1
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Frommer J, Oppenheimer R, Allott BM, Núñez-Pertíñez S, Wilks TR, Cox LR, Bath J, O'Reilly RK, Turberfield AJ. A New Architecture for DNA-Templated Synthesis in Which Abasic Sites Protect Reactants from Degradation. Angew Chem Int Ed Engl 2024; 63:e202317482. [PMID: 38346169 DOI: 10.1002/anie.202317482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Indexed: 03/01/2024]
Abstract
The synthesis of artificial sequence-defined polymers that match and extend the functionality of proteins is an important goal in materials science. One way of achieving this is to program a sequence of chemical reactions between precursor building blocks by means of attached oligonucleotide adapters. However, hydrolysis of the reactive building blocks has so far limited the length and yield of product that can be obtained using DNA-templated reactions. Here, we report an architecture for DNA-templated synthesis in which reactants are tethered at internal abasic sites on opposite strands of a DNA duplex. We show that an abasic site within a DNA duplex can protect a nearby thioester from degradation, significantly increasing the yield of a DNA-templated reaction. This protective effect has the potential to overcome the challenges associated with programmable, sequence-controlled synthesis of long non-natural polymers by extending the lifetime of the reactive building blocks.
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Affiliation(s)
- Jennifer Frommer
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Robert Oppenheimer
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
| | - Benjamin M Allott
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Samuel Núñez-Pertíñez
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Thomas R Wilks
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Liam R Cox
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Jonathan Bath
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
| | - Rachel K O'Reilly
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Andrew J Turberfield
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot, Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK
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2
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Baranda Pellejero L, Nijenhuis MAD, Ricci F, Gothelf KV. Protein-Templated Reactions Using DNA-Antibody Conjugates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2200971. [PMID: 35344264 DOI: 10.1002/smll.202200971] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/10/2022] [Indexed: 06/14/2023]
Abstract
DNA-templated chemical reactions have found wide applications in drug discovery, programmed multistep synthesis, nucleic acid detection, and targeted drug delivery. The control of these reactions has, however, been limited to nucleic acid hybridization as a means to direct the proximity between reactants. In this work a system capable of translating protein-protein binding events into a DNA-templated reaction which leads to the covalent formation of a product is introduced. Protein-templated reactions by employing two DNA-antibody conjugates that are both able to recognize the same target protein and to colocalize a pair of reactant DNA strands able to undergo a click reaction are achieved. Two individual systems, each responsive to human serum albumin (HSA) and human IgG, are engineered and it is demonstrated that, while no reaction occurs in the absence of proteins, both protein-templated reactions can occur simultaneously in the same solution without any inter-system crosstalk.
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Affiliation(s)
- Lorena Baranda Pellejero
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Minke A D Nijenhuis
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Kurt V Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus, 8000, Denmark
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3
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Helmi S, Turberfield AJ. Template-directed conjugation of heterogeneous oligonucleotides to a homobifunctional molecule for programmable supramolecular assembly. NANOSCALE 2022; 14:4463-4468. [PMID: 35253832 DOI: 10.1039/d2nr00197g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanoscience aspires to mimic nature's control over functional molecular assemblies. Here we present a templating technique for the efficient attachment of two different oligonucleotides to a homobifunctional molecule, enabling its controlled and programmable placement within a DNA nanostructure. We demonstrate its application to a range of organic molecules with different conjugation chemistries and water solubilities. We show that the two oligonucleotide adapters can be used to integrate a bifunctional cyanine dye into a self-assembled three-dimensional DNA origami nanostructure, giving control of both position and orientation. We also demonstrate the use of both adapters to exert dynamic control over the environment of the target molecule by means of a series of strand-displacement reactions.
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Affiliation(s)
- Seham Helmi
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, New Biochemistry Building, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew J Turberfield
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, New Biochemistry Building, South Parks Road, Oxford OX1 3QU, UK
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4
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Kim J, Ahn SY, Um SH. Bead-Immobilized Multimodal Molecular Beacon-Equipped DNA Machinery for Specific RNA Target Detection: A Prototypical Molecular Nanobiosensor. NANOMATERIALS 2021; 11:nano11061617. [PMID: 34203018 PMCID: PMC8235652 DOI: 10.3390/nano11061617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/12/2021] [Accepted: 06/18/2021] [Indexed: 12/28/2022]
Abstract
A variety of nanostructured diagnostic tools have been developed for the precise detection of known genetic variants. Molecular beacon systems are very promising tools due to their specific selectivity coupled with relatively lower cost and time requirements than existing molecular detection tools such as next generation sequencing or real-time PCR (polymerase chain reaction). However, they are prone to errors induced by secondary structure responses to environmental fluctuations, such as temperature and pH. Herein, we report a temperature-insensitive, bead-immobilized, molecular beacon-equipped novel DNA nanostructure for detection of cancer miRNA variants with the consideration of thermodynamics. This system consists of three parts: a molecular beacon for cancer-specific RNA capture, a stem body as a core template, and a single bead for solid-support. This DNA system was selectively bound to nanosized beads using avidin-biotin chemistry. Synthetic DNA nanostructures, designed based on the principle of fluorescence-resonance enhanced transfer, were effectively applied for in vitro cancer-specific RNA detection. Several parameters were optimized for higher performance, with a focus on thermodynamic stability. Theoretical issues regarding the secondary structure of a single molecular beacon and its combinatory forms were also studied. This study provides design guidelines for new sensing systems of miRNA variation for next-generation biotechnological applications.
