aggregates on the plasmonic substrate. The method is able to achieve ideal sensitivities at subfemtomolar levels for four miRNAs, with multiplexed assay capability for an integrated liquid biopsy. The on-chip digital profiling of serum miRNAs in mapping and barcoding formats enable both clear discrimination of untreated cancer patients from the healthy cohort and precise classification of tumor stages, metastatic conditions, and subtypes, with an overall accuracy of 94%. The SERS-based microfluidic barcoding system therefore holds great promise in early cancer screening, diagnosis, and prognosis.
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Affiliation(s)
- Xiaohui Lu
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Dongdong Zhang
- Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin 300071, China
| | - Xiaofeng Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Chanyu Yao
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Zheng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong 518060, China
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4
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Jahnke K, Göpfrich K. Engineering DNA-based cytoskeletons for synthetic cells. Interface Focus 2023; 13:20230028. [PMID: 37577007 PMCID: PMC10415745 DOI: 10.1098/rsfs.2023.0028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/30/2023] [Indexed: 08/15/2023] Open
Abstract
The development and bottom-up assembly of synthetic cells with a functional cytoskeleton sets a major milestone to understand cell mechanics and to develop man-made machines on the nano- and microscale. However, natural cytoskeletal components can be difficult to purify, deliberately engineer and reconstitute within synthetic cells which therefore limits the realization of multifaceted functions of modern cytoskeletons in synthetic cells. Here, we review recent progress in the development of synthetic cytoskeletons made from deoxyribonucleic acid (DNA) as a complementary strategy. In particular, we explore the capabilities and limitations of DNA cytoskeletons to mimic functions of natural cystoskeletons like reversible assembly, cargo transport, force generation, mechanical support and guided polymerization. With recent examples, we showcase the power of rationally designed DNA cytoskeletons for bottom-up assembled synthetic cells as fully engineerable entities. Nevertheless, the realization of dynamic instability, self-replication and genetic encoding as well as contractile force generating motors remains a fruitful challenge for the complete integration of multifunctional DNA-based cytoskeletons into synthetic cells.
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Affiliation(s)
- Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Department of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Center for Molecular Biology (ZMBH), Heidelberg University, Im Neuenheimer Feld 329, 69120 Heidelberg, Germany
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5
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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6
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Peil A, Zhan P, Duan X, Krahne R, Garoli D, M Liz-Marzán L, Liu N. Transformable Plasmonic Helix with Swinging Gold Nanoparticles. Angew Chem Int Ed Engl 2023; 62:e202213992. [PMID: 36423337 DOI: 10.1002/anie.202213992] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 11/25/2022]
Abstract
Control over multiple optical elements that can be dynamically rearranged to yield substantial three-dimensional structural transformations is of great importance to realize reconfigurable plasmonic nanoarchitectures with sensitive and distinct optical feedback. In this work, we demonstrate a transformable plasmonic helix system, in which multiple gold nanoparticles (AuNPs) can be directly transported by DNA swingarms to target positions without undergoing consecutive stepwise movements. The swingarms allow for programmable AuNP translocations in large leaps within plasmonic nanoarchitectures, giving rise to tailored circular dichroism spectra. Our work provides an instructive bottom-up solution to building complex dynamic plasmonic systems, which can exhibit prominent optical responses through cooperative rearrangements of the constituent optical elements with high fidelity and programmability.
