1
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Haymaker A, Bardin AA, Gonen T, Martynowycz MW, Nannenga BL. Structure determination of a DNA crystal by MicroED. Structure 2023; 31:1499-1503.e2. [PMID: 37541248 PMCID: PMC10805983 DOI: 10.1016/j.str.2023.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023]
Abstract
Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG)2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG)2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.
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Affiliation(s)
- Alison Haymaker
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Andrey A Bardin
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Brent L Nannenga
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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2
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Yang Q, Chang X, Lee JY, Saji M, Zhang F. DNA T-shaped crossover tiles for 2D tessellation and nanoring reconfiguration. Nat Commun 2023; 14:7675. [PMID: 37996416 PMCID: PMC10667507 DOI: 10.1038/s41467-023-43558-8] [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: 03/02/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
DNA tiles serve as the fundamental building blocks for DNA self-assembled nanostructures such as DNA arrays, origami, and designer crystals. Introducing additional binding arms to DNA crossover tiles holds the promise of unlocking diverse nano-assemblies and potential applications. Here, we present one-, two-, and three-layer T-shaped crossover tiles, by integrating T junction with antiparallel crossover tiles. These tiles carry over the orthogonal binding directions from T junction and retain the rigidity from antiparallel crossover tiles, enabling the assembly of various 2D tessellations. To demonstrate the versatility of the design rules, we create 2-state reconfigurable nanorings from both single-stranded tiles and single-unit assemblies. Moreover, four sets of 4-state reconfiguration systems are constructed, showing effective transformations between ladders and/or rings with pore sizes spanning ~20 nm to ~168 nm. These DNA tiles enrich the design tools in nucleic acid nanotechnology, offering exciting opportunities for the creation of artificial dynamic DNA nanopores.
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Affiliation(s)
- Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Jung Yeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Minu Saji
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA.
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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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4
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Haymaker A, Bardin AA, Gonen T, Martynowycz MW, Nannenga BL. Structure determination of a DNA crystal by MicroED. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538338. [PMID: 37163108 PMCID: PMC10168392 DOI: 10.1101/2023.04.25.538338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG) 2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG) 2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.
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5
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Walczak M, Brady RA, Leathers A, Kotar J, Di Michele L. Influence of hydrophobic moieties on the crystallization of amphiphilic DNA nanostructures. J Chem Phys 2023; 158:084501. [PMID: 36859089 DOI: 10.1063/5.0132484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Three-dimensional crystalline frameworks with nanoscale periodicity are valuable for many emerging technologies, from nanophotonics to nanomedicine. DNA nanotechnology has emerged as a prime route for constructing these materials, with most approaches taking advantage of the structural rigidity and bond directionality programmable for DNA building blocks. Recently, we have introduced an alternative strategy reliant on flexible, amphiphilic DNA junctions dubbed C-stars, whose ability to crystallize is modulated by design parameters, such as nanostructure topology, conformation, rigidity, and size. While C-stars have been shown to form ordered phases with controllable lattice parameter, response to stimuli, and embedded functionalities, much of their vast design space remains unexplored. Here, we investigate the effect of changing the chemical nature of the hydrophobic modifications and the structure of the DNA motifs in the vicinity of these moieties. While similar design variations should strongly alter key properties of the hydrophobic interactions between C-stars, such as strength and valency, only limited differences in self-assembly behavior are observed. This finding suggests that long-range order in C-star crystals is likely imposed by structural features of the building block itself rather than the specific characteristics of the hydrophobic tags. Nonetheless, we find that altering the hydrophobic regions influences the ability of C-star crystals to uptake hydrophobic molecular cargoes, which we exemplify by studying the encapsulation of antibiotic penicillin V. Besides advancing our understanding of the principles governing the self-assembly of amphiphilic DNA building blocks, our observations thus open up new routes to chemically program the materials without affecting their structure.
