1
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Wang J, Wang DX, Liu B, Jing X, Chen DY, Tang AN, Cui YX, Kong DM. Recent advances in constructing high-order DNA structures. Chem Asian J 2022; 17:e202101315. [PMID: 34989140 DOI: 10.1002/asia.202101315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/04/2022] [Indexed: 11/07/2022]
Abstract
Molecular self-assembly is widely used in the fields of biosensors, molecular devices, efficient catalytic materials, and medical biomaterials. As the carrier of genetic information, DNA is a kind of biomacromolecule composed of deoxyribonucleotide units. DNA nanotechnology extends DNA of its original properties as a molecule that stores and transmits genetic information from its biological environment. By taking advantage of its unique base pairing and inherent biocompatibility to produce structurally-defined supramolecular structures. With the continuously development of DNA technology, the assembly method of DNA nanostructures is not only limited on the basis of DNA hybridization but also other biochemical interactions. In this review, we summarize the latest methods used to construct high-order DNA nanostructures. The problems of DNA nanostructures are discussed and the future directions in this field are provided.
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Affiliation(s)
- Jing Wang
- Nankai University, Department of Chemistry, CHINA
| | | | - Bo Liu
- Nankai University, College of Chemistry, CHINA
| | - Xiao Jing
- Nankai University, College of Chemistry, CHINA
| | - Dan-Ye Chen
- Nankai University, College of Chemistry, CHINA
| | - An-Na Tang
- Nankai University, College of Chemistry, CHINA
| | - Yun-Xi Cui
- Nankai University, College of Chemistry, CHINA
| | - De Ming Kong
- Nankai University, Key Laboratory of Functional Polymer Materials, Weijin road 94, 30071, Tianjin, CHINA
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2
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Keller A, Linko V. Challenges and Perspectives of DNA Nanostructures in Biomedicine. Angew Chem Int Ed Engl 2020; 59:15818-15833. [PMID: 32112664 PMCID: PMC7540699 DOI: 10.1002/anie.201916390] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Indexed: 01/12/2023]
Abstract
DNA nanotechnology holds substantial promise for future biomedical engineering and the development of novel therapies and diagnostic assays. The subnanometer-level addressability of DNA nanostructures allows for their precise and tailored modification with numerous chemical and biological entities, which makes them fit to serve as accurate diagnostic tools and multifunctional carriers for targeted drug delivery. The absolute control over shape, size, and function enables the fabrication of tailored and dynamic devices, such as DNA nanorobots that can execute programmed tasks and react to various external stimuli. Even though several studies have demonstrated the successful operation of various biomedical DNA nanostructures both in vitro and in vivo, major obstacles remain on the path to real-world applications of DNA-based nanomedicine. Here, we summarize the current status of the field and the main implementations of biomedical DNA nanostructures. In particular, we focus on open challenges and untackled issues and discuss possible solutions.
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Affiliation(s)
- Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Strasse 10033098PaderbornGermany
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
- HYBER CentreDepartment of Applied PhysicsAalto UniversityP. O. Box 1510000076AaltoFinland
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3
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Keller A, Linko V. Herausforderungen und Perspektiven von DNA‐Nanostrukturen in der Biomedizin. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Adrian Keller
- Technische und Makromolekulare Chemie Universität Paderborn Warburger Straße 100 33098 Paderborn Deutschland
| | - Veikko Linko
- Biohybrid Materials Department of Bioproducts and Biosystems Aalto University P. O. Box 16100 00076 Aalto Finnland
- HYBER Centre Department of Applied Physics Aalto University P. O. Box 15100 00076 Aalto Finnland
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4
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Li J, Mohammed-Elsabagh M, Paczkowski F, Li Y. Circular Nucleic Acids: Discovery, Functions and Applications. Chembiochem 2020; 21:1547-1566. [PMID: 32176816 DOI: 10.1002/cbic.202000003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/13/2020] [Indexed: 12/14/2022]
Abstract
Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Freeman Paczkowski
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
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5
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Kim Y, Yin P. Enhancing Biocompatible Stability of DNA Nanostructures Using Dendritic Oligonucleotides and Brick Motifs. Angew Chem Int Ed Engl 2019; 59:700-703. [PMID: 31595637 PMCID: PMC6940523 DOI: 10.1002/anie.201911664] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Indexed: 12/26/2022]
Abstract
The use of DNA‐based nanomaterials in biomedical applications is continuing to grow, yet more emphasis is being put on the need for guaranteed structural stability of DNA nanostructures in physiological conditions. Various methods have been developed to stabilize DNA origami against low concentrations of divalent cations and the presence of nucleases. However, existing strategies typically require the complete encapsulation of nanostructures, which makes accessing the encased DNA strands difficult, or chemical modification, such as covalent crosslinking of DNA strands. We present a stabilization method involving the synthesis of DNA brick nanostructures with dendritic oligonucleotides attached to the outer surface. We find that nanostructures assembled from DNA brick motifs remain stable against denaturation without any chemical modifications. Furthermore, densely coating the outer surface of DNA brick nanostructures with dendritic oligonucleotides prevents nuclease digestion.
