1
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Kalra S, Donnelly A, Singh N, Matthews D, Del Villar-Guerra R, Bemmer V, Dominguez C, Allcock N, Cherny D, Revyakin A, Rusling DA. Functionalizing DNA Origami by Triplex-Directed Site-Specific Photo-Cross-Linking. J Am Chem Soc 2024; 146:13617-13628. [PMID: 38695163 PMCID: PMC11100008 DOI: 10.1021/jacs.4c03413] [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] [Received: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Here, we present a cross-linking approach to covalently functionalize and stabilize DNA origami structures in a one-pot reaction. Our strategy involves adding nucleotide sequences to adjacent staple strands, so that, upon assembly of the origami structure, the extensions form short hairpin duplexes targetable by psoralen-labeled triplex-forming oligonucleotides bearing other functional groups (pso-TFOs). Subsequent irradiation with UVA light generates psoralen adducts with one or both hairpin staples leading to site-specific attachment of the pso-TFO (and attached group) to the origami with ca. 80% efficiency. Bis-adduct formation between strands in proximal hairpins further tethers the TFO to the structure and generates "superstaples" that improve the structural integrity of the functionalized complex. We show that directing cross-linking to regions outside of the origami core dramatically reduces sensitivity of the structures to thermal denaturation and disassembly by T7 RNA polymerase. We also show that the underlying duplex regions of the origami core are digested by DNase I and thus remain accessible to read-out by DNA-binding proteins. Our strategy is scalable and cost-effective, as it works with existing DNA origami structures, does not require scaffold redesign, and can be achieved with just one psoralen-modified oligonucleotide.
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Affiliation(s)
- Shantam Kalra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Amber Donnelly
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Nishtha Singh
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Daniel Matthews
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Rafael Del Villar-Guerra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Victoria Bemmer
- Centre
for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, U.K.
| | - Cyril Dominguez
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Natalie Allcock
- Core
Biotechnology Services Electron Microscopy Facility, University of Leicester, Leicester LE1 7RH, U.K.
| | - Dmitry Cherny
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Andrey Revyakin
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - David A. Rusling
- School
of Medicine, Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K.
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2
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Pérez-Romero A, Cano-Muñoz M, López-Chamorro C, Conejero-Lara F, Palacios O, Dobado JA, Galindo MA. Selective Formation of Pd-DNA Hybrids Using Tailored Palladium-Mediated Base Pairs: Towards Heteroleptic Pd-DNA Systems. Angew Chem Int Ed Engl 2024; 63:e202400261. [PMID: 38246884 DOI: 10.1002/anie.202400261] [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] [Received: 01/04/2024] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 01/23/2024]
Abstract
The formation of highly organized metal-DNA structures has significant implications in bioinorganic chemistry, molecular biology and material science due to their unique properties and potential applications. In this study, we report on the conversion of single-stranded polydeoxycytidine (dC15 ) into a Pd-DNA supramolecular structure using the [Pd(Aqa)] complex (Aqa=8-amino-4-hydroxyquinoline-2-carboxylic acid) through a self-assembly process. The resulting Pd-DNA assembly closely resembles a natural double helix, with continuous [Pd(Aqa)(C)] (C=cytosine) units serving as palladium-mediated base pairs, forming interbase hydrogen bonds and intrastrand stacking interactions. Notably, the design of the [Pd(Aqa)] complex favours the interaction with cytosine, distinguishing it from our previously reported [Pd(Cheld)] complex (Cheld=chelidamic acid). This finding opens possibilities for creating heteroleptic Pd-DNA hybrids where different complexes specifically bind to nucleobases. We confirmed the Pd-DNA supramolecular structural assembly and selective binding of the complexes using NMR spectroscopy, circular dichroism, mass spectrometry, isothermal titration calorimetry, and DFT calculations.
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Affiliation(s)
- Antonio Pérez-Romero
- Departamento de Química Inorgánica., Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente., Facultad de Ciencias., Universidad de Granada, Avda Fuentenueva s/n, 18071, Granada, Spain
| | - Mario Cano-Muñoz
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente., Facultad de Ciencias., Universidad de Granada, Avda Fuentenueva s/n, 18071, Granada, Spain
| | - Carmen López-Chamorro
- Departamento de Química Inorgánica., Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente., Facultad de Ciencias., Universidad de Granada, Avda Fuentenueva s/n, 18071, Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física, Instituto de Biotecnología y Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente., Facultad de Ciencias., Universidad de Granada, Avda Fuentenueva s/n, 18071, Granada, Spain
| | - Oscar Palacios
- Departament de Química, Facultat de Ciències., Universitat Autònoma de Barcelona., Campus Ballaterra s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - José A Dobado
- Grupo de Modelización y Diseño Molecular, Departamento de Química Orgánica., Facultad de Ciencias., Universidad de Granada., Avda Fuentenueva s/n, 18071, Granada, Spain
| | - Miguel A Galindo
- Departamento de Química Inorgánica., Unidad de Excelencia Química Aplicada a Biomedicina y Medioambiente., Facultad de Ciencias., Universidad de Granada, Avda Fuentenueva s/n, 18071, Granada, Spain
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3
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Simmons CR, Buchberger A, Henry SJW, Novacek A, Fahmi NE, MacCulloch T, Stephanopoulos N, Yan H. Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals. J Am Chem Soc 2023; 145:26075-26085. [PMID: 37987645 PMCID: PMC10789492 DOI: 10.1021/jacs.3c07802] [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: 11/22/2023]
Abstract
The structural analysis of guest molecules in rationally designed and self-assembling DNA crystals has proven an elusive goal since its conception. Oligonucleotide frameworks provide an especially attractive route toward studying DNA-binding molecules by using three-dimensional lattices with defined sequence and structure. In this work, we site-specifically position a suite of minor groove binding molecules, and solve their structures via X-ray crystallography as a proof-of-principle toward scaffolding larger guest species. Two crystal motifs were used to precisely immobilize the molecules DAPI, Hoechst, and netropsin at defined positions in the lattice, allowing us to control occupancy within the crystal. We also solved the structure of a three-ring imidazole-pyrrole-pyrrole polyamide molecule, which sequence-specifically packs in an antiparallel dimeric arrangement within the minor groove. Finally, we engineered a crystal designed to position both netropsin and the polyamide at two distinct locations within the same lattice. Our work elucidates the design principles for the spatial arrangement of functional guests within lattices and opens new potential opportunities for the use of DNA crystals to display and structurally characterize small molecules, peptides, and ultimately proteins of unknown structure.