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Affiliation(s)
- Andreas Peil
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Pengfei Zhan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Xiaoyang Duan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
| | - Roman Krahne
- Instituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Denis Garoli
- Instituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy
| | - Luis M Liz-Marzán
- CIC BiomaGUNE, Paseo Miramón 182, 20014, Donostia/San Sebastián, Spain.,Biomedical Networking Center, Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Paseo Miramón 182, 20014, Donostia/San Sebastián, Spain.,Ikerbasque, Basque Foundation for Science, 43009, Bilbao, Spain
| | - Na Liu
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.,Max Planck Institute for Solid State Research, Heisenbergstraße 1, 70569, Stuttgart, Germany
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7
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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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8
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Stasi M, Monferrer A, Babl L, Wunnava S, Dirscherl CF, Braun D, Schwille P, Dietz H, Boekhoven J. Regulating DNA-Hybridization Using a Chemically Fueled Reaction Cycle. J Am Chem Soc 2022; 144:21939-21947. [PMID: 36442850 PMCID: PMC9732876 DOI: 10.1021/jacs.2c08463] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular machines, such as ATPases or motor proteins, couple the catalysis of a chemical reaction, most commonly hydrolysis of nucleotide triphosphates, to their conformational change. In essence, they continuously convert a chemical fuel to drive their motion. An outstanding goal of nanotechnology remains to synthesize a nanomachine with similar functions, precision, and speed. The field of DNA nanotechnology has given rise to the engineering precision required for such a device. Simultaneously, the field of systems chemistry developed fast chemical reaction cycles that convert fuel to change the function of molecules. In this work, we thus combined a chemical reaction cycle with the precision of DNA nanotechnology to yield kinetic control over the conformational state of a DNA hairpin. Future work on such systems will result in out-of-equilibrium DNA nanodevices with precise functions.
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Affiliation(s)
- Michele Stasi
- School
of Natural Sciences, Department of Chemistry, Technical University of Munich, Garching85748, Germany
| | - Alba Monferrer
- School
of Natural Sciences, Department of Physics, Technical University of Munich, Am Coulombwall 4, Garching85748, Germany,Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, Garching85748, Germany
| | - Leon Babl
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried82152,Germany
| | - Sreekar Wunnava
- Center
for NanoScience (CeNS) and Systems Biophysics, Ludwig-Maximilian University Munich, Munich80799, Germany
| | | | - Dieter Braun
- Center
for NanoScience (CeNS) and Systems Biophysics, Ludwig-Maximilian University Munich, Munich80799, Germany
| | - Petra Schwille
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried82152,Germany
| | - Hendrik Dietz
- School
of Natural Sciences, Department of Physics, Technical University of Munich, Am Coulombwall 4, Garching85748, Germany,Munich
Institute of Biomedical Engineering, Technical
University of Munich, Boltzmannstraße 11, Garching85748, Germany
| | - Job Boekhoven
- School
of Natural Sciences, Department of Chemistry, Technical University of Munich, Garching85748, Germany,
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9
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Zhang J, Song C, Wang L. DNA-mediated dynamic plasmonic nanostructures: assembly, actuation, optical properties, and biological applications. Phys Chem Chem Phys 2022; 24:23959-23979. [PMID: 36168789 DOI: 10.1039/d2cp02100e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent advances in DNA technology have made it possible to combine with the plasmonics to fabricate reconfigurable dynamic nanodevices with extraordinary property and function. These DNA-mediated plasmonic nanostructures have been investigated for a variety of unique and beneficial physicochemical properties and their dynamic behavior has been controlled by endogenous or exogenous stimuli for a variety of interesting biological applications. In this perspective, the recent efforts to use the DNA nanostructures as molecular linkers for fabricating dynamic plasmonic nanostructures are reviewed. Next, the actuation media for triggering the dynamic behavior of plasmonic nanostructures and the dynamic response in optical features are summarized. Finally, the applications, remaining challenges and perspectives of the DNA-mediated dynamic plasmonic nanostructures are discussed.
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Affiliation(s)
- Jingjing Zhang
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Chunyuan Song
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
| | - Lianhui Wang
- State Key Lab for Organic Electronics & Information Displays (KLOEID), Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, Nanjing, 210023, China.