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Affiliation(s)
- Jeonghun Kim
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea; (J.K.); (S.Y.A.)
| | - So Yeon Ahn
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea; (J.K.); (S.Y.A.)
| | - Soong Ho Um
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea; (J.K.); (S.Y.A.)
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Gyeonggi-do, Korea
- Correspondence:
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5
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Du Y, Pan J, Qiu H, Mao C, Choi JH. Mechanistic Understanding of Surface Migration Dynamics with DNA Walkers. J Phys Chem B 2021; 125:507-517. [PMID: 33428424 DOI: 10.1021/acs.jpcb.0c09048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yancheng Du
- School of Mechanical Engineering, Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Jing Pan
- Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Hengming Qiu
- School of Mechanical Engineering, Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
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6
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Kassem S, Lee ATL, Leigh DA, Markevicius A, Tetlow DJ, Toriumi N. Site-to-site peptide transport on a molecular platform using a small-molecule robotic arm. Chem Sci 2020; 12:2065-2070. [PMID: 34163969 PMCID: PMC8179245 DOI: 10.1039/d0sc05906d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Peptides attached to a cysteine hydrazide ‘transporter module’ are transported selectively in either direction between two chemically similar sites on a molecular platform, enabled by the discovery of new operating methods for a molecular transporter that functions through ratcheting. Substrate repositioning is achieved using a small-molecule robotic arm controlled by a protonation-mediated rotary switch and attachment/release dynamic covalent chemistry. A polar solvent mixtures were found to favour Z to E isomerization of the doubly-protonated switch, transporting cargo in one direction (arbitrarily defined as ‘forward’) in up to 85% yield, while polar solvent mixtures were unexpectedly found to favour E to Z isomerization enabling transport in the reverse (‘backward’) direction in >98% yield. Transport of the substrates proceeded in a matter of hours (compared to 6 days even for simple cargoes with the original system) without the peptides at any time dissociating from the machine nor exchanging with others in the bulk. Under the new operating conditions, key intermediates of the switch are sufficiently stabilized within the macrocycle formed between switch, arm, substrate and platform that they can be identified and structurally characterized by 1H NMR. The size of the peptide cargo has no significant effect on the rate or efficiency of transport in either direction. The new operating conditions allow detailed physical organic chemistry of the ratcheted transport mechanism to be uncovered, improve efficiency, and enable the transport of more complex cargoes than was previously possible. Peptides are transported in either direction between chemically similar sites on a molecular platform, substrate repositioning is achieved using a cysteine hydrazide transporter module and a small-molecule robotic arm controlled by a rotary switch.![]()
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Affiliation(s)
- Salma Kassem
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - Alan T L Lee
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - David A Leigh
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | | | - Daniel J Tetlow
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - Naoyuki Toriumi
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
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7
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Rossetti M, Bertucci A, Patiño T, Baranda L, Porchetta A. Programming DNA-Based Systems through Effective Molarity Enforced by Biomolecular Confinement. Chemistry 2020; 26:9826-9834. [PMID: 32428310 DOI: 10.1002/chem.202001660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/12/2020] [Indexed: 12/12/2022]
Abstract
The fundamental concept of effective molarity is observed in a variety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To control molecular encountering and promote effective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of a number of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Bertucci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Tania Patiño
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Lorena Baranda
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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8
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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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9
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Herges R. Molecular assemblers: molecular machines performing chemical synthesis. Chem Sci 2020; 11:9048-9055. [PMID: 34123157 PMCID: PMC8163427 DOI: 10.1039/d0sc03094e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/14/2020] [Indexed: 01/04/2023] Open
Abstract
Molecular assemblers were proposed by K. Eric Drexler in 1986, based on the ideas of R. Feynman. In his (quite lurid) book "Engines of Creation: The Coming Era of Nanotechnology" and follow-up publications Drexler proposes molecular machines capable of positioning reactive molecules with atomic precision and to build larger, more sophisticated structures via mechanosynthesis. These imaginative visions started a hot controversy. The debate culminated in a cover story of Chemical & Engineering News in 2003 (ref. 1) with the key question: "Are molecular assemblers - devices capable of positioning atoms and molecules for precisely defined reactions - possible?" with Drexler as the proponent and Nobelist Richard E. Smalley being the opponent. Smalley raised two major objections: the "fat fingers" and the "sticky fingers" problem. To grab and guide each individual atom the assembler must have many nano-fingers. Smalley argued that there is just not enough room in the nanometer-sized reaction region to accommodate all the fingers of all the manipulators necessary to have complete control of the chemistry. The sticky finger issue arises from the problem that …"the atoms of the manipulator hands will adhere to the atom that is being moved. So it will often be impossible to release the building block in precisely the right spot." Smalley concludes that the fat and the sticky finger problems are fundamental and cannot be avoided. While some of the statements of E. Drexler are bold and probably not very realistic, his ideas are inspiring and might be a good starting point to assess on how far laboratory chemistry has advanced towards real "molecular assemblers" within the last two decades.
