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Lee J, Kim J, Posnjak G, Ershova A, Hayakawa D, Shih WM, Rogers WB, Ke Y, Liedl T, Lee S. DNA Origami Colloidal Crystals: Opportunities and Challenges. NANO LETTERS 2024. [PMID: 39704025 DOI: 10.1021/acs.nanolett.4c05041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2024]
Abstract
Over the last three decades, colloidal crystallization has provided an easy-to-craft platform for mesoscale engineering of photonic and phononic crystals. Nevertheless, the crystal lattices achieved thus far with commodity colloids are largely limited to symmetric and densely packed structures, restricting their functionalities. To obtain non-close-packed crystals and the resulting complexity of the available structures, directional binding between "patchy" colloids has been pursued. However, the conventional "patchy" colloids have been restricted to micrometer-scale spherical particles or clusters. In this Mini-Review, we argue that the time has come to widen the scope of the colloidal palette and include particles made using DNA origami. By benefiting from its unprecedented ability to control nanoscale shapes and patch placement and incorporate various nanomaterials, DNA origami enables novel engineering of colloidal crystallization, particularly for photonic and phononic applications. This mini-review summarizes the recent progress on using DNA origami for colloidal crystallization, together with its challenges and opportunities.
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Affiliation(s)
- Jaewon Lee
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Jangwon Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Gregor Posnjak
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, München 80539, Bayern, Germany
| | - Anastasia Ershova
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute & Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daichi Hayakawa
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - William M Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Cancer Biology, Dana-Farber Cancer Institute & Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - W Benjamin Rogers
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 30322 Atlanta, United States
| | - Tim Liedl
- Faculty of Physics and CeNS, Ludwig-Maximilian-University Munich, München 80539, Bayern, Germany
| | - Seungwoo Lee
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Integrative Energy Engineering, Department of Biomicrosystem Technology, and KU Photonics Center, Korea University, Seoul 02841, Republic of Korea
- Center for Optoelectronic Materials and Devices, Post-Silicon Semiconductor Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
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Luo X, Dai W, Lin T, Li L, Zhang Y. Role of Deoxyribonucleic Acid Origami for Alleviating Kidney and Liver Injury in Diabetic Sepsis. J Proteome Res 2024; 23:4626-4636. [PMID: 39264033 DOI: 10.1021/acs.jproteome.4c00543] [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] [Indexed: 09/13/2024]
Abstract
Treating diabetic sepsis (DS) can be challenging because of the persistent infection of multiple organs. To address this complicated pathological condition, it is necessary to develop advanced materials and gain a better understanding of their roles. In this study, we developed a two-dimensional planar material with a rectangular deoxyribonucleic acid origami nanostructure (termed Rec-DON). Rec-DON was used to improve liver and renal function in DS mice, as it preferentially accumulates in these organs, and has superior anti-inflammatory activity and the ability to scavenge reactive oxygen species. The role of Rec-DON in the treatment of DS mice was investigated via quantitative proteomics. This study revealed that Rec-DON can regulate key proteins located primarily in the cytoplasm and mitochondrion, involved in protein transport, antigen processing and presentation, and steroid metabolic process, and can also bind to various proteins to restore liver and renal function in DS mice. This study presented Rec-DON as a liver and kidney targeting material and revealed its role in alleviating multiorgan injury in DS.
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Affiliation(s)
- Xinmei Luo
- Health Management Center, General Practice Medical Center and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wenshu Dai
- Health Management Center, General Practice Medical Center and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tianhai Lin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ling Li
- Department of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Yong Zhang
- Health Management Center, General Practice Medical Center and Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu 610041, China
- Department of Nephrology, Kidney Research Institute, West China Hospital of Sichuan University, Chengdu 610041, China
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Hayakawa D, Videbæk TE, Grason GM, Rogers WB. Symmetry-Guided Inverse Design of Self-Assembling Multiscale DNA Origami Tilings. ACS NANO 2024; 18:19169-19178. [PMID: 38981100 PMCID: PMC11271658 DOI: 10.1021/acsnano.4c04515] [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: 04/05/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
Recent advances enable the creation of nanoscale building blocks with complex geometries and interaction specificities for self-assembly. This nearly boundless design space necessitates design principles for defining the mutual interactions between multiple particle species to target a user-specified complex structure or pattern. In this article, we develop a symmetry-based method to generate the interaction matrices that specify the assembly of two-dimensional tilings, which we illustrate using equilateral triangles. By exploiting the allowed 2D symmetries, we develop an algorithmic approach by which any periodic 2D tiling can be generated from an arbitrarily large number of subunit species, notably addressing an unmet challenge of engineering 2D crystals with periodicities that can be arbitrarily larger than the subunit size. To demonstrate the utility of our design approach, we encode specific interactions between triangular subunits synthesized by DNA origami and show that we can guide their self-assembly into tilings with a wide variety of symmetries, using up to 12 unique species of triangles. By conjugating specific triangles with gold nanoparticles, we fabricate gold-nanoparticle supracrystals whose lattice parameter spans up to 300 nm. Finally, to generate economical design rules, we compare the design economy of various tilings. In particular, we show that (1) higher symmetries allow assembly of larger unit cells with fewer subunits and (2) linear supracrystals can be designed more economically using linear primitive unit cells. This work provides a simple algorithmic approach to designing periodic assemblies, aiding in the multiscale assembly of supracrystals of nanostructured "meta-atoms" with engineered plasmonic functions.