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Affiliation(s)
- Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
| | - Alex Buchberger
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Skylar J W Henry
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Alexandra Novacek
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Nour Eddine Fahmi
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287,United States
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4
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Simmons CR, Buchberger A, Henry SJW, Novacek A, Fahmi NE, MacCulloch T, Stephanopoulos N, Yan H. Site-specific arrangement and structure determination of minor groove binding molecules in self-assembled three-dimensional DNA crystals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561756. [PMID: 37873139 PMCID: PMC10592734 DOI: 10.1101/2023.10.10.561756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The structural analysis of guest molecules in rationally designed and self-assembling DNA crystals has proven elusive since its conception. Oligonucleotide frameworks provide an especially attractive route towards studying DNA-binding molecules by using three-dimensional lattices with defined sequence and structure. In this work, we site-specifically position a suite of minor groove binding molecules, and solve their structures via x-ray crystallography, as a proof-of-principle towards scaffolding larger guest species. Two crystal motifs were used to precisely immobilize the molecules DAPI, Hoechst, and netropsin at defined positions in the lattice, allowing us to control occupancy within the crystal. We also solved the structure of a three-ring imidazole-pyrrole-pyrrole polyamide molecule, which sequence-specifically packs in an anti-parallel dimeric arrangement within the minor groove. Finally, we engineered a crystal designed to position both netropsin and the polyamide at two distinct locations within the same lattice. Our work elucidates the design principles for the spatial arrangement of functional guests within lattices and opens new potential opportunities for the use of DNA crystals to display and structurally characterize small molecules, peptides, and ultimately proteins of unknown structure.
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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: 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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6
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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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7
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Zhao Y, Chandrasekaran AR, Rusling DA, Woloszyn K, Hao Y, Hernandez C, Vecchioni S, Ohayon YP, Mao C, Seeman NC, Sha R. The Formation and Displacement of Ordered DNA Triplexes in Self-Assembled Three-Dimensional DNA Crystals. J Am Chem Soc 2023; 145:3599-3605. [PMID: 36731121 PMCID: PMC10032566 DOI: 10.1021/jacs.2c12667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Reconfigurable structures engineered through DNA hybridization and self-assembly offer both structural and dynamic applications in nanotechnology. Here, we have demonstrated that strand displacement of triplex-forming oligonucleotides (TFOs) can be translated to a robust macroscopic DNA crystal by coloring the crystals with covalently attached fluorescent dyes. We show that three different types of triplex strand displacement are feasible within the DNA crystals and the bound TFOs can be removed and/or replaced by (a) changing the pH from 5 to 7, (b) the addition of the Watson-Crick complement to a TFO containing a short toehold, and (c) the addition of a longer TFO that uses the duplex edge as a toehold. We have also proved by X-ray diffraction that the structure of the crystals remains as designed in the presence of the TFOs.
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Affiliation(s)
- Yue Zhao
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Arun Richard Chandrasekaran
- The RNA Institute, University of Albany, State University of New York, Albany, New York 12222, United States
| | - David A Rusling
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K
| | - Karol Woloszyn
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yudong Hao
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Carina Hernandez
- 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
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, 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
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, United States
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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: 1] [Impact Index Per Article: 0.5] [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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10
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Xiu D, Zhao S, Li Z, Xu Y, Wang Y, Zhu Z, Zhang M, Snow CD, Belfiore LA, Tang J. Conditionally designed luminescent DNA crystals doped by Ln 3+(Eu 3+/Tb 3+) complexes or fluorescent proteins with smart drug sensing property. J Mater Chem B 2022; 10:6443-6452. [PMID: 35703105 DOI: 10.1039/d2tb00847e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, a designed porous DNA crystal with high intrinsic biocompatibility was used as the scaffold material to load fluorescent guest molecules to detect anti-cancer drugs. It is shown here that the synthesized crystals have the characteristics consistent with the designed large solvent channels, and can therefore accommodate guest molecules such as fluorescent proteins that cannot be accommodated by less porous crystals. Eu(TTA)3phen and Tb(acac)3phen lanthanide complexes were individually noncovalently loaded into the porous crystals, resulting in hybrid luminescent DNA crystals. Emodin, an anti-cancer, anti-tumor, anti-inflammatory drug, was found to quench lanthanide complexes in solution or in crystals. Notably, emodin is the active ingredient of Lianhua Qingwen Capsule, an anti-COVID-19 drug candidate. Therefore, the porous DNA crystals reported here have potential applications as a biocompatible and theranostic delivery biomaterial for functional macromolecules.