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Affiliation(s)
- Rainer Herges
- Otto-Diels-Institute of Organic Chemistry, Kiel University 24118 Kiel Germany
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10
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Surin M, Ulrich S. From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies. ChemistryOpen 2020; 9:480-498. [PMID: 32328404 PMCID: PMC7175023 DOI: 10.1002/open.202000013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsCenter of Innovation and Research in Materials and Polymers (CIRMAP)University of Mons-UMONS7000MonsBelgium
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11
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Xu X, Winterwerber P, Ng D, Wu Y. DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials. Top Curr Chem (Cham) 2020; 378:31. [PMID: 32146596 PMCID: PMC7060966 DOI: 10.1007/s41061-020-0292-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/17/2020] [Indexed: 12/21/2022]
Abstract
DNA nanotechnology, based on sequence-specific DNA recognition, could allow programmed self-assembly of sophisticated nanostructures with molecular precision. Extension of this technique to the preparation of broader types of nanomaterials would significantly improve nanofabrication technique to lower nanometer scale and even achieve single molecule operation. Using such exquisite DNA nanostructures as templates, chemical synthesis of polymer and inorganic nanomaterials could also be programmed with unprecedented accuracy and flexibility. This review summarizes recent advances in the synthesis and assembly of polymer and inorganic nanomaterials using DNA nanostructures as templates, and discusses the current challenges and future outlook of DNA templated nanotechnology.
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Affiliation(s)
- Xuemei Xu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan, 430074, People's Republic of China
| | - Pia Winterwerber
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - David Ng
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Yuzhou Wu
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road 1037, Hongshan, Wuhan, 430074, People's Republic of China.
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.
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12
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Liu B, Shi Q, Hu L, Huang Z, Zhu X, Zhang Z. Engineering digital polymer based on thiol–maleimide Michael coupling toward effective writing and reading. Polym Chem 2020. [DOI: 10.1039/c9py01939a] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Based on thiol–maleimide Michael coupling, a digital polymer allowing efficient message writing and reading was rationally designed.
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Affiliation(s)
- Baolei Liu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
| | - Qiunan Shi
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
| | - Lihua Hu
- Analysis and Testing Center
- Soochow University
- Suzhou 215123
- China
| | - Zhihao Huang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
| | - Xiulin Zhu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
- Global Institute of Software Technology
| | - Zhengbiao Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University, Suzhou
- China
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13
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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14
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One-shot synthesis of sequence-controlled polymers with versatile succimide motifs for post-modifications. REACT FUNCT POLYM 2019. [DOI: 10.1016/j.reactfunctpolym.2018.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Ren K, Zhang Y, Zhang X, Liu Y, Yang M, Ju H. In Situ SiRNA Assembly in Living Cells for Gene Therapy with MicroRNA Triggered Cascade Reactions Templated by Nucleic Acids. ACS NANO 2018; 12:10797-10806. [PMID: 30354052 DOI: 10.1021/acsnano.8b02403] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The in situ generation of siRNAs in living cells can greatly enhance the specificity and efficiency of gene therapy. Inspired by the natural molecular machines that organize different compartments sequentially in a limited space to facilitate cellular process, this work constructs a DNA nanomachine (DNM) by alternately hybridizing two pairs of DNA/RNA hybrids to a DNA scaffold generated by rolling circle amplification for highly efficient in situ siRNA assembly in living cells. After target cell-specific delivery of DNM, intracellular specific microRNA can work as a trigger to operate the DNM by initiating DNA cascade displacement reaction between DNA/RNA hybrids along the scaffold for continuous generation of siRNAs. Using miR-21 as a model, efficient siRNAs generation is achieved via DNA templated cascade reaction, which demonstrated impressive suppressions to VEGF mRNA and protein expressions in cells and in vivo tumor growth and indicated promising application of the designed strategy in gene therapy.