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Affiliation(s)
- Youngeun Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan circle, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan circle, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
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6
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Kim Y, Yin P. Enhancing Biocompatible Stability of DNA Nanostructures Using Dendritic Oligonucleotides and Brick Motifs. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Youngeun Kim
- Wyss Institute for Biologically Inspired Engineering Harvard University 3 Blackfan circle Boston MA 02115 USA
- Department of Systems Biology Harvard Medical School Boston MA 02115 USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering Harvard University 3 Blackfan circle Boston MA 02115 USA
- Department of Systems Biology Harvard Medical School Boston MA 02115 USA
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7
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Mishra S, Feng Y, Endo M, Sugiyama H. Advances in DNA Origami–Cell Interfaces. Chembiochem 2019; 21:33-44. [DOI: 10.1002/cbic.201900481] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/19/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Shubham Mishra
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
| | - Yihong Feng
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
| | - Masayuki Endo
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceInstitute for Integrated Cell-Material SciencesKyoto University Kitashirakawa-Oiwakecho Kyoto 606-8502 Japan
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8
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Wolfrum M, Schwarz RJ, Schwarz M, Kramer M, Richert C. Stabilizing DNA nanostructures through reversible disulfide crosslinking. NANOSCALE 2019; 11:14921-14928. [PMID: 31360975 DOI: 10.1039/c9nr05143k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Designed DNA nanostructures can be generated in a wide range of sizes and shapes and have the potential to become exciting tools in material sciences, catalysis and medicine. However, DNA nanostructures are thermally labile assemblies of delicate biomacromolecules, and the lability hampers the use in many applications. Disulfide crosslinking is nature's successful approach to stabilize folded proteins against denaturation. It is therefore interesting to ask whether similar approaches can be used to stabilize DNA nanostructures. Here we report the synthesis of two 2'-deoxynucleoside phosphoramidites and two nucleosides linked to controlled pore glass that can be used to prepare oligodeoxynucleotides with protected thiol groups via automated DNA synthesis. Strands with one, two, three or four thiol-bearing nucleotides were prepared. One nicked duplex and three different nanostructures were assembled, the protected thiols were liberated under non-denaturing conditions, and disulfide crosslinking was induced with oxygen. Up to 19 crosslinks were thus placed in folded DNA structures up to 1456 nucleotides in size. The crosslinked structures had increased thermal stability, with UV-melting points 9-50 °C above that of the control structure. Disulfides were converted back to free thiols under reducing conditions. The redox-dependent increase in stability makes crosslinked DNA nanostructures attractive for the construction of responsive materials and biomedical applications.
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Affiliation(s)
- Manpreet Wolfrum
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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9
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Nguyen L, Döblinger M, Liedl T, Heuer‐Jungemann A. Siliciumdioxidwachstum auf DNA‐Origamitemplaten durch Sol‐Gel‐Chemie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Linh Nguyen
- Fakultät für Physik und Center for NanoScience (CeNS)Ludwig-Maximilians-Universität Geschwister-Scholl-Platz 1 80539 München Deutschland
| | - Markus Döblinger
- Fakultät für Chemie und Center for NanoScience (CeNS)Ludwig-Maximilians-Universität Butenandtstraße 5–13 81377 München Deutschland
| | - Tim Liedl
- Fakultät für Physik und Center for NanoScience (CeNS)Ludwig-Maximilians-Universität Geschwister-Scholl-Platz 1 80539 München Deutschland
| | - Amelie Heuer‐Jungemann
- Fakultät für Physik und Center for NanoScience (CeNS)Ludwig-Maximilians-Universität Geschwister-Scholl-Platz 1 80539 München Deutschland
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10
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Nguyen L, Döblinger M, Liedl T, Heuer-Jungemann A. DNA-Origami-Templated Silica Growth by Sol-Gel Chemistry. Angew Chem Int Ed Engl 2018; 58:912-916. [PMID: 30398705 DOI: 10.1002/anie.201811323] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Indexed: 12/15/2022]
Abstract
Improving the stability of DNA origami structures with respect to thermal, chemical, and mechanical demands will be essential to fully explore the real-life applicability of DNA nanotechnology. Here we present a strategy to increase the mechanical resilience of individual DNA origami objects and 3D DNA origami crystals in solution as well as in the dry state. By encapsulating DNA origami in a protective silica shell using sol-gel chemistry, all the objects maintain their structural integrity. This allowed for a detailed structural analysis of the crystals in a dry state, thereby revealing their true 3D shape without lattice deformation and drying-induced collapse. Analysis by energy-dispersive X-ray spectroscopy showed a uniform silica coating whose thickness could be controlled through the precursor concentrations and reaction time. This strategy thus facilitates shape-controlled bottom-up synthesis of designable biomimetic silica structures through transcription from DNA origami.
