1
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Cai B, Rong X, Sun Y, Liu L, Li Z. Engineered 3D DNA Crystals: A Molecular Design Perspective. SMALL METHODS 2025:e2401455. [PMID: 39777863 DOI: 10.1002/smtd.202401455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 12/24/2024] [Indexed: 01/11/2025]
Abstract
Recent advances in biomolecular self-assembly have transformed material science, enabling the creation of novel materials with unparalleled precision and functionality. Among these innovations, 3D DNA crystals have emerged as a distinctive class of macroscopic materials, engineered through the bottom-up approach by DNA self-assembly. These structures uniquely combine precise molecular ordering with high programmability, establishing their importance in advanced material design. This review delves into the molecular design of engineered 3D DNA crystals, classifying current crystal structures based on "crystal bond orientations" and examining key aspects of in-silico molecular design, self-assembly, and crystal modifications. The functionalization of 3D DNA crystals for applications in crystallization scaffolding, biocatalysis, biosensing, electrical and optical devices, as well as in the emerging fields of DNA computing and data storage are explored. Finally, the ongoing challenges are addressed and future directions to advance the field of engineered 3D DNA crystals are proposed.
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Affiliation(s)
- Baoshuo Cai
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiao Rong
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yifan Sun
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Longfei Liu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06484, USA
- Nanobiology Institute, Yale University, West Haven, CT, 06484, USA
| | - Zhe Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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2
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Orun A, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD. Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals. ACS NANOSCIENCE AU 2024; 4:338-348. [PMID: 39430379 PMCID: PMC11487669 DOI: 10.1021/acsnanoscienceau.4c00013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 10/22/2024]
Abstract
Biomolecular crystals can serve as materials for a plethora of applications including precise guest entrapment. However, as grown, biomolecular crystals are fragile in solutions other than their growth conditions. For crystals to achieve their full potential as hosts for other molecules, crystals can be made stronger with bioconjugation. Building on our previous work using carbodiimide 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC) for chemical ligation, here, we investigate DNA junction architecture through sticky base overhang lengths and the role of scaffold proteins in cross-linking within two classes of biomolecular crystals: cocrystals of DNA-binding proteins and pure DNA crystals. Both crystal classes contain DNA junctions where DNA strands stack up end-to-end. Ligation yields were studied as a function of sticky base overhang length and terminal phosphorylation status. The best ligation performance for both crystal classes was achieved with longer sticky overhangs and terminal 3'phosphates. Notably, EDC chemical ligation was achieved in crystals with pore sizes too small for intracrystal transport of ligase enzyme. Postassembly cross-linking produced dramatic stability improvements for both DNA crystals and cocrystals in water and blood serum. The results presented may help crystals containing DNA achieve broader application utility, including as structural biology scaffolds.
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Affiliation(s)
- Abigail
R. Orun
- Department
of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Caroline K. Slaughter
- Department
of Cell and Molecular Biology, Colorado
State University, Fort Collins, Colorado 80523, United States
| | - Ethan T. Shields
- Department
of Biomedical Engineering, Colorado State
University, Fort Collins, Colorado 80523, United States
| | - Ananya Vajapayajula
- Department
of Chemical and Biological Engineering, Colorado State University, Fort
Collins, Colorado 80523, United States
| | - Sara Jones
- Department
of Chemical and Biological Engineering, Colorado State University, Fort
Collins, Colorado 80523, United States
| | - Rojina Shrestha
- Department
of Cell and Molecular Biology, Colorado
State University, Fort Collins, Colorado 80523, United States
| | - Christopher D. Snow
- Department
of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
- Department
of Cell and Molecular Biology, Colorado
State University, Fort Collins, Colorado 80523, United States
- Department
of Biomedical Engineering, Colorado State
University, Fort Collins, Colorado 80523, United States
- Department
of Chemical and Biological Engineering, Colorado State University, Fort
Collins, Colorado 80523, United States
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3
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Lyu J, Zhu T, Zhou Y, Zhao T, Fei M, Zhong X, He H. Controlling the Crystal Growth of DNA Molecules via Strategic Chemical Modifications. Chemistry 2024; 30:e202400012. [PMID: 38477176 DOI: 10.1002/chem.202400012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Intermolecular interactions are critical to the crystallization of biomolecules, yet the precise control of biomolecular crystal growth based on these interactions remains elusive. To understand the connections between the crystallization kinetics and the strength of intermolecular interactions, herein we have employed DNA triangular crystals and modified ones as a versatile tool to investigate how the strength of intermolecular interaction affects crystal growth. Interestingly, we have found that the 2'-O-methylation at sticky ends of the DNA triangle could strengthen its intermolecular interaction, resulting in the accelerated formation of smaller crystals. Conversely, phosphorothioate modification could weaken the sticky-end cohesion and delay the nucleation, resulting in formation of fewer but larger crystals. In addition, these modification effects were consistently observed in the crystallization of a DNA decamer. In one word, our experimental results demonstrate that the strength of intermolecular interaction directly impacts crystal growth. It suggests that 2'-O-methylation and phosphorothioate modification represents a rational strategy for controlling DNA molecules grow into desired crystals and it also facilitates structural determination.