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Affiliation(s)
- Michal Walczak
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ryan A Brady
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Adrian Leathers
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jurij Kotar
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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6
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Stabilizing DNA–Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA. CRYSTALS 2021. [DOI: 10.3390/cryst12010049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein and DNA co-crystals are most commonly prepared to reveal structural and functional details of DNA-binding proteins when subjected to X-ray diffraction. However, biomolecular crystals are notoriously unstable in solution conditions other than their native growth solution. To achieve greater application utility beyond structural biology, biomolecular crystals should be made robust against harsh conditions. To overcome this challenge, we optimized chemical DNA ligation within a co-crystal. Co-crystals from two distinct DNA-binding proteins underwent DNA ligation with the carbodiimide crosslinking agent 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) under various optimization conditions: 5′ vs. 3′ terminal phosphate, EDC concentration, EDC incubation time, and repeated EDC dose. This crosslinking and DNA ligation route did not destroy crystal diffraction. In fact, the ligation of DNA across the DNA–DNA junctions was clearly revealed via X-ray diffraction structure determination. Furthermore, crystal macrostructure was fortified. Neither the loss of counterions in pure water, nor incubation in blood serum, nor incubation at low pH (2.0 or 4.5) led to apparent crystal degradation. These findings motivate the use of crosslinked biomolecular co-crystals for purposes beyond structural biology, including biomedical applications.
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7
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Construction and Analysis of Double Helix for Triangular Bipyramid and Pentangular Bipyramid. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:5609593. [PMID: 32549907 PMCID: PMC7255045 DOI: 10.1155/2020/5609593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/08/2020] [Accepted: 02/14/2020] [Indexed: 12/11/2022]
Abstract
DNA cages can be joined together to make larger 3D nanostructures on which molecular electronic circuits and tiny containers are built for drug delivery. The mathematical models for these promising nanomaterials play important roles in clarifying their assembly mechanism and understanding their structures. In this study, we propose a mathematical and computer method to construct permissible topological structures with double-helical edges for a triangular bipyramid and pentangular bipyramid. Furthermore, we remove the same topological links, without eliminating the nonrepeated ones for a triangular bipyramid and pentangular bipyramid. By analyzing characteristics of these unique links, some self-assembly and statistic rules are discussed. This study may obtain some new insights into the DNA assembly from the viewpoint of mathematics, promoting the comprehending and design efficiency of DNA polyhedra with required topological structures.
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8
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An J, Choi J, Hwang D, Park J, Pemble CW, Duong THM, Kim KR, Ahn H, Chung HS, Ahn DR. The crystal structure of a natural DNA polymerase complexed with mirror DNA. Chem Commun (Camb) 2020; 56:2186-2189. [PMID: 31971182 DOI: 10.1039/c9cc09351f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The intrinsic l-DNA binding properties of a natural DNA polymerase was discovered. The binding affinity of Dpo4 polymerase for l-DNA was comparable to that for d-DNA. The crystal structure of Dpo4/l-DNA complex revealed a dimer formed by the little finger domain that provides a binding site for l-DNA.
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Affiliation(s)
- Jinsu An
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Jaewoo Choi
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Dohyeon Hwang
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Jihyun Park
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Charles W Pemble
- Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, TX, USA
| | - Thi Hoai Men Duong
- Department of Pharmacy, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi 13024, Republic of Korea
| | - Kyoung-Ran Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea.
| | - Heechul Ahn
- Department of Pharmacy, Dongguk University-Seoul, 32 Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi 13024, Republic of Korea
| | - Hak Suk Chung
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Dae-Ro Ahn
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea. and Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology (UST), Seoul 02792, Republic of Korea
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9
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Ernst P, Plückthun A, Mittl PRE. Structural analysis of biological targets by host:guest crystal lattice engineering. Sci Rep 2019; 9:15199. [PMID: 31645583 PMCID: PMC6811568 DOI: 10.1038/s41598-019-51017-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/23/2019] [Indexed: 11/17/2022] Open
Abstract
To overcome the laborious identification of crystallisation conditions for protein X-ray crystallography, we developed a method where the examined protein is immobilised as a guest molecule in a universal host lattice. We applied crystal engineering to create a generic crystalline host lattice under reproducible, predefined conditions and analysed the structures of target guest molecules of different size, namely two 15-mer peptides and green fluorescent protein (sfGFP). A fusion protein with an N-terminal endo-α-N-acetylgalactosaminidase (EngBF) domain and a C-terminal designed ankyrin repeat protein (DARPin) domain establishes the crystal lattice. The target is recruited into the host lattice, always in the same crystal form, through binding to the DARPin. The target structures can be determined rapidly from difference Fourier maps, whose quality depends on the size of the target and the orientation of the DARPin.