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10
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Abstract
The cytoskeleton is an essential component of a cell. It controls the cell shape, establishes the internal organization, and performs vital biological functions. Building synthetic cytoskeletons that mimic key features of their natural counterparts delineates a crucial step towards synthetic cells assembled from the bottom up. To this end, DNA nanotechnology represents one of the most promising routes, given the inherent sequence specificity, addressability and programmability of DNA. Here we demonstrate functional DNA-based cytoskeletons operating in microfluidic cell-sized compartments. The synthetic cytoskeletons consist of DNA tiles self-assembled into filament networks. These filaments can be rationally designed and controlled to imitate features of natural cytoskeletons, including reversible assembly and ATP-triggered polymerization, and we also explore their potential for guided vesicle transport in cell-sized confinement. Also, they possess engineerable characteristics, including assembly and disassembly powered by DNA hybridization or aptamer–target interactions and autonomous transport of gold nanoparticles. This work underpins DNA nanotechnology as a key player in building synthetic cells. ![]()
Cytoskeletons are essential components of cells that perform a variety of tasks, and artificial cytoskeletons that perform these functions are required for the bottom-up assembly of synthetic cells. Now, a multi-functional cytoskeleton mimic has been engineered from DNA, consisting of confined DNA filaments that are capable of reversible self-assembly and transport of gold nanoparticles and vesicular cargo.
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11
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Lussier F, Schröter M, Diercks NJ, Jahnke K, Weber C, Frey C, Platzman I, Spatz JP. pH-Triggered Assembly of Endomembrane Multicompartments in Synthetic Cells. ACS Synth Biol 2022; 11:366-382. [PMID: 34889607 PMCID: PMC8787813 DOI: 10.1021/acssynbio.1c00472] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 11/29/2022]
Abstract
By using electrostatic interactions as driving force to assemble vesicles, the droplet-stabilized method was recently applied to reconstitute and encapsulate proteins, or compartments, inside giant unilamellar vesicles (GUVs) to act as minimal synthetic cells. However, the droplet-stabilized approach exhibits low production efficiency associated with the troublesome release of the GUVs from the stabilized droplets, corresponding to a major hurdle for the droplet-stabilized approach. Herein, we report the use of pH as a potential trigger to self-assemble droplet-stabilized GUVs (dsGUVs) by either bulk or droplet-based microfluidics. Moreover, pH enables the generation of compartmentalized GUVs with flexibility and robustness. By co-encapsulating pH-sensitive small unilamellar vesicles (SUVs), negatively charged SUVs, and/or proteins, we show that acidification of the droplets efficiently produces dsGUVs while sequestrating the co-encapsulated material. Most importantly, the pH-mediated assembly of dsGUVs significantly improves the production efficiency of free-standing GUVs (i.e., released from the stabilizing-droplets) compared to its previous implementation.
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Affiliation(s)
- Félix Lussier
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Martin Schröter
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Nicolas J. Diercks
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Kevin Jahnke
- Biophysical
Engineering Group, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, D-69120 Heidelberg, Germany
| | - Cornelia Weber
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Christoph Frey
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Ilia Platzman
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
| | - Joachim P. Spatz
- Department
of Cellular Biophysics, Max Planck Institute
for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
- Institute
for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, D-69120 Heidelberg, Germany
- Max
Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany
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12
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Marini M, Legittimo F, Torre B, Allione M, Limongi T, Scaltrito L, Pirri CF, di Fabrizio E. DNA Studies: Latest Spectroscopic and Structural Approaches. MICROMACHINES 2021; 12:mi12091094. [PMID: 34577737 PMCID: PMC8465297 DOI: 10.3390/mi12091094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/28/2021] [Accepted: 09/04/2021] [Indexed: 11/16/2022]
Abstract
This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.
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Affiliation(s)
- Monica Marini
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
- Correspondence: ; Tel.: +39-011-090-43-22
| | - Francesca Legittimo
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
| | - Bruno Torre
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
| | - Marco Allione
- Istituto Italiano di Tecnologia (IIT), Via Livorno 60, 10144 Torino, Italy;
| | - Tania Limongi
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
| | - Luciano Scaltrito
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
| | - Candido Fabrizio Pirri
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
- Istituto Italiano di Tecnologia (IIT), Via Livorno 60, 10144 Torino, Italy;
| | - Enzo di Fabrizio
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (F.L.); (B.T.); (T.L.); (L.S.); (C.F.P.); (E.d.F.)