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Affiliation(s)
- Kewei Ren
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Yue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Xiaobo Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Min Yang
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy , University College London , London WC1N 1AX , United Kingdom
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
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16
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Chandra P, Jonas AM, Fernandes AE. Sequence and Surface Confinement Direct Cooperativity in Catalytic Precision Oligomers. J Am Chem Soc 2018; 140:5179-5184. [DOI: 10.1021/jacs.8b00872] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Prakash Chandra
- Institute of Condensed Matter and Nanosciences, Bio- and Soft Matter, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Alain M. Jonas
- Institute of Condensed Matter and Nanosciences, Bio- and Soft Matter, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Antony E. Fernandes
- Institute of Condensed Matter and Nanosciences, Bio- and Soft Matter, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
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17
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Sayers J, Payne RJ, Winssinger N. Peptide nucleic acid-templated selenocystine-selenoester ligation enables rapid miRNA detection. Chem Sci 2017; 9:896-903. [PMID: 29629156 PMCID: PMC5873163 DOI: 10.1039/c7sc02736b] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022] Open
Abstract
The development of a rapid and chemoselective selenocystine-selenoester peptide ligation that operates at nanomolar reactant concentrations has been developed by utilising PNA templation. Kinetic analysis of the templated peptide ligation revealed that the selenocystine-selenoester reaction was 10 times faster than traditional native chemical ligation at cysteine and to our knowledge is the fastest templated ligation reaction reported to date. The efficiency and operational simplicity of this technology is highlighted through the formation of hairpin molecular architectures and in a novel paper-based lateral flow assay for the rapid and sequence specific detection of oligonucleotides, including miRNA in cell lysates.
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Affiliation(s)
- Jessica Sayers
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia . .,Department of Organic Chemistry , Faculty of Science , NCCR Chemical Biology , University of Geneva , Quai Ernest Ansermet 30 , 1211 Geneva , Switzerland .
| | - Richard J Payne
- School of Chemistry , The University of Sydney , Sydney , NSW 2006 , Australia .
| | - Nicolas Winssinger
- Department of Organic Chemistry , Faculty of Science , NCCR Chemical Biology , University of Geneva , Quai Ernest Ansermet 30 , 1211 Geneva , Switzerland .
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18
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O’Reilly RK, Turberfield AJ, Wilks TR. The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery. Acc Chem Res 2017; 50:2496-2509. [PMID: 28915003 PMCID: PMC5746846 DOI: 10.1021/acs.accounts.7b00280] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Precise control over reactivity and molecular
structure is a fundamental
goal of the chemical sciences. Billions of years of evolution by natural
selection have resulted in chemical systems capable of information
storage, self-replication, catalysis, capture and production of light,
and even cognition. In all these cases, control over molecular structure
is required to achieve a particular function: without structural control,
function may be impaired, unpredictable, or impossible. The
search for molecules with a desired function is often achieved
by synthesizing a combinatorial library, which contains many or all
possible combinations of a set of chemical building blocks (BBs),
and then screening this library to identify “successful”
structures. The largest libraries made by conventional synthesis are
currently of the order of 108 distinct molecules. To put
this in context, there are 1013 ways of arranging the 21
proteinogenic amino acids in chains up to 10 units long. Given that
we know that a number of these compounds have potent biological activity,
it would be highly desirable to be able to search them all to identify
leads for new drug molecules. Large libraries of oligonucleotides
can be synthesized combinatorially and translated into peptides using
systems based on biological replication such as mRNA display, with
selected molecules identified by DNA sequencing; but these methods
are limited to BBs that are compatible with cellular machinery. In
order to search the vast tracts of chemical space beyond nucleic acids
and natural peptides, an alternative approach is required. DNA-templated
synthesis (DTS) could enable us to meet this challenge.
DTS controls chemical product formation by using the specificity of
DNA hybridization to bring selected reactants into close proximity,
and is capable of the programmed synthesis of many distinct products
in the same reaction vessel. By making use of dynamic, programmable
DNA processes, it is possible to engineer a system that can translate
instructions coded as a sequence of DNA bases into a chemical structure—a
process analogous to the action of the ribosome in living organisms
but with the potential to create a much more chemically diverse set
of products. It is also possible to ensure that each product molecule
is tagged with its identifying DNA sequence. Compound libraries synthesized
in this way can be exposed to selection against suitable targets,
enriching successful molecules. The encoding DNA can then be amplified
using the polymerase chain reaction and decoded by DNA sequencing.
More importantly, the DNA instruction sequences can be mutated and
reused during multiple rounds of amplification, translation, and selection.
In other words, DTS could be used as the foundation for a system of
synthetic molecular evolution, which could allow us to efficiently
search a vast chemical space. This has huge potential to revolutionize
materials discovery—imagine being able to evolve molecules
for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety
of reactions can be performed on a DNA template. Complex architectures
and autonomous “DNA robots” have been implemented for
the controlled assembly of BBs, and these mechanisms have in turn
enabled the one-pot synthesis of large combinatorial libraries. Indeed,
DTS libraries are being exploited by pharmaceutical companies and
have already found their way into drug lead discovery programs. This
Account explores the processes involved in DTS and highlights the
challenges that remain in creating a general system for molecular
discovery by evolution.