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Affiliation(s)
- Jiazhen Lyu
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Tingyu Zhu
- School of Stomatology, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Yan Zhou
- School of Pharmacy, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Ting Zhao
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Meiling Fei
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Xiaowu Zhong
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
| | - Hongfei He
- School of Laboratory Medicine, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College & Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, PR China
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4
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Chen J, Dai Z, Lv H, Jin Z, Tang Y, Xie X, Shi J, Wang F, Li Q, Liu X, Fan C. Programming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification. Proc Natl Acad Sci U S A 2024; 121:e2312596121. [PMID: 38437555 PMCID: PMC10945798 DOI: 10.1073/pnas.2312596121] [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: 07/27/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Self-assembled DNA crystals offer a precise chemical platform at the ångström-scale for DNA nanotechnology, holding enormous potential in material separation, catalysis, and DNA data storage. However, accurately controlling the crystallization kinetics of such DNA crystals remains challenging. Herein, we found that atomic-level 5-methylcytosine (5mC) modification can regulate the crystallization kinetics of DNA crystal by tuning the hybridization rates of DNA motifs. We discovered that by manipulating the axial and combination of 5mC modification on the sticky ends of DNA tensegrity triangle motifs, we can obtain a series of DNA crystals with controllable morphological features. Through DNA-PAINT and FRET-labeled DNA strand displacement experiments, we elucidate that atomic-level 5mC modification enhances the affinity constant of DNA hybridization at both the single-molecule and macroscopic scales. This enhancement can be harnessed for kinetic-driven control of the preferential growth direction of DNA crystals. The 5mC modification strategy can overcome the limitations of DNA sequence design imposed by limited nucleobase numbers in various DNA hybridization reactions. This strategy provides a new avenue for the manipulation of DNA crystal structure, valuable for the advancement of DNA and biomacromolecular crystallography.
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Affiliation(s)
- Jielin Chen
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Zheze Dai
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hui Lv
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
- Zhangjiang Laboratory, Shanghai201210, China
| | - Zhongchao Jin
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yuqing Tang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Jiye Shi
- Division of Physical Biology, Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai201800, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
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5
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Kong H, Sun B, Yu F, Wang Q, Xia K, Jiang D. Exploring the Potential of Three-Dimensional DNA Crystals in Nanotechnology: Design, Optimization, and Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302021. [PMID: 37327311 PMCID: PMC10460852 DOI: 10.1002/advs.202302021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/23/2023] [Indexed: 06/18/2023]
Abstract
DNA has been used as a robust material for the building of a variety of nanoscale structures and devices owing to its unique properties. Structural DNA nanotechnology has reported a wide range of applications including computing, photonics, synthetic biology, biosensing, bioimaging, and therapeutic delivery, among others. Nevertheless, the foundational goal of structural DNA nanotechnology is exploiting DNA molecules to build three-dimensional crystals as periodic molecular scaffolds to precisely align, obtain, or collect desired guest molecules. Over the past 30 years, a series of 3D DNA crystals have been rationally designed and developed. This review aims to showcase various 3D DNA crystals, their design, optimization, applications, and the crystallization conditions utilized. Additionally, the history of nucleic acid crystallography and potential future directions for 3D DNA crystals in the era of nanotechnology are discussed.