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Affiliation(s)
- Daichi Hayakawa
- Martin
A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Thomas E. Videbæk
- Martin
A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Gregory M. Grason
- Department
of Polymer Science and Engineering, University
of Massachusetts, Amherst, Massachusetts 01003, United States
| | - W. Benjamin Rogers
- Martin
A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
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Pinto DEP, Araújo NAM, Šulc P, Russo J. Inverse Design of Self-Folding 3D Shells. PHYSICAL REVIEW LETTERS 2024; 132:118201. [PMID: 38563942 DOI: 10.1103/physrevlett.132.118201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/29/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024]
Abstract
Self-folding is an emerging paradigm for the inverse design of three-dimensional structures. While most efforts have concentrated on the shape of the net, our approach introduces a new design dimension-bond specificity between the edges. We transform this design process into a Boolean satisfiability problem to derive solutions for various target structures. This method significantly enhances the yield of the folding process. Furthermore, by linearly combining independent solutions, we achieve designs for shape-shifting nets wherein the dominant structure evolves with varying external conditions. This approach is demonstrated through coarse-grained simulations on two examples of triangular and square nets capable of folding into multiple target shapes.
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Affiliation(s)
- Diogo E P Pinto
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Nuno A M Araújo
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA
- TU Munich, School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - John Russo
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Ge Y, Jia B, Zhang P, Chen B, Liu L, Shi Y, Huang S, Liu X, Wang R, Xie Y, Li Z, Dong J. TBX15 facilitates malignant progression of glioma by transcriptional activation of TXDNC5. iScience 2024; 27:108950. [PMID: 38327797 PMCID: PMC10847739 DOI: 10.1016/j.isci.2024.108950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/03/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
T-box transcription factor 15 (TBX15) plays important role in various cancers; however, its expression and role in glioma is still unclear. In this study, our findings indicated that TBX15 was increased in gliomas compared to normal brain tissues, and high levels of TBX15 were related to poor survival. Furthermore, TBX15 silencing in glioma cells not only inhibited their proliferation, migration, and invasion in vitro, but also weakened their ability to recruit macrophages and polarize the latter to the M2 subtype. Mechanism study indicated that thioredoxin domain containing 5 (TXNDC5) lies downstream of TBX15. Furthermore, rescue assays verified that the role of TBX15 in glioma cells is dependent on TXNDC5. Moreover, sh-TBX15 loaded into DNA origami nanocarrier suppressed the malignant phenotype of glioma in vitro and in vivo. Taken together, the TBX15/TXNDC5 axis is involved in the genesis and progression of glioma, and is a potential therapeutic target.
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Affiliation(s)
- Yuyuan Ge
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Bin Jia
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Peng Zhang
- Department of Neurosurgery, People’s Hospital of Rugao, Nantong 226500, China
- Department of Neurosurgery, Rugao Clinical College, Jiangsu Health Vocational College, Nantong 226500, China
| | - Baomin Chen
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Liang Liu
- Department of Neurosurgery, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Yan Shi
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Shilu Huang
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Xinglei Liu
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Ran Wang
- Department of Neurosurgery, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Yandong Xie
- Department of Neurosurgery, Affiliated Nanjing Brain Hospital, Nanjing Medical University, Nanjing 210029, China
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Jun Dong
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou 215004, China
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Berg WR, Berengut JF, Bai C, Wimberger L, Lee LK, Rizzuto FJ. Light-Activated Assembly of DNA Origami into Dissipative Fibrils. Angew Chem Int Ed Engl 2023; 62:e202314458. [PMID: 37903739 DOI: 10.1002/anie.202314458] [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: 09/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Hierarchical DNA nanostructures offer programmable functions at scale, but making these structures dynamic, while keeping individual components intact, is challenging. Here we show that the DNA A-motif-protonated, self-complementary poly(adenine) sequences-can propagate DNA origami into one-dimensional, micron-length fibrils. When coupled to a small molecule pH regulator, visible light can activate the hierarchical assembly of our DNA origami into dissipative fibrils. This system is recyclable and does not require DNA modification. By employing a modular and waste-free strategy to assemble and disassemble hierarchical structures built from DNA origami, we offer a facile and accessible route to developing well-defined, dynamic, and large DNA assemblies with temporal control. As a general tool, we envision that coupling the A-motif to cycles of dissipative protonation will allow the transient construction of diverse DNA nanostructures, finding broad applications in dynamic and non-equilibrium nanotechnology.
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Affiliation(s)
- Willi R Berg
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
- Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstraße 34-36, 14195, Berlin, Germany
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Changzhuang Bai
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Laura Wimberger
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Biomedical Sciences, University of New South Wales, Sydney, 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, 2052, Australia
| | - Felix J Rizzuto
- School of Chemistry, University of New South Wales, Sydney, 2052, Australia
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