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Affiliation(s)
- Rachel K. O’Reilly
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew J. Turberfield
- Clarendon
Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Thomas R. Wilks
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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19
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De Bo G, Gall MAY, Kitching MO, Kuschel S, Leigh DA, Tetlow DJ, Ward JW. Sequence-Specific β-Peptide Synthesis by a Rotaxane-Based Molecular Machine. J Am Chem Soc 2017; 139:10875-10879. [DOI: 10.1021/jacs.7b05850] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Guillaume De Bo
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Malcolm A. Y. Gall
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Matthew O. Kitching
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sonja Kuschel
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Daniel J. Tetlow
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - John W. Ward
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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20
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Ji Y, Zhang L, Gu X, Zhang W, Zhou N, Zhang Z, Zhu X. Sequence-Controlled Polymers with Furan-Protected Maleimide as a Latent Monomer. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610305] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yuxuan Ji
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Liuqiao Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Xue Gu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Wei Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Nianchen Zhou
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Zhengbiao Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Xiulin Zhu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
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21
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Ji Y, Zhang L, Gu X, Zhang W, Zhou N, Zhang Z, Zhu X. Sequence-Controlled Polymers with Furan-Protected Maleimide as a Latent Monomer. Angew Chem Int Ed Engl 2017; 56:2328-2333. [DOI: 10.1002/anie.201610305] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/01/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Yuxuan Ji
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Liuqiao Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Xue Gu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Wei Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Nianchen Zhou
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Zhengbiao Zhang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
| | - Xiulin Zhu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials; Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application; College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou 215123 China
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22
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Kamonsutthipaijit N, Anderson HL. Template-directed synthesis of linear porphyrin oligomers: classical, Vernier and mutual Vernier. Chem Sci 2017; 8:2729-2740. [PMID: 28553508 PMCID: PMC5426366 DOI: 10.1039/c6sc05355f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/20/2017] [Indexed: 12/22/2022] Open
Abstract
We demonstrate a variety of template-directed strategies for preparing linear monodisperse butadiyne-linked porphyrin oligomers by Glaser–Hay coupling, based on the coordination of pyridine-substituted nickel(ii) porphyrins to zinc(ii) porphyrins.
Three different types of template-directed syntheses of linear porphyrin oligomers are presented. In the classical approach the product has the same number of binding sites as the template, whereas in Vernier reactions the product has the lowest common multiple of the numbers of binding sites in the template and the building block. Mutual Vernier templating is like Vernier templating except that both strands of the Vernier complex undergo coupling simultaneously, so that it becomes impossible to say which is the ‘template’ and which is the ‘building block’. The template-directed synthesis of monodisperse linear oligomers is more difficult than that of cyclic oligomers, because the products of linear templating have reactive ends. All three types of templating are demonstrated here, and used to prepare a nickel(ii) porphyrin dodecamer with 4-pyridyl substituents on all twelve porphyrin units. The stabilities and cooperativities of the double-strand complexes involved in these reactions were investigated by UV-vis-NIR titration. The four-rung ladder duplex has a stability constant of about 2 × 1018 M–1 in dichloromethane at 298 K.
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Affiliation(s)
| | - Harry L Anderson
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , Oxford OX1 3TA , UK .
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23
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Takada T, Ido M, Ashida A, Nakamura M, Yamana K. DNA-Templated Synthesis of Perylenediimide Stacks Utilizing Abasic Sites as Binding Pockets and Reactive Sites. Chembiochem 2016; 17:2230-2233. [DOI: 10.1002/cbic.201600454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Misa Ido
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Akane Ashida
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Mitsunobu Nakamura
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
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24
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Trinh T, Chidchob P, Bazzi HS, Sleiman HF. DNA micelles as nanoreactors: efficient DNA functionalization with hydrophobic organic molecules. Chem Commun (Camb) 2016; 52:10914-7. [PMID: 27533528 DOI: 10.1039/c6cc04970b] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report a micelle-templated method to enhance the reactivity of DNA with highly hydrophobic molecules. Lipids, chromophores and polymers can be conjugated to DNA in high yield and under mild conditions. This method expands the range of DNA-templated reactions for DNA-encoded libraries, oligonucleotide and drug delivery, nanopore mimetics and DNA nanotechnology.
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Affiliation(s)
- Tuan Trinh
- Department of Chemistry and Center for Self-Assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.
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25
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Meng W, Muscat RA, McKee ML, Milnes PJ, El-Sagheer AH, Bath J, Davis BG, Brown T, O'Reilly RK, Turberfield AJ. An autonomous molecular assembler for programmable chemical synthesis. Nat Chem 2016; 8:542-8. [PMID: 27219697 DOI: 10.1038/nchem.2495] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 02/24/2016] [Indexed: 12/21/2022]
Abstract
Molecular machines that assemble polymers in a programmed sequence are fundamental to life. They are also an achievable goal of nanotechnology. Here, we report synthetic molecular machinery made from DNA that controls and records the formation of covalent bonds. We show that an autonomous cascade of DNA hybridization reactions can create oligomers, from building blocks linked by olefin or peptide bonds, with a sequence defined by a reconfigurable molecular program. The system can also be programmed to achieve combinatorial assembly. The sequence of assembly reactions and thus the structure of each oligomer synthesized is recorded in a DNA molecule, which enables this information to be recovered by PCR amplification followed by DNA sequencing.