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Affiliation(s)
- Dan Xiu
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Sibo Zhao
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Zhenhua Li
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Yanan Xu
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Yao Wang
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Zhijun Zhu
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Min Zhang
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
| | - Christopher D Snow
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523, USA.
| | - Laurence A Belfiore
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China. .,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523, USA.
| | - Jianguo Tang
- Institute of Hybrid Materials, National Center of International Research for Hybrid Materials Technology, National Base of International Science & Technology Cooperation, College of Materials Science and Engineering, Qingdao University, Qingdao, 266071, P. R. China.
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11
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Zheng J, Cheng X, Zhang H, Bai X, Ai R, Shao L, Wang J. Gold Nanorods: The Most Versatile Plasmonic Nanoparticles. Chem Rev 2021; 121:13342-13453. [PMID: 34569789 DOI: 10.1021/acs.chemrev.1c00422] [Citation(s) in RCA: 148] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gold nanorods (NRs), pseudo-one-dimensional rod-shaped nanoparticles (NPs), have become one of the burgeoning materials in the recent years due to their anisotropic shape and adjustable plasmonic properties. With the continuous improvement in synthetic methods, a variety of materials have been attached around Au NRs to achieve unexpected or improved plasmonic properties and explore state-of-the-art technologies. In this review, we comprehensively summarize the latest progress on Au NRs, the most versatile anisotropic plasmonic NPs. We present a representative overview of the advances in the synthetic strategies and outline an extensive catalogue of Au-NR-based heterostructures with tailored architectures and special functionalities. The bottom-up assembly of Au NRs into preprogrammed metastructures is then discussed, as well as the design principles. We also provide a systematic elucidation of the different plasmonic properties associated with the Au-NR-based structures, followed by a discussion of the promising applications of Au NRs in various fields. We finally discuss the future research directions and challenges of Au NRs.
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Affiliation(s)
- Jiapeng Zheng
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Xizhe Cheng
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Han Zhang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Xiaopeng Bai
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Ruoqi Ai
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
| | - Lei Shao
- Beijing Computational Science Research Center, Beijing 100193, China
| | - Jianfang Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China
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12
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13
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Rusling DA. Triplex-forming properties and enzymatic incorporation of a base-modified nucleotide capable of duplex DNA recognition at neutral pH. Nucleic Acids Res 2021; 49:7256-7266. [PMID: 34233006 PMCID: PMC8287925 DOI: 10.1093/nar/gkab572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/31/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
The sequence-specific recognition of duplex DNA by unmodified parallel triplex-forming oligonucleotides is restricted to low pH conditions due to a necessity for cytosine protonation in the third strand. This has severely restricted their use as gene-targeting agents, as well as for the detection and/or functionalisation of synthetic or genomic DNA. Here I report that the nucleobase 6-amino-5-nitropyridin-2-one (Z) finally overcomes this constraint by acting as an uncharged mimic of protonated cytosine. Synthetic TFOs containing the nucleobase enabled stable and selective triplex formation at oligopurine-oligopyrimidine sequences containing multiple isolated or contiguous GC base pairs at neutral pH and above. Moreover, I demonstrate a universal strategy for the enzymatic assembly of Z-containing TFOs using its commercially available deoxyribonucleotide triphosphate. These findings seek to improve not only the recognition properties of TFOs but also the cost and/or expertise associated with their chemical syntheses.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
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14
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Lu S, Shen J, Fan C, Li Q, Yang X. DNA Assembly-Based Stimuli-Responsive Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100328. [PMID: 34258165 PMCID: PMC8261508 DOI: 10.1002/advs.202100328] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.