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13
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Jahnke K, Ritzmann N, Fichtler J, Nitschke A, Dreher Y, Abele T, Hofhaus G, Platzman I, Schröder RR, Müller DJ, Spatz JP, Göpfrich K. Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells. Nat Commun 2021; 12:3967. [PMID: 34172734 PMCID: PMC8233306 DOI: 10.1038/s41467-021-24103-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
Bottom-up and top-down approaches to synthetic biology each employ distinct methodologies with the common aim to harness living systems. Here, we realize a strategic merger of both approaches to convert light into proton gradients for the actuation of synthetic cellular systems. We genetically engineer E. coli to overexpress the light-driven inward-directed proton pump xenorhodopsin and encapsulate them in artificial cell-sized compartments. Exposing the compartments to light-dark cycles, we reversibly switch the pH by almost one pH unit and employ these pH gradients to trigger the attachment of DNA structures to the compartment periphery. For this purpose, a DNA triplex motif serves as a nanomechanical switch responding to the pH-trigger of the E. coli. When DNA origami plates are modified with the pH-sensitive triplex motif, the proton-pumping E. coli can trigger their attachment to giant unilamellar lipid vesicles (GUVs) upon illumination. A DNA cortex is formed upon DNA origami polymerization, which sculpts and deforms the GUVs. We foresee that the combination of bottom-up and top down approaches is an efficient way to engineer synthetic cells.
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Affiliation(s)
- Kevin Jahnke
- grid.414703.50000 0001 2202 0959Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Noah Ritzmann
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Julius Fichtler
- grid.414703.50000 0001 2202 0959Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Anna Nitschke
- grid.414703.50000 0001 2202 0959Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Yannik Dreher
- grid.414703.50000 0001 2202 0959Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Tobias Abele
- grid.414703.50000 0001 2202 0959Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Götz Hofhaus
- Centre for Advanced Materials, Heidelberg, Germany
| | - Ilia Platzman
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Department of Cellular Biophysics, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Institute for Molecular Systems Engineering (IMSE), Heidelberg University, Heidelberg, Germany
| | | | - Daniel J. Müller
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland
| | - Joachim P. Spatz
- grid.414703.50000 0001 2202 0959Max Planck Institute for Medical Research, Department of Cellular Biophysics, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Institute for Molecular Systems Engineering (IMSE), Heidelberg University, Heidelberg, Germany ,grid.4372.20000 0001 2105 1091Max Planck School Matter to Life, Heidelberg, Germany
| | - Kerstin Göpfrich
- grid.414703.50000 0001 2202 0959Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
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14
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Agarwal S, Klocke MA, Pungchai PE, Franco E. Dynamic self-assembly of compartmentalized DNA nanotubes. Nat Commun 2021; 12:3557. [PMID: 34117248 PMCID: PMC8196065 DOI: 10.1038/s41467-021-23850-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 05/20/2021] [Indexed: 02/05/2023] Open
Abstract
Bottom-up synthetic biology aims to engineer artificial cells capable of responsive behaviors by using a minimal set of molecular components. An important challenge toward this goal is the development of programmable biomaterials that can provide active spatial organization in cell-sized compartments. Here, we demonstrate the dynamic self-assembly of nucleic acid (NA) nanotubes inside water-in-oil droplets. We develop methods to encapsulate and assemble different types of DNA nanotubes from programmable DNA monomers, and demonstrate temporal control of assembly via designed pathways of RNA production and degradation. We examine the dynamic response of encapsulated nanotube assembly and disassembly with the support of statistical analysis of droplet images. Our study provides a toolkit of methods and components to build increasingly complex and functional NA materials to mimic life-like functions in synthetic cells.
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Affiliation(s)
- Siddharth Agarwal
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Melissa A Klocke
- Department of Mechanical Engineering, University of California, Riverside, CA, USA
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA
| | - Passa E Pungchai
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Elisa Franco
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
- Department of Mechanical Engineering, University of California, Riverside, CA, USA.