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Affiliation(s)
- Wenjing Meng
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Richard A Muscat
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Mireya L McKee
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Phillip J Milnes
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Jonathan Bath
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Rachel K O'Reilly
- Department of Chemistry, University of Warwick, Coventry, West Midlands CV4 7AL, UK
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26
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Funke JJ, Dietz H. Placing molecules with Bohr radius resolution using DNA origami. NATURE NANOTECHNOLOGY 2016; 11:47-52. [PMID: 26479026 DOI: 10.1038/nnano.2015.240] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/09/2015] [Indexed: 05/17/2023]
Abstract
Molecular self-assembly with nucleic acids can be used to fabricate discrete objects with defined sizes and arbitrary shapes. It relies on building blocks that are commensurate to those of biological macromolecular machines and should therefore be capable of delivering the atomic-scale placement accuracy known today only from natural and designed proteins. However, research in the field has predominantly focused on producing increasingly large and complex, but more coarsely defined, objects and placing them in an orderly manner on solid substrates. So far, few objects afford a design accuracy better than 5 nm, and the subnanometre scale has been reached only within the unit cells of designed DNA crystals. Here, we report a molecular positioning device made from a hinged DNA origami object in which the angle between the two structural units can be controlled with adjuster helices. To test the positioning capabilities of the device, we used photophysical and crosslinking assays that report the coordinate of interest directly with atomic resolution. Using this combination of placement and analysis, we rationally adjusted the average distance between fluorescent molecules and reactive groups from 1.5 to 9 nm in 123 discrete displacement steps. The smallest displacement step possible was 0.04 nm, which is slightly less than the Bohr radius. The fluctuation amplitudes in the distance coordinate were also small (±0.5 nm), and within a factor of two to three of the amplitudes found in protein structures.
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Affiliation(s)
- Jonas J Funke
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748 Garching near Munich, Germany
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748 Garching near Munich, Germany
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27
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Hua Z, Pitto-Barry A, Kang Y, Kirby N, Wilks TR, O'Reilly RK. Micellar nanoparticles with tuneable morphologies through interactions between nucleobase-containing synthetic polymers in aqueous solution. Polym Chem 2016. [DOI: 10.1039/c6py00716c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report the preparation of nucleobase-containing synthetic amphiphilic diblock copolymers using RAFT polymerization.
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Affiliation(s)
- Zan Hua
- Department of Chemistry
- University of Warwick
- Coventry
- UK
| | | | - Yan Kang
- Department of Chemistry
- University of Warwick
- Coventry
- UK
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28
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Lu CH, Cecconello A, Qi XJ, Wu N, Jester SS, Famulok M, Matthies M, Schmidt TL, Willner I. Switchable Reconfiguration of a Seven-Ring Interlocked DNA Catenane Nanostructure. NANO LETTERS 2015; 15:7133-7137. [PMID: 26360345 DOI: 10.1021/acs.nanolett.5b03280] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The synthesis, purification, and structure characterization of a seven-ring interlocked DNA catenane is described. The design of the seven-ring catenane allows the dynamic reconfiguration of any of the four rings (R1, R3, R4, and R6) on the catenane scaffold, or the simultaneous switching of any combination of two, three, or all four rings to yield 16 different isomeric states of the catenane. The dynamic reconfiguration across the states is achieved by implementing the strand-displacement process in the presence of appropriate fuel/antifuel strands and is probed by fluorescence spectroscopy. Each of the 16 isomers of the catenane can be transformed into any of the other isomers, thus allowing for 240 dynamic transitions within the system.
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Affiliation(s)
- Chun-Hua Lu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Alessandro Cecconello
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Xiu-Juan Qi
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
- The Key Laboratory of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry, Fuzhou University , Fuzhou 350002, China
| | - Na Wu
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Stefan-Sven Jester
- Kekulé Institut für Organische Chemie und Biochemie, University of Bonn , Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
| | - Michael Famulok
- LIMES Program Unit Chemical Biology & Medicinal Chemistry, c/o Kekulé Institut für Organische Chemie und Biochemie, University of Bonn , Gerhard-Domagk-Straße 1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research (CAESAR) , Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Michael Matthies
- Cluster of Excellence Centre for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
| | - Thorsten-Lars Schmidt
- Cluster of Excellence Centre for Advancing Electronics Dresden (cfaed), Technische Universität Dresden , 01062 Dresden, Germany
| | - Itamar Willner
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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29
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Affiliation(s)
- Sundus Erbas-Cakmak
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - David A. Leigh
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Charlie T. McTernan
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alina
L. Nussbaumer
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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30
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Cheng C, McGonigal PR, Schneebeli ST, Li H, Vermeulen NA, Ke C, Stoddart JF. An artificial molecular pump. NATURE NANOTECHNOLOGY 2015; 10:547-53. [PMID: 25984834 DOI: 10.1038/nnano.2015.96] [Citation(s) in RCA: 350] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/10/2015] [Indexed: 05/24/2023]
Abstract
Carrier proteins consume fuel in order to pump ions or molecules across cell membranes, creating concentration gradients. Their control over diffusion pathways, effected entirely through noncovalent bonding interactions, has inspired chemists to devise artificial systems that mimic their function. Here, we report a wholly artificial compound that acts on small molecules to create a gradient in their local concentration. It does so by using redox energy and precisely organized noncovalent bonding interactions to pump positively charged rings from solution and ensnare them around an oligomethylene chain, as part of a kinetically trapped entanglement. A redox-active viologen unit at the heart of a dumbbell-shaped molecular pump plays a dual role, first attracting and then repelling the rings during redox cycling, thereby enacting a flashing energy ratchet mechanism with a minimalistic design. Our artificial molecular pump performs work repetitively for two cycles of operation and drives rings away from equilibrium toward a higher local concentration.