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Affiliation(s)
- Linh Nguyen
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Markus Döblinger
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Butenandtstrasse 5-13, 81377, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Amelie Heuer-Jungemann
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
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11
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Benn F, Haley NEC, Lucas AE, Silvester E, Helmi S, Schreiber R, Bath J, Turberfield AJ. Chiral DNA Origami Nanotubes with Well-Defined and Addressable Inside and Outside Surfaces. Angew Chem Int Ed Engl 2018; 57:7687-7690. [DOI: 10.1002/anie.201800275] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/16/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Florence Benn
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Natalie E. C. Haley
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Alexandra E. Lucas
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Emma Silvester
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Seham Helmi
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Robert Schreiber
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Jonathan Bath
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Andrew J. Turberfield
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
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12
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Benn F, Haley NEC, Lucas AE, Silvester E, Helmi S, Schreiber R, Bath J, Turberfield AJ. Chiral DNA Origami Nanotubes with Well-Defined and Addressable Inside and Outside Surfaces. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Florence Benn
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Natalie E. C. Haley
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Alexandra E. Lucas
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Emma Silvester
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Seham Helmi
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Robert Schreiber
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Jonathan Bath
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
| | - Andrew J. Turberfield
- University of Oxford; Department of Physics; Clarendon Laboratory; Parks Road Oxford OX1 3PU UK
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13
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Agarwal NP, Matthies M, Gür FN, Osada K, Schmidt TL. Block Copolymer Micellization as a Protection Strategy for DNA Origami. Angew Chem Int Ed Engl 2017; 56:5460-5464. [DOI: 10.1002/anie.201608873] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 01/01/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Nayan P. Agarwal
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Michael Matthies
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Fatih N. Gür
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Kensuke Osada
- Department of Bioengineering; University of Tokyo; Japan
| | - Thorsten L. Schmidt
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
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14
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Agarwal NP, Matthies M, Gür FN, Osada K, Schmidt TL. Block Copolymer Micellization as a Protection Strategy for DNA Origami. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201608873] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Nayan P. Agarwal
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Michael Matthies
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Fatih N. Gür
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
| | - Kensuke Osada
- Department of Bioengineering; University of Tokyo; Japan
| | - Thorsten L. Schmidt
- Center for Advancing Electronics Dresden (cfaed); Technische Universität Dresden; 01062 Dresden Germany
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15
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Taylor AI, Beuron F, Peak-Chew SY, Morris EP, Herdewijn P, Holliger P. Nanostructures from Synthetic Genetic Polymers. Chembiochem 2016; 17:1107-10. [PMID: 26992063 PMCID: PMC4973672 DOI: 10.1002/cbic.201600136] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/22/2022]
Abstract
Nanoscale objects of increasing complexity can be constructed from DNA or RNA. However, the scope of potential applications could be enhanced by expanding beyond the moderate chemical diversity of natural nucleic acids. Here, we explore the construction of nano-objects made entirely from alternative building blocks: synthetic genetic polymers not found in nature, also called xeno nucleic acids (XNAs). Specifically, we describe assembly of 70 kDa tetrahedra elaborated in four different XNA chemistries (2'-fluro-2'-deoxy-ribofuranose nucleic acid (2'F-RNA), 2'-fluoroarabino nucleic acids (FANA), hexitol nucleic acids (HNA), and cyclohexene nucleic acids (CeNA)), as well as mixed designs, and a ∼600 kDa all-FANA octahedron, visualised by electron microscopy. Our results extend the chemical scope for programmable nanostructure assembly, with implications for the design of nano-objects and materials with an expanded range of structural and physicochemical properties, including enhanced biostability.