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Affiliation(s)
- Shasha Lu
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jianlei Shen
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Chunhai Fan
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineDepartment of UrologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qian Li
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Xiurong Yang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
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15
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Chandrasekaran AR, Mathivanan J, Ebrahimi P, Vilcapoma J, Chen AA, Halvorsen K, Sheng J. Hybrid DNA/RNA nanostructures with 2'-5' linkages. NANOSCALE 2020; 12:21583-21590. [PMID: 33089274 PMCID: PMC7644649 DOI: 10.1039/d0nr05846g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Nucleic acid nanostructures with different chemical compositions have shown utility in biological applications as they provide additional assembly parameters and enhanced stability. The naturally occurring 2'-5' linkage in RNA is thought to be a prebiotic analogue and has potential use in antisense therapeutics. Here, we report the first instance of DNA/RNA motifs containing 2'-5' linkages. We synthesized and incorporated RNA strands with 2'-5' linkages into different DNA motifs with varying number of branch points (a duplex, four arm junction, double crossover motif and tensegrity triangle motif). Using experimental characterization and molecular dynamics simulations, we show that hybrid DNA/RNA nanostructures can accommodate interspersed 2'-5' linkages with relatively minor effect on the formation of these structures. Further, the modified nanostructures showed improved resistance to ribonuclease cleavage, indicating their potential use in the construction of robust drug delivery vehicles with prolonged stability in physiological conditions.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- To whom correspondence should be addressed: (ARC), (JS)
| | - Johnsi Mathivanan
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Parisa Ebrahimi
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Alan A. Chen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222
- To whom correspondence should be addressed: (ARC), (JS)
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16
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Chandrasekaran AR, Halvorsen K. Nuclease Degradation Analysis of DNA Nanostructures Using Gel Electrophoresis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2020; 82:e115. [PMID: 32931657 PMCID: PMC8034824 DOI: 10.1002/cpnc.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Custom-built DNA nanostructures are now used in applications such as biosensing, molecular computation, biomolecular analysis, and drug delivery. While the functionality and biocompatibility of DNA makes DNA nanostructures useful in such applications, the field faces a challenge in making biostable DNA nanostructures. Being a natural material, DNA is most suited for biological applications, but is also easily degraded by nucleases. Several methods have been employed to study the nuclease degradation rates and enhancement of nuclease resistance. This protocol describes the use of gel electrophoresis to analyze the extent of nuclease degradation of DNA nanostructures and to report degradation times, kinetics of nuclease digestion, and evaluation of biostability enhancement factors. © 2020 Wiley Periodicals LLC. Basic Protocol: Timed analysis of nuclease degradation of DNA nanostructures Support Protocol: Calculating biostability enhancement factors.
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Affiliation(s)
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York
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17
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Abstract
DNA is now well-established as a nanoscale building material with applications in fields such as biosensing and molecular computation. Molecular processes such as logic gates, nucleic acid circuits, and multiplexed detection have used different readout strategies to measure the output signal. In biosensing, this output can be the diagnosis of a disease biomarker, whereas in molecular computation, the output can be the result of a mathematical operation carried out using DNA. Recent developments have shown that the output of such processes can be displayed graphically as a macroscopic symbol or an alphanumeric character on multiwell plates, microarray chips, gels, lateral flow devices, and DNA origami surfaces. This review discusses the concepts behind such graphical readouts of molecular events, available display platforms, and the advantages and challenges in adapting such methods for practical use. Graphical display systems have the potential to be used in the creation of intelligent computing and sensing devices by which nanoscale binding events are translated into macroscopic visual readouts.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
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18
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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19
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Wang Y, Guo X, Kou B, Zhang L, Xiao SJ. Small Circular DNA Molecules as Triangular Scaffolds for the Growth of 3D Single Crystals. Biomolecules 2020; 10:biom10060814. [PMID: 32466440 PMCID: PMC7355631 DOI: 10.3390/biom10060814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/14/2020] [Accepted: 05/22/2020] [Indexed: 12/30/2022] Open
Abstract
DNA is a very useful molecule for the programmed self-assembly of 3D (three dimension) nanoscale structures. The organised 3D DNA assemblies and crystals enable scientists to conduct studies for many applications such as enzymatic catalysis, biological immune analysis and photoactivity. The first self-assembled 3D DNA single crystal was reported by Seeman and his colleagues, based on a rigid triangle tile with the tile side length of two turns. Till today, successful designs of 3D single crystals by means of programmed self-assembly are countable, and still remain as the most challenging task in DNA nanotechnology, due to the highly constrained conditions for rigid tiles and precise packing. We reported here the use of small circular DNA molecules instead of linear ones as the core triangle scaffold to grow 3D single crystals. Several crystallisation parameters were screened, DNA concentration, incubation time, water-vapour exchange speed, and pH of the sampling buffer. Several kinds of DNA single crystals with different morphologies were achieved in macroscale. The crystals can provide internal porosities for hosting guest molecules of Cy3 and Cy5 labelled triplex-forming oligonucleotides (TFOs). Success of small circular DNA molecules in self-assembling 3D single crystals encourages their use in DNA nanotechnology regarding the advantage of rigidity, stability, and flexibility of circular tiles.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
| | - Xin Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
| | - Bo Kou
- School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing 211167, China;
| | - Ling Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
- Correspondence:
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20
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Liu J, Feng W, Zhang W. A single-molecule study reveals novel rod-like structures formed by a thrombin aptamer repeat sequence. NANOSCALE 2020; 12:4159-4166. [PMID: 32022812 DOI: 10.1039/c9nr09054a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thrombin aptamers (TBAs) have attracted much attention due to their various applications. The structures and properties of long ssDNA chains with multiple TBA repeat sequences are interesting and distinct from those of their monomers. Due to the complexity of the sample system, it is quite difficult to reveal the structure of such a long-chain ssDNA using traditional methods. In this work, we investigated the repeated ssDNA by using single-molecule magnetic tweezers and AFM imaging. To do that we developed the polymerase change-rolling circle amplification (PC-RCA) synthetic method and prepared two-end modified repeated ssDNA. The rod-like G4 structures formed by intramolecular stacking of the repeat sequence were for the first time identified. This novel structure is different from those higher-order quadruplex structures formed by G-tetrads or loop-mediated interactions. It is also quite interesting to find that the increase of the TBA copy number can unitize the diversity of TBA conformation to the best-fit binding structure for thrombin. The methodology developed in this work can be used for studying other repeat sequences in the genome, such as telomeric DNA as well as interactions of ssDNA with the binding molecule.