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Affiliation(s)
- Chuyang Cheng
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Paul R McGonigal
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Severin T Schneebeli
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Hao Li
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Nicolaas A Vermeulen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Chenfeng Ke
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - J Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
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31
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Guo Y, Wu J, Ju H. Target-driven DNA association to initiate cyclic assembly of hairpins for biosensing and logic gate operation. Chem Sci 2015; 6:4318-4323. [PMID: 29218202 PMCID: PMC5707516 DOI: 10.1039/c5sc01215e] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 05/11/2015] [Indexed: 01/22/2023] Open
Abstract
Target-driven DNA association is designed for initiating the cyclic assembly of hairpins for target detection and logic gate operation.
A target-driven DNA association was designed to initiate cyclic assembly of hairpins, which led to an enzyme-free amplification strategy for detection of a nucleic acid or aptamer substrate and flexible construction of logic gates. The cyclic system contained two ssDNA (S1 and S2) and two hairpins (H1 and H2). These ssDNA could co-recognize the target to produce an S1–target–S2 structure, which brought their toehold and branch-migration domains into close proximity to initiate the cyclic assembly of hairpins. The assembly product further induced the dissociation of a double-stranded probe DNA (Q:F) via toehold-mediated strand displacement to switch the fluorescence signal. This method could detect DNA and ATP as model analytes down to 21.6 pM and 38 nM, respectively. By designing different DNA input strands, the “AND”, “INHIBIT” and “NAND” logic gates could be activated to achieve the output signal. The proposed biosensing and logic gate operation platform showed potential applications in disease diagnosis.
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Affiliation(s)
- Yuehua Guo
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , P. R. China . ; ; Tel: +86 25 83593593
| | - Jie Wu
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , P. R. China . ; ; Tel: +86 25 83593593
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , P. R. China . ; ; Tel: +86 25 83593593
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32
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Qi XJ, Lu CH, Cecconello A, Yang HH, Willner I. A two-ring interlocked DNA catenane rotor undergoing switchable transitions across three states. Chem Commun (Camb) 2015; 50:4717-20. [PMID: 24676286 DOI: 10.1039/c4cc00880d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A two-ring (α/β) interlocked DNA catenane rotor system is described. Using appropriate fuel and anti-fuel strands, the triggered switchable rotation across three states S1, S2 and S3 associated with the circular track of ring α is demonstrated.
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Affiliation(s)
- Xiu-Juan Qi
- The Key Laboratory of Analysis and Detection Technology for Food Safety of the MOE, College of Chemistry, Fuzhou University, Fuzhou 350002, China
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33
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Abstract
This review discusses the template-directed preparation of sequence-defined polymers.
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Li D, Wang X, Shi F, Sha R, Seeman NC, Canary JW. Templated DNA ligation with thiol chemistry. Org Biomol Chem 2014; 12:8823-7. [DOI: 10.1039/c4ob01552e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Martinez-Veracoechea FJ, Mognetti BM, Angioletti-Uberti S, Varilly P, Frenkel D, Dobnikar J. Designing stimulus-sensitive colloidal walkers. SOFT MATTER 2014; 10:3463-3470. [PMID: 24647520 DOI: 10.1039/c3sm53096e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Colloidal particles with DNA "legs" that can bind reversibly to receptors on a surface can be made to 'walk' if there is a gradient in receptor concentration. We use a combination of theory and Monte Carlo simulations to explore how controllable parameters, e.g. coating density and binding strength, affect the dynamics of such colloids. We find that competition between thermodynamic and kinetic trends imply that there is an optimal value for both the binding strength and the number of "legs" for which transport is the fastest. Using available thermodynamic data on DNA binding, we indicate how directionally reversible, temperature-controlled transport of colloidal walkers can be achieved. In particular, the present results should make it possible to design a chromatographic technique that can be used to separate colloids with different DNA functionalizations.