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Affiliation(s)
- Patrick Ernst
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
| | - Peer R E Mittl
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
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10
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Deng T. Configuration of DNA polyhedra of truncated tetrahedron, cuboctahedron, truncated octahedron. J Theor Biol 2019; 472:4-10. [PMID: 30928351 DOI: 10.1016/j.jtbi.2019.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 11/28/2022]
Abstract
The synthesis of DNA polyhedra has attracted more interest because of its wide application prospect, but its formation mechanism from mathematical viewpoint remains poorly understood. This paper presents the assembly process and mechanism of DNA truncated tetrahedron, cuboctahedron and truncated octahedron by the means of mathematics and computer program. Firstly, based on the assumption that the total number of all the crossings within each face of a DNA polyhedron must be an even number, potential types for three DNA polyhedra above are calculated by computer programs; Secondly, the projections of the truncated tetrahedron, the cuboctahedron and the truncated octahedron are plotted based on data fetched by the program; Thirdly, the component number, the odd-crossing edge number and even-crossing edge number for the corresponding polyhedral links are computed by analysis of their projections. This study gets some assembly mechanism on the structure of DNA double helix, promoting the comprehending and design efficiency of DNA polyhedra.
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Affiliation(s)
- Tao Deng
- Key Laboratory of China's Ethnic Languages and Information Technology of Ministry of Education, Northwest Minzu University, Lanzhou 730000, PR China; Key Laboratory of Streaming Data Computing Technologies and Application, Northwest Minzu University, Lanzhou 730030, PR China; School of Mathematics and Computer Science, Northwest Minzu University, Lanzhou 730030, PR China.
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11
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Zhang F, Simmons CR, Gates J, Liu Y, Yan H. Self-Assembly of a 3D DNA Crystal Structure with Rationally Designed Six-Fold Symmetry. Angew Chem Int Ed Engl 2018; 57:12504-12507. [PMID: 30066355 DOI: 10.1002/anie.201807223] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 01/17/2023]
Abstract
Programming self-assembled designer DNA crystals with various lattices and functions is one of the most important goals for nanofabrication using nucleic acids. The resulting porous materials possess atomic precision for several potential applications that rely on crystalline lattices and cavities. Herein, we present a rationally designed and self-assembled 3D DNA crystal lattice with hexagonal symmetry. In our design, two 21-base oligonucleotides are used to form a duplex motif that further assembles into a 3D array. The interactions between the strands are programmed using Watson-Crick base-pairing. The six-fold symmetry, as well as the chirality, is directed by the Holliday junctions formed between the duplex motifs. The rationally designed DNA crystal provides a new avenue that could create self-assembled macromolecular 3D crystalline lattices with atomic precision. In addition, the structure contains a highly organized array of well-defined cavities that are suitable for future applications with immobilized guests.
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Affiliation(s)
- Fei Zhang
- School of Molecular Sciences and Biodesign Institution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85281, USA
| | - Chad R Simmons
- School of Molecular Sciences and Biodesign Institution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85281, USA
| | - Jade Gates
- School of Molecular Sciences and Biodesign Institution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85281, USA
| | - Yan Liu
- School of Molecular Sciences and Biodesign Institution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85281, USA
| | - Hao Yan
- School of Molecular Sciences and Biodesign Institution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ, 85281, USA
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12
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Zhang F, Simmons CR, Gates J, Liu Y, Yan H. Self‐Assembly of a 3D DNA Crystal Structure with Rationally Designed Six‐Fold Symmetry. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fei Zhang
- School of Molecular Sciences and Biodesign Institution Arizona State University 1001 S McAllister Ave Tempe AZ 85281 USA
| | - Chad R. Simmons
- School of Molecular Sciences and Biodesign Institution Arizona State University 1001 S McAllister Ave Tempe AZ 85281 USA
| | - Jade Gates
- School of Molecular Sciences and Biodesign Institution Arizona State University 1001 S McAllister Ave Tempe AZ 85281 USA
| | - Yan Liu
- School of Molecular Sciences and Biodesign Institution Arizona State University 1001 S McAllister Ave Tempe AZ 85281 USA
| | - Hao Yan
- School of Molecular Sciences and Biodesign Institution Arizona State University 1001 S McAllister Ave Tempe AZ 85281 USA
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13
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Liu Y, O'Keeffe M, Treacy MMJ, Yaghi OM. The geometry of periodic knots, polycatenanes and weaving from a chemical perspective: a library for reticular chemistry. Chem Soc Rev 2018; 47:4642-4664. [DOI: 10.1039/c7cs00695k] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The geometry of the most regular polycatenanes and weavings, as an extended family of discrete knots and catenanes, is described in terms of sticks and corners in their optimal embeddings.
