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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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2
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Lu B, Ohayon YP, Woloszyn K, Yang CF, Yoder JB, Rothschild LJ, Wind SJ, Hendrickson WA, Mao C, Seeman NC, Canary JW, Sha R, Vecchioni S. Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals. J Am Chem Soc 2023; 145:17945-17953. [PMID: 37530628 DOI: 10.1021/jacs.3c05478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Metal-mediated DNA (mmDNA) presents a pathway toward engineering bioinorganic and electronic behavior into DNA devices. Many chemical and biophysical forces drive the programmable chelation of metals between pyrimidine base pairs. Here, we developed a crystallographic method using the three-dimensional (3D) DNA tensegrity triangle motif to capture single- and multi-metal binding modes across granular changes to environmental pH using anomalous scattering. Leveraging this programmable crystal, we determined 28 biomolecular structures to capture mmDNA reactions. We found that silver(I) binds with increasing occupancy in T-T and U-U pairs at elevated pH levels, and we exploited this to capture silver(I) and mercury(II) within the same base pair and to isolate the titration points for homo- and heterometal base pair modes. We additionally determined the structure of a C-C pair with both silver(I) and mercury(II). Finally, we extend our paradigm to capture cadmium(II) in T-T pairs together with mercury(II) at high pH. The precision self-assembly of heterobimetallic DNA chemistry at the sub-nanometer scale will enable atomistic design frameworks for more elaborate mmDNA-based nanodevices and nanotechnologies.
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Affiliation(s)
- Brandon Lu
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, Illinois 60439, United States
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, California 94035, United States
| | - Shalom J Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - James W Canary
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York 10003, United States
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3
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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: 0] [Impact Index Per Article: 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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Vecchioni S, Lu B, Livernois W, Ohayon YP, Yoder JB, Yang CF, Woloszyn K, Bernfeld W, Anantram MP, Canary JW, Hendrickson WA, Rothschild LJ, Mao C, Wind SJ, Seeman NC, Sha R. Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2210938. [PMID: 37268326 DOI: 10.1002/adma.202210938] [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: 11/03/2022] [Revised: 03/06/2023] [Indexed: 06/04/2023]
Abstract
DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag+ and Hg2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.
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Affiliation(s)
- Simon Vecchioni
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Brandon Lu
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Livernois
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Jesse B Yoder
- IMCA-CAT, Argonne National Lab, Argonne, IL, 60439, USA
| | - Chu-Fan Yang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - William Bernfeld
- Department of Chemistry, New York University, New York, NY, 10003, USA
- ASPIRE Program, King School, Stamford, CT, 06905, USA
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, 98195, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Lynn J Rothschild
- NASA Ames Research Center, Planetary Sciences Branch, Moffett Field, CA, 94035, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Math, Columbia University, New York, NY, 10027, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
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5
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Schlick T. Innovations in biophysics: A sampling of ideas celebrating Ned Seeman's legacy. Biophys J 2022; 121:E1-E2. [PMID: 36493782 PMCID: PMC9808539 DOI: 10.1016/j.bpj.2022.11.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Affiliation(s)
- Tamar Schlick
- Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York.
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