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Affiliation(s)
- Jianyu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China.
| | - Wei Feng
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China.
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21
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Feldner T, Wolfrum M, Richert C. Turning DNA Binding Motifs into a Material for Flow Cells. Chemistry 2019; 25:15288-15294. [PMID: 31483908 PMCID: PMC6916365 DOI: 10.1002/chem.201903631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/03/2019] [Indexed: 01/18/2023]
Abstract
Nanoscale assemblies of DNA strands are readily designed and can be generated in a wide range of shapes and sizes. Turning them into solids that bind biomolecules reversibly, so that they can act as active material in flow cells, is a challenge. Among the biomolecular ligands, cofactors are of particular interest because they are often the most expensive reagents of biochemical transformations, for which controlled release and recycling are desirable. We have recently described DNA triplex motifs that bind adenine-containing cofactors, such as NAD, FAD and ATP, reversibly with low micromolar affinity. We sought ways to convert the soluble DNA motifs into a macroporous solid for cofactor binding. While assemblies of linear and branched DNA motifs produced hydrogels with undesirable properties, long DNA triplexes treated with protamine gave materials suitable for flow cells. Using exchangeable cells in a flow system, thermally controlled loading and discharge were demonstrated. Employing a flow cell loaded with ATP, bioluminescence was induced through thermal release of the cofactor. The results show that materials generated from functional DNA structures can be successfully employed in macroscopic devices.
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Affiliation(s)
- Tobias Feldner
- Institut für Organische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Manpreet Wolfrum
- Institut für Organische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Clemens Richert
- Institut für Organische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
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22
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Ali M, Afshan N, Jiang C, Zheng H, Xiao SJ. 2D DNA lattice arrays assembled from DNA dumbbell tiles using poly(A-T)-rich stems. NANOSCALE 2019; 11:22216-22221. [PMID: 31728476 DOI: 10.1039/c9nr07911d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Poly(A-T)-rich sequences have been applied as stems of DNA dumbbell tiles for construction of single crystalline 2D DNA lattice arrays in slightly acidic solutions. These arrays show much higher stability and better organised crystalline lattice structures than those assembled from DNA dumbbell tiles with randomly sequenced stems in slightly alkaline environments. DNA nanotechnology probably provides a useful platform to study the mechanical properties of DNA duplexes with specific sequences.
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Affiliation(s)
- Mashooq Ali
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, Jiangsu, China.
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23
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Wang T, Shan J, Wang L, Zhang X, Li G. On the kinetics of catalytic hydrogenation over Pd nanoparticles regulated by various nucleosides. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Ji W, Li D, Lai W, Yao X, Alam MF, Zhang W, Pei H, Li L, Chandrasekaran AR. pH-Operated Triplex DNA Device on MoS 2 Nanosheets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5050-5053. [PMID: 30879305 DOI: 10.1021/acs.langmuir.8b04272] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We report a triplex-based DNA device coupled with molybdenum disulfide (MoS2) nanosheets for use as a pH-sensing platform. The device transitions from a duplex state at pH 8 to a triplex state at pH 5. The interaction of the device with MoS2 nanosheets in the two states is read out as a fluorescence signal from a pH-insensitive dye attached to the device. We characterized the operation of the DNA device on MoS2 nanosheets, analyzed the pH response, and tested the reversibility of the system. Our strategy can lead to the creation of a suite of biosensors where the sensing element is a triplex DNA device and the signal response is modulated by inorganic nanomaterials.
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Affiliation(s)
- Wei Ji
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Dan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Xiaowei Yao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Md Fazle Alam
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Weijia Zhang
- Institutes of Biomedical Sciences and Zhongshan Hospital , Fudan University , Shanghai 200032 , P. R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering , East China Normal University , 500 Dongchuan Road , Shanghai 200241 , P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany , State University of New York , Albany , New York 12222 , United States
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25
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Kanamori T, Takamura A, Tago N, Masaki Y, Ohkubo A, Sekine M, Seio K. Fluorescence enhancement of oligodeoxynucleotides modified with green fluorescent protein chromophore mimics upon triplex formation. Org Biomol Chem 2018; 15:1190-1197. [PMID: 28084483 DOI: 10.1039/c6ob01278g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Green fluorescent protein (GFP)-based molecular-rotor chromophores were attached to the 5-positions of deoxyuridines, and subsequently, incorporated into the middle positions of oligodeoxynucleotides. These oligonucleotides were designed to form triplex DNA in order to encapsulate the GFP chromophores, mimicking GFP structures. Upon triplex formation, the embedded GFP chromophores exhibited fluorescence enhancement, suggesting the potential application of these fluorescent probes for the detection of nucleic acids.