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Affiliation(s)
- Yuzhong Liu
- Department of Chemistry
- University of California-Berkeley
- Materials Sciences Division
- Lawrence Berkeley National Laboratory
- Kavli Energy NanoSciences Institute
| | | | | | - Omar M. Yaghi
- Department of Chemistry
- University of California-Berkeley
- Materials Sciences Division
- Lawrence Berkeley National Laboratory
- Kavli Energy NanoSciences Institute
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14
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Huang J, Ding HM, Xu Y, Zeng D, Zhu H, Zang DM, Bao SS, Ma YQ, Zheng LM. Chiral expression from molecular to macroscopic level via pH modulation in terbium coordination polymers. Nat Commun 2017; 8:2131. [PMID: 29242533 PMCID: PMC5730601 DOI: 10.1038/s41467-017-02260-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 11/16/2017] [Indexed: 12/21/2022] Open
Abstract
Chiral expression from the molecular to macroscopic level is common in biological systems, but is difficult to realise for coordination polymers (CPs). The assembly of homochiral CPs in both crystalline and helical forms can provide a bridge for understanding the relationship between the molecular and macroscopic scales of chirality. Herein, we report homochiral helices of [Tb(R- or S-pempH)3]∙2H2O (R - or S -1) (pempH2 = (1-phenylethylamino)methylphosphonic acid) and their crystalline counterparts (R - or S -3), which are formed at different pH of the reaction mixtures under hydrothermal conditions. By combining the experiments and molecular simulations, we propose that the formation of helices of R -1 or S -1 occurs via a hierarchical self-assembly route, which involves twisted packing due to the geometric incompatibility of the different types of chains. The observed chiral transcription from molecules to morphologies is significant for understanding bio-related self-assembly processes on the nano- to macro-scale.
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Affiliation(s)
- Jian Huang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Hong-Ming Ding
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China.,Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou, 215006, China
| | - Yan Xu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Dai Zeng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Hui Zhu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Dong-Mian Zang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Song-Song Bao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China.
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China. .,Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou, 215006, China.
| | - Li-Min Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China.
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15
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Structure of the Holliday junction: applications beyond recombination. Biochem Soc Trans 2017; 45:1149-1158. [PMID: 28842529 DOI: 10.1042/bst20170048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/24/2022]
Abstract
The Holliday junction (HJ) is an essential element in recombination and related mechanisms. The structure of this four-stranded DNA assembly, which is now well-defined alone and in complex with proteins, has led to its applications in areas well outside of molecular recombination, including nanotechnology and biophysics. This minireview explores some interesting recent research on the HJ, as it has been adapted to design regular two- or three-dimensional lattices for crystal engineering, and more complex systems through DNA origami. In addition, the sequence dependence of the structure is discussed in terms how it can be applied to characterize the geometries and energies of various noncovalent interactions, including halogen bonds in oxidatively damaged (halogenated) bases and hydrogen bonds associated with the epigenetic 5-hydroxylmethylcytosine base.
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16
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McNeil R, Paukstelis PJ. Core-Shell and Layer-by-Layer Assembly of 3D DNA Crystals. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1701019. [PMID: 28520255 DOI: 10.1002/adma.201701019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/23/2017] [Indexed: 06/07/2023]
Abstract
A long-standing goal of DNA nanotechnology has been to assemble 3D crystals to be used as molecular scaffolds. The DNA 13-mer, BET66, self-assembles via Crick-Watson and noncanonical base pairs to form crystals. The crystals contain solvent channels that run through them in multiple directions, allowing them to accommodate tethered guest molecules. Here, the first example of biomacromolecular core-shell crystal growth is described, by showing that these crystals can be assembled with two or more discrete layers. This approach leads to structurally identical layers on the DNA level, but with each layer differentiated based on the presence or absence of conjugated guest molecules. The crystal solvent channels also allow layer-specific postcrystallization covalent attachment of guest molecules. Through controlling the guest-molecule identity, concentration, and layer thickness, this study opens up a new method for using DNA to create multifunctional periodic biomaterials with tunable optical, chemical, and physical properties.
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Affiliation(s)
- Ronald McNeil
- Chemistry & Biochemistry Department, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD, 20742, USA
| | - Paul J Paukstelis
- Chemistry & Biochemistry Department, Center for Biomolecular Structure and Organization, Maryland NanoCenter, University of Maryland, College Park, MD, 20742, USA
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Affiliation(s)
- Diana Zhang
- Department of Chemistry & Biochemistry and Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
| | - Paul J. Paukstelis
- Department of Chemistry & Biochemistry and Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742, United States
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