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Affiliation(s)
- Huating Kong
- Shanghai Synchrotron Radiation FacilityShanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204China
| | - Bo Sun
- Shanghai Synchrotron Radiation FacilityShanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204China
| | - Feng Yu
- Shanghai Synchrotron Radiation FacilityShanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204China
| | - Qisheng Wang
- Shanghai Synchrotron Radiation FacilityShanghai Advanced Research InstituteChinese Academy of SciencesShanghai201204China
| | - Kai Xia
- Shanghai Frontier Innovation Research InstituteShanghai201108China
- Shanghai Stomatological HospitalFudan UniversityShanghai200031China
| | - Dawei Jiang
- Wuhan Union HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430022China
- Hubei Key Laboratory of Molecular ImagingWuhan430022China
- Key Laboratory of Biological Targeted Therapythe Ministry of EducationWuhan430022China
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6
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Orun A, Shields ET, Dmytriw S, Vajapayajula A, Slaughter CK, Snow CD. Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds. ACS NANO 2023; 17:13110-13120. [PMID: 37407546 PMCID: PMC10373652 DOI: 10.1021/acsnano.2c07282] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
High-precision nanomaterials to entrap DNA-binding molecules are sought after for applications such as controlled drug delivery and scaffold-assisted structural biology. Here, we engineered protein-DNA cocrystals to serve as scaffolds for DNA-binding molecules. The designed cocrystals, isoreticular cocrystals, contain DNA-binding protein and cognate DNA blocks where the DNA-DNA junctions stack end-to-end. Furthermore, the crystal symmetry allows topology preserving (isoreticular) expansion of the DNA stack without breaking protein-protein contacts, hence providing larger solvent channels for guest diffusion. Experimentally, the resulting designed isoreticular cocrystal adopted an interpenetrating I222 lattice, a phenomenon previously observed in metal-organic frameworks (MOFs). The interpenetrating lattice crystallized dependably in the same space group despite myriad modifications at the DNA-DNA junctions. Assembly was modular with respect to the DNA inserted for expansion, providing an interchangeable DNA sequence for guest-specified scaffolding. Also, the DNA-DNA junctions were tunable, accommodating varied sticky base overhang lengths and terminal phosphorylation. As a proof of concept, we used the interpenetrating scaffold crystals to separately entrap three distinct guest molecules during crystallization. Isoreticular cocrystal design offers a route to a programmable scaffold for DNA-binding molecules, and the design principles may be applied to existing cocrystals to develop scaffolding materials.
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Affiliation(s)
- Abigail
R. Orun
- Department
of Chemistry, Colorado State University, 1301 Center Ave., Fort Collins, Colorado 80523, United States
| | - Ethan T. Shields
- Department
of Biomedical Engineering, Colorado State
University, 1376 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Sara Dmytriw
- Department
of Biomedical Engineering, Colorado State
University, 1376 Campus Delivery, Fort Collins, Colorado 80523, United States
- Department
of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort
Collins, Colorado 80523, United States
| | - Ananya Vajapayajula
- Department
of Biomedical Engineering, Colorado State
University, 1376 Campus Delivery, Fort Collins, Colorado 80523, United States
- Department
of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort
Collins, Colorado 80523, United States
| | - Caroline K. Slaughter
- Department
of Cell and Molecular Biology, Colorado
State University, Fort Collins, Colorado 80523, United States
| | - Christopher D. Snow
- Department
of Chemistry, Colorado State University, 1301 Center Ave., Fort Collins, Colorado 80523, United States
- Department
of Biomedical Engineering, Colorado State
University, 1376 Campus Delivery, Fort Collins, Colorado 80523, United States
- Department
of Chemical and Biological Engineering, Colorado State University, 1370 Campus Delivery, Fort
Collins, Colorado 80523, United States
- Department
of Cell and Molecular Biology, Colorado
State University, Fort Collins, Colorado 80523, United States
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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: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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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8
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Lu B, Vecchioni S, Ohayon YP, Canary JW, Sha R. The wending rhombus: Self-assembling 3D DNA crystals. Biophys J 2022; 121:4759-4765. [PMID: 36004779 PMCID: PMC9808540 DOI: 10.1016/j.bpj.2022.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
In this perspective, we provide a summary of recent developments in self-assembling three-dimensional (3D) DNA crystals. Starting from the inception of this subfield, we describe the various advancements in structure that have led to an increase in the diversity of macromolecular crystal motifs formed through self-assembly, and we further comment on the future directions of the field, which exploit noncanonical base pairing interactions beyond Watson-Crick. We then survey the current applications of self-assembling 3D DNA crystals in reversibly active nanodevices and materials engineering and provide an outlook on the direction researchers are taking these structures. Finally, we compare 3D DNA crystals with DNA origami and suggest how these distinct subfields might work together to enhance biomolecule structure solution, nanotechnological motifs, and their applications.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York
| | - James W Canary
- Department of Chemistry, New York University, New York, New York.
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York.
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9
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Li R, Zheng M, Madhvacharyula AS, Du Y, Mao C, Choi JH. Mechanical deformation behaviors and structural properties of ligated DNA crystals. Biophys J 2022; 121:4078-4090. [PMID: 36181269 PMCID: PMC9675025 DOI: 10.1016/j.bpj.2022.09.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022] Open
Abstract
DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here, we investigate the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We perform coarse-grained molecular dynamics simulations and confirm the results with nanoindentation experiments using atomic force microscopy. We observe various deformation modes, including untension, linear elasticity, duplex dissociation, and single-stranded component stretch. We find that the mechanical properties of a DNA architecture are correlated with those of its components. However, the structure shows complex behaviors which may not be predicted by components alone and the architectural design must be considered.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana
| | - Mengxi Zheng
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | | | - Yancheng Du
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana.
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