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Affiliation(s)
- Takashi Kanamori
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Akihiro Takamura
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Nobuhiro Tago
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Yoshiaki Masaki
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Akihiro Ohkubo
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-Cho, Midori-ku, Yokohama 226-8501, Japan.
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26
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Chandrasekaran AR, Rusling DA. Triplex-forming oligonucleotides: a third strand for DNA nanotechnology. Nucleic Acids Res 2018; 46:1021-1037. [PMID: 29228337 PMCID: PMC5814803 DOI: 10.1093/nar/gkx1230] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/21/2017] [Accepted: 11/30/2017] [Indexed: 11/14/2022] Open
Abstract
DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.
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Affiliation(s)
| | - David A Rusling
- Biological Sciences, Institute for Life Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
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27
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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28
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He X, Sha R, Zhuo R, Mi Y, Chaikin PM, Seeman NC. Exponential growth and selection in self-replicating materials from DNA origami rafts. NATURE MATERIALS 2017; 16:993-997. [PMID: 28920942 DOI: 10.1038/nmat4986] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating. At pH 5.3, the replication rate of species I is ∼1.3-1.4 times faster than that of species II. At pH 7.8, the replication rates are reversed. When mixed together in the same vial, the progeny of species I replicate preferentially at pH 7.8; similarly at pH 5.3, the progeny of species II take over the system. This addressable selectivity should be adaptable to the selection and evolution of multi-component self-replicating materials in the nanoscopic-to-microscopic size range.
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Affiliation(s)
- Xiaojin He
- Department of Chemistry, New York University, New York, New York 10003, USA
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
- Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemistry, Tongji University, Shanghai, 100024, China
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Rebecca Zhuo
- Department of Chemistry, New York University, New York, New York 10003, USA
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
| | - Yongli Mi
- Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemistry, Tongji University, Shanghai, 100024, China
| | - Paul M Chaikin
- Center for Soft Matter Research, New York University, New York, New York 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, USA
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29
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Wang X, Sha R, Kristiansen M, Hernandez C, Hao Y, Mao C, Canary JW, Seeman NC. An Organic Semiconductor Organized into 3D DNA Arrays by “Bottom‐up” Rational Design. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Xiao Wang
- Department of Chemistry New York University New York NY 10003 USA
| | - Ruojie Sha
- Department of Chemistry New York University New York NY 10003 USA
| | | | - Carina Hernandez
- Department of Chemistry New York University New York NY 10003 USA
| | - Yudong Hao
- Department of Chemistry New York University New York NY 10003 USA
| | - Chengde Mao
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
| | - James W. Canary
- Department of Chemistry New York University New York NY 10003 USA
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30
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Wang X, Sha R, Kristiansen M, Hernandez C, Hao Y, Mao C, Canary JW, Seeman NC. An Organic Semiconductor Organized into 3D DNA Arrays by “Bottom‐up” Rational Design. Angew Chem Int Ed Engl 2017; 56:6445-6448. [DOI: 10.1002/anie.201700462] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Xiao Wang
- Department of Chemistry New York University New York NY 10003 USA
| | - Ruojie Sha
- Department of Chemistry New York University New York NY 10003 USA
| | | | - Carina Hernandez
- Department of Chemistry New York University New York NY 10003 USA
| | - Yudong Hao
- Department of Chemistry New York University New York NY 10003 USA
| | - Chengde Mao
- Department of Chemistry Purdue University West Lafayette IN 47907 USA
| | - James W. Canary
- Department of Chemistry New York University New York NY 10003 USA
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31
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Valsangkar V, Chandrasekaran AR, Wang R, Haruehanroengra P, Levchenko O, Halvorsen K, Sheng J. Click-based functionalization of a 2'-O-propargyl-modified branched DNA nanostructure. J Mater Chem B 2017; 5:2074-2077. [PMID: 32263680 DOI: 10.1039/c6tb03277j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA has emerged as a versatile building block for programmable self-assembly. DNA-based nanostructures have been widely applied in biosensing, bioimaging, drug delivery, molecular computation and macromolecular scaffolding. A variety of strategies have been developed to functionalize these nanostructures. In this study, we report a facile click-based strategy to incorporate a metal chelating ligand and a fluorescent tag into a three-point-star DNA tile containing 2'-O-propargyl groups. Such a strategy opens up the possibility of functionalizing pre-assembled DNA strands to construct platforms for metal or drug delivery.
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Affiliation(s)
- Vibhav Valsangkar
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, USA.