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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15
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Plesa T, Stan GB, Ouldridge TE, Bae W. Quasi-robust control of biochemical reaction networks via stochastic morphing. J R Soc Interface 2021; 18:20200985. [PMID: 33849334 PMCID: PMC8086924 DOI: 10.1098/rsif.2020.0985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/18/2021] [Indexed: 01/09/2023] Open
Abstract
One of the main objectives of synthetic biology is the development of molecular controllers that can manipulate the dynamics of a given biochemical network that is at most partially known. When integrated into smaller compartments, such as living or synthetic cells, controllers have to be calibrated to factor in the intrinsic noise. In this context, biochemical controllers put forward in the literature have focused on manipulating the mean (first moment) and reducing the variance (second moment) of the target molecular species. However, many critical biochemical processes are realized via higher-order moments, particularly the number and configuration of the probability distribution modes (maxima). To bridge the gap, we put forward the stochastic morpher controller that can, under suitable timescale separations, morph the probability distribution of the target molecular species into a predefined form. The morphing can be performed at a lower-resolution, allowing one to achieve desired multi-modality/multi-stability, and at a higher-resolution, allowing one to achieve arbitrary probability distributions. Properties of the controller, such as robustness and convergence, are rigorously established, and demonstrated on various examples. Also proposed is a blueprint for an experimental implementation of stochastic morpher.
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Affiliation(s)
- Tomislav Plesa
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Guy-Bart Stan
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Thomas E. Ouldridge
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, UK
| | - Wooli Bae
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2AZ, UK
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16
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17
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Ryssy J, Natarajan AK, Wang J, Lehtonen AJ, Nguyen MK, Klajn R, Kuzyk A. Light-Responsive Dynamic DNA-Origami-Based Plasmonic Assemblies. Angew Chem Int Ed Engl 2021; 60:5859-5863. [PMID: 33320988 PMCID: PMC7986157 DOI: 10.1002/anie.202014963] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Indexed: 12/11/2022]
Abstract
DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA‐based systems responsive to light has remained challenging. Herein, we describe the remote manipulation of native (non‐photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine‐based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA‐based devices and nanomaterials.
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Affiliation(s)
- Joonas Ryssy
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland
| | - Ashwin K Natarajan
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland
| | - Jinhua Wang
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Arttu J Lehtonen
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland
| | - Minh-Kha Nguyen
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland.,Faculty of Chemical Engineering, HCMC University of Technology, VNU-HCM, Ho Chi Minh City, 700000, Vietnam
| | - Rafal Klajn
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Anton Kuzyk
- Department of Neuroscience and Biomedical Engineering, School of Science, Aalto University, 00076, Aalto, Finland
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18
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Frey C, Pfeil J, Neckernuss T, Geiger D, Weishaupt K, Platzman I, Marti O, Spatz JP. Label‐free monitoring and manipulation of microfluidic water‐in‐oil droplets. VIEW 2020. [DOI: 10.1002/viw.20200101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Christoph Frey
- Department of Cellular Biophysics Max Planck Institute for Medical Research Heidelberg Germany
- Institute for Molecular Systems Engineering University of Heidelberg Heidelberg Germany
| | - Jonas Pfeil
- Institute of Experimental Physics University of Ulm Ulm Germany
| | | | - Daniel Geiger
- Institute of Experimental Physics University of Ulm Ulm Germany
| | - Klaus Weishaupt
- Department of Cellular Biophysics Max Planck Institute for Medical Research Heidelberg Germany
- Institute for Molecular Systems Engineering University of Heidelberg Heidelberg Germany
| | - Ilia Platzman
- Department of Cellular Biophysics Max Planck Institute for Medical Research Heidelberg Germany
- Institute for Molecular Systems Engineering University of Heidelberg Heidelberg Germany
| | - Othmar Marti
- Institute of Experimental Physics University of Ulm Ulm Germany
| | - Joachim P. Spatz
- Department of Cellular Biophysics Max Planck Institute for Medical Research Heidelberg Germany
- Institute for Molecular Systems Engineering University of Heidelberg Heidelberg Germany
- Max Planck School Matter to Life Heidelberg Germany
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