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Affiliation(s)
- Alexander I Taylor
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Department of Biology/Centre for Applied Synthetic Biology, Concordia University, 7141 Rue Sherbrooke, Montreal, H4B 1R6, Canada.
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories), 237 Fulham Road, London, SW3 6JB, UK
| | - Sew-Yeu Peak-Chew
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories), 237 Fulham Road, London, SW3 6JB, UK
| | - Piet Herdewijn
- Rega Institute, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
- Institute of Systems and Synthetic Biology, Université Evry, 5 rue Henri Desbrueres, 91030, Evry Cedex, France
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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16
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Kalinowski M, Haug R, Said H, Piasecka S, Kramer M, Richert C. Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures. Chembiochem 2016; 17:1150-5. [PMID: 27225865 DOI: 10.1002/cbic.201600061] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 01/25/2023]
Abstract
The folding of long DNA strands into designed nanostructures has evolved into an art. Being based on linear chains only, the resulting nanostructures cannot readily be transformed into covalently linked frameworks. Covalently linking strands in the context of folded DNA structures requires a robust method that avoids sterically demanding reagents or enzymes. Here we report chemical ligation of the 3'-amino termini of oligonucleotides and 5'-phosphorylated partner strands in templated reactions that produce phosphoramidate linkages. These reactions produce inter-nucleotide linkages that are isoelectronic and largely isosteric to phosphodiesters. Ligations were performed at three levels of complexity, including the extension of branched DNA hybrids and the ligation of six scaffold strands in a small origami.
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Affiliation(s)
- Matthäus Kalinowski
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Rüdiger Haug
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Hassan Said
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Sylwia Piasecka
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Markus Kramer
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany.
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17
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Wu ZS, Shen Z, Tram K, Salena BJ, Li Y. Topological DNA Assemblies Containing Identical or Fraternal Twins. Chembiochem 2016; 17:1142-5. [PMID: 26994736 DOI: 10.1002/cbic.201600036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Zai-Sheng Wu
- Departments of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- Cancer Metastasis Alert and Prevention Center; Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment; Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy; College of Chemistry; Fuzhou University; Fuzhou 350002 China
| | - Zhifa Shen
- Departments of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
- School of Laboratory Medicine and Life Sciences; Wenzhou Medical University; Wenzhou Chashan University Town Wenzhou Zhejiang 325035 China
| | - Kha Tram
- Departments of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Bruno J. Salena
- Department of Medicine; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
| | - Yingfu Li
- Departments of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 4K1 Canada
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18
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De Stefano M, Vesterager Gothelf K. Dynamic Chemistry of Disulfide Terminated Oligonucleotides in Duplexes and Double-Crossover Tiles. Chembiochem 2016; 17:1122-6. [PMID: 26994867 DOI: 10.1002/cbic.201600076] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Indexed: 02/03/2023]
Abstract
Designed nanostructures formed by self-assembly of multiple DNA strands suffer from low stability at elevated temperature and under other denaturing conditions. Here, we propose a method for covalent coupling of DNA strands in such structures by the formation of disulfide bonds; this allows disassembly of the structure under reducing conditions. The dynamic chemistry of disulfides and thiols was applied to crosslink DNA strands with terminal disulfide modifications. The formation of disulfide-linked DNA duplexes consisting of three strands is demonstrated, as well as a more-complex DNA double-crossover tile. All the strands in the fully disulfide-linked structures are covalently and geometrically interlocked, and it is demonstrated that the structures are stable under heating and in the presence of denaturants. Such a reversible system can be exploited in applications where higher DNA stability is needed only temporarily, such as delivery of cargoes to cells by DNA nanostructures.
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Affiliation(s)
- Mattia De Stefano
- Danish National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Kurt Vesterager Gothelf
- Danish National Research Foundation, Center for DNA Nanotechnology, Department of Chemistry and iNANO, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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Zhang D, Paukstelis PJ. Enhancing DNA Crystal Durability through Chemical Crosslinking. Chembiochem 2016; 17:1163-70. [DOI: 10.1002/cbic.201500610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Diana Zhang
- Department of Chemistry & Biochemistry; University of Maryland; 8314 Paint Branch Drive College Park 20742 MD USA
| | - Paul J. Paukstelis
- Department of Chemistry & Biochemistry; University of Maryland; 8314 Paint Branch Drive College Park 20742 MD USA
- Maryland NanoCenter; University of Maryland; College Park 20742 MD USA
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