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32
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Stahl E, Praetorius F, de Oliveira Mann CC, Hopfner KP, Dietz H. Impact of Heterogeneity and Lattice Bond Strength on DNA Triangle Crystal Growth. ACS NANO 2016; 10:9156-9164. [PMID: 27583560 DOI: 10.1021/acsnano.6b04787] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One key goal of DNA nanotechnology is the bottom-up construction of macroscopic crystalline materials. Beyond applications in fields such as photonics or plasmonics, DNA-based crystal matrices could possibly facilitate the diffraction-based structural analysis of guest molecules. Seeman and co-workers reported in 2009 the first designed crystal matrices based on a 38 kDa DNA triangle that was composed of seven chains. The crystal lattice was stabilized, unprecedentedly, by Watson-Crick base pairing. However, 3D crystallization of larger designed DNA objects that include more chains such as DNA origami remains an unsolved problem. Larger objects would offer more degrees of freedom and design options with respect to tailoring lattice geometry and for positioning other objects within a crystal lattice. The greater rigidity of multilayer DNA origami could also positively influence the diffractive properties of crystals composed of such particles. Here, we rationally explore the role of heterogeneity and Watson-Crick interaction strengths in crystal growth using 40 variants of the original DNA triangle as model multichain objects. Crystal growth of the triangle was remarkably robust despite massive chemical, geometrical, and thermodynamical sample heterogeneity that we introduced, but the crystal growth sensitively depended on the sequences of base pairs next to the Watson-Crick sticky ends of the triangle. Our results point to weak lattice interactions and high concentrations as decisive factors for achieving productive crystallization, while sample heterogeneity and impurities played a minor role.
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Affiliation(s)
- Evi Stahl
- Physik Department and Institute for Advanced Study, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany
| | - Florian Praetorius
- Physik Department and Institute for Advanced Study, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany
| | - Carina C de Oliveira Mann
- Department of Biochemistry and Gene Center, Ludwig-Maximilians-Universität , Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry and Gene Center, Ludwig-Maximilians-Universität , Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Hendrik Dietz
- Physik Department and Institute for Advanced Study, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany
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33
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34
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Chandrasekaran AR, Wady H, Subramanian HKK. Nucleic Acid Nanostructures for Chemical and Biological Sensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2689-2700. [PMID: 27040036 DOI: 10.1002/smll.201503854] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/23/2016] [Indexed: 06/05/2023]
Abstract
The nanoscale features of DNA have made it a useful molecule for bottom-up construction of nanomaterials, for example, two- and three-dimensional lattices, nanomachines, and nanodevices. One of the emerging applications of such DNA-based nanostructures is in chemical and biological sensing, where they have proven to be cost-effective, sensitive and have shown promise as point-of-care diagnostic tools. DNA is an ideal molecule for sensing not only because of its specificity but also because it is robust and can function under a broad range of biologically relevant temperatures and conditions. DNA nanostructure-based sensors provide biocompatibility and highly specific detection based on the molecular recognition properties of DNA. They can be used for the detection of single nucleotide polymorphism and to sense pH both in solution and in cells. They have also been used to detect clinically relevant tumor biomarkers. In this review, recent advances in DNA-based biosensors for pH, nucleic acids, tumor biomarkers and cancer cell detection are introduced. Some challenges that lie ahead for such biosensors to effectively compete with established technologies are also discussed.
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Affiliation(s)
| | - Heitham Wady
- Upstate Medical University, State University of New York, Syracuse, NY, 13210, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California, Riverside, CA, 92521, USA
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35
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute; University at Albany, State University of New York; 1400 Washington Avenue Albany NY 12222 USA
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36
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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37
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Yamagata Y, Emura T, Hidaka K, Sugiyama H, Endo M. Triple Helix Formation in a Topologically Controlled DNA Nanosystem. Chemistry 2016; 22:5494-8. [PMID: 26938310 DOI: 10.1002/chem.201505030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 12/11/2022]
Abstract
In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace.
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Affiliation(s)
- Yutaro Yamagata
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan. .,Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan.
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38
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Chandrasekaran AR. Programmable DNA scaffolds for spatially-ordered protein assembly. NANOSCALE 2016; 8:4436-4446. [PMID: 26852879 DOI: 10.1039/c5nr08685j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.
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39
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Gong X, Zhou W, Chai Y, Yuan R, Xiang Y. MicroRNA-induced cascaded and catalytic self-assembly of DNA nanostructures for enzyme-free and sensitive fluorescence detection of microRNA from tumor cells. Chem Commun (Camb) 2016; 52:2501-4. [PMID: 26739755 DOI: 10.1039/c5cc08861e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The presence of target microRNA triggers cascaded and catalytic self-assembly of two DNA motifs into DNA nanostructures, which serves as a remarkable signal amplification means for the highly sensitive monitoring of the target microRNA and the detection of low numbers of tumor cells.
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Affiliation(s)
- Xue Gong
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
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40
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Abdallah HO, Ohayon YP, Chandrasekaran AR, Sha R, Fox KR, Brown T, Rusling DA, Mao C, Seeman NC. Stabilisation of self-assembled DNA crystals by triplex-directed photo-cross-linking. Chem Commun (Camb) 2016; 52:8014-7. [DOI: 10.1039/c6cc03695c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cross-linked crystals: triplex-forming oligonucleotides can direct cross-linking reactions within or between tiles of a DNA crystal, improving their thermal stability.
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Affiliation(s)
| | | | | | - Ruojie Sha
- Department of Chemistry
- New York University
- New York
- USA
| | - Keith R. Fox
- Centre for Biological Sciences
- University of Southampton
- Southampton
- UK
| | - Tom Brown
- Department of Chemistry
- University of Oxford
- Chemistry Research Laboratory
- Oxford
- UK
| | - David A. Rusling
- Centre for Biological Sciences
- University of Southampton
- Southampton
- UK
| | - Chengde Mao
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
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41
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Chandrasekaran AR. Designer DNA Architectures: Applications in Nanomedicine. Nanobiomedicine (Rij) 2016; 3:6. [PMID: 29942381 PMCID: PMC5998270 DOI: 10.5772/63228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022] Open
Abstract
DNA has been used as a material for the construction of nanoscale objects. These nanostructures are programmable and allow the conjugation of biomolecular guests to improve their functionality. DNA nanostructures display a wide variety of characteristics, such as cellular permeability, biocompatibility and stability, and responsiveness to external stimuli, making them excellent candidates for applications in nanomedicine.
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42
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Chandrasekaran AR, Zavala J, Halvorsen K. Programmable DNA Nanoswitches for Detection of Nucleic Acid Sequences. ACS Sens 2015. [DOI: 10.1021/acssensors.5b00178] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA
Institute, University
at Albany, State University of New York, Albany, New York 12222, United States
| | - Johnny Zavala
- The RNA
Institute, University
at Albany, State University of New York, Albany, New York 12222, United States
| | - Ken Halvorsen
- The RNA
Institute, University
at Albany, State University of New York, Albany, New York 12222, United States
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43
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Zhao J, Chandrasekaran AR, Li Q, Li X, Sha R, Seeman NC, Mao C. Post‐Assembly Stabilization of Rationally Designed DNA Crystals. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jiemin Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | | | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Xiang Li
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003 (USA)
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003 (USA)
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
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44
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Zhao J, Chandrasekaran AR, Li Q, Li X, Sha R, Seeman NC, Mao C. Post‐Assembly Stabilization of Rationally Designed DNA Crystals. Angew Chem Int Ed Engl 2015; 54:9936-9. [PMID: 26136359 DOI: 10.1002/anie.201503610] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/05/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Jiemin Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | | | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Xiang Li
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003 (USA)
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003 (USA)
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
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45
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DNA-Encoded Tuning of Geometric and Plasmonic Properties of Nanoparticles Growing from Gold Nanorod Seeds. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500838] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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46
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Song T, Tang L, Tan LH, Wang X, Satyavolu NSR, Xing H, Wang Z, Li J, Liang H, Lu Y. DNA-Encoded Tuning of Geometric and Plasmonic Properties of Nanoparticles Growing from Gold Nanorod Seeds. Angew Chem Int Ed Engl 2015; 54:8114-8. [DOI: 10.1002/anie.201500838] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/03/2015] [Indexed: 01/12/2023]
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47
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Affiliation(s)
- Yuhe R. Yang
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design
and Biomimetics, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States
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48
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Abstract
The ability to predictably control the coassembly of multiple nanoscale building blocks, especially those with disparate chemical and physical properties such as biomolecules and inorganic nanoparticles, has far-reaching implications in catalysis, sensing, and photonics, but a generalizable strategy for engineering specific contacts between these particles is an outstanding challenge. This is especially true in the case of proteins, where the types of possible interparticle interactions are numerous, diverse, and complex. Herein, we explore the concept of trading protein-protein interactions for DNA-DNA interactions to direct the assembly of two nucleic-acid-functionalized proteins with distinct surface chemistries into six unique lattices composed of catalytically active proteins, or of a combination of proteins and DNA-modified gold nanoparticles. The programmable nature of DNA-DNA interactions used in this strategy allows us to control the lattice symmetries and unit cell constants, as well as the compositions and habit, of the resulting crystals. This study provides a potentially generalizable strategy for constructing a unique class of materials that take advantage of the diverse morphologies, surface chemistries, and functionalities of proteins for assembling functional crystalline materials.
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49
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Rusling DA, Fox KR. Sequence-specific recognition of DNA nanostructures. Methods 2014; 67:123-33. [PMID: 24583116 DOI: 10.1016/j.ymeth.2014.02.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/04/2014] [Accepted: 02/20/2014] [Indexed: 01/02/2023] Open
Abstract
DNA is the most exploited biopolymer for the programmed self-assembly of objects and devices that exhibit nanoscale-sized features. One of the most useful properties of DNA nanostructures is their ability to be functionalized with additional non-nucleic acid components. The introduction of such a component is often achieved by attaching it to an oligonucleotide that is part of the nanostructure, or hybridizing it to single-stranded overhangs that extend beyond or above the nanostructure surface. However, restrictions in nanostructure design and/or the self-assembly process can limit the suitability of these procedures. An alternative strategy is to couple the component to a DNA recognition agent that is capable of binding to duplex sequences within the nanostructure. This offers the advantage that it requires little, if any, alteration to the nanostructure and can be achieved after structure assembly. In addition, since the molecular recognition of DNA can be controlled by varying pH and ionic conditions, such systems offer tunable properties that are distinct from simple Watson-Crick hybridization. Here, we describe methodology that has been used to exploit and characterize the sequence-specific recognition of DNA nanostructures, with the aim of generating functional assemblies for bionanotechnology and synthetic biology applications.
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Affiliation(s)
- David A Rusling
- Centre for Biological Sciences and Institute for Life Sciences, Life Sciences Building 85, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - Keith R Fox
- Centre for Biological Sciences and Institute for Life Sciences, Life Sciences Building 85, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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