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Bryksin AV, Brown AC, Baksh MM, Finn M, Barker TH. Learning from nature - novel synthetic biology approaches for biomaterial design. Acta Biomater 2014; 10:1761-9. [PMID: 24463066 DOI: 10.1016/j.actbio.2014.01.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/16/2014] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
Abstract
Many biomaterials constructed today are complex chemical structures that incorporate biologically active components derived from nature, but the field can still be said to be in its infancy. The need for materials that bring sophisticated properties of structure, dynamics and function to medical and non-medical applications will only grow. Increasing appreciation of the functionality of biological systems has caused biomaterials researchers to consider nature for design inspiration, and many examples exist of the use of biomolecular motifs. Yet evolution, nature's only engine for the creation of new designs, has been largely ignored by the biomaterials community. Molecular evolution is an emerging tool that enables one to apply nature's engineering principles to non-natural situations using variation and selection. The purpose of this review is to highlight the most recent advances in the use of molecular evolution in synthetic biology applications for biomaterial engineering, and to discuss some of the areas in which this approach may be successfully applied in the future.
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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Nguyen T, Håkansson P, Edge R, Collison D, Goodman BA, Burns JR, Stulz E. EPR based distance measurement in Cu-porphyrin–DNA. NEW J CHEM 2014. [DOI: 10.1039/c4nj00673a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Measurement of EPR spectra of Cu-porphyrin–DNA reveals intermolecular interactions between the DNA strands with average distances of 6.5–8.9 Å.
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Affiliation(s)
- ThaoNguyen Nguyen
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Pär Håkansson
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Ruth Edge
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - David Collison
- School of Chemistry and Photon Science Institute
- The University of Manchester
- Manchester, UK
| | - Bernard A. Goodman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources
- Guangxi University
- Nanning 530005, China
| | - Jonathan R. Burns
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
| | - Eugen Stulz
- School of Chemistry and Instituted of Life Sciences
- University of Southampton
- Southampton, UK
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Vázquez O, Seitz O. Cytotoxic peptide–PNA conjugates obtained by RNA-programmed peptidyl transfer with turnover. Chem Sci 2014. [DOI: 10.1039/c4sc00299g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A RNA triggered chemical peptidyl transfer reaction leads to a cytotoxic peptide conjugate that requires turnover in RNA for bioactivity.
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Affiliation(s)
- O. Vázquez
- Institut für Chemie
- Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| | - O. Seitz
- Institut für Chemie
- Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
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Leigh DA, Lewandowska U, Lewandowski B, Wilson MR. Synthetic Molecular Walkers. MOLECULAR MACHINES AND MOTORS 2014; 354:111-38. [DOI: 10.1007/128_2014_546] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Sicilia G, Grainger-Boultby C, Francini N, Magnusson JP, Saeed AO, Fernández-Trillo F, Spain SG, Alexander C. Programmable polymer-DNA hydrogels with dual input and multiscale responses. Biomater Sci 2014; 2:203-211. [DOI: 10.1039/c3bm60126a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Barluenga S, Winssinger N. Picture Perfect: DNA-Templated Photoaffinity Labeling. Chembiochem 2013; 14:1927-8. [DOI: 10.1002/cbic.201300416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Indexed: 12/18/2022]
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Spillmann CM, Ancona MG, Buckhout-White S, Algar WR, Stewart MH, Susumu K, Huston AL, Goldman ER, Medintz IL. Achieving effective terminal exciton delivery in quantum dot antenna-sensitized multistep DNA photonic wires. ACS NANO 2013; 7:7101-7118. [PMID: 23844838 DOI: 10.1021/nn402468t] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Assembling DNA-based photonic wires around semiconductor quantum dots (QDs) creates optically active hybrid architectures that exploit the unique properties of both components. DNA hybridization allows positioning of multiple, carefully arranged fluorophores that can engage in sequential energy transfer steps while the QDs provide a superior energy harvesting antenna capacity that drives a Förster resonance energy transfer (FRET) cascade through the structures. Although the first generation of these composites demonstrated four-sequential energy transfer steps across a distance >150 Å, the exciton transfer efficiency reaching the final, terminal dye was estimated to be only ~0.7% with no concomitant sensitized emission observed. Had the terminal Cy7 dye utilized in that construct provided a sensitized emission, we estimate that this would have equated to an overall end-to-end ET efficiency of ≤ 0.1%. In this report, we demonstrate that overall energy flow through a second generation hybrid architecture can be significantly improved by reengineering four key aspects of the composite structure: (1) making the initial DNA modification chemistry smaller and more facile to implement, (2) optimizing donor-acceptor dye pairings, (3) varying donor-acceptor dye spacing as a function of the Förster distance R0, and (4) increasing the number of DNA wires displayed around each central QD donor. These cumulative changes lead to a 2 orders of magnitude improvement in the exciton transfer efficiency to the final terminal dye in comparison to the first-generation construct. The overall end-to-end efficiency through the optimized, five-fluorophore/four-step cascaded energy transfer system now approaches 10%. The results are analyzed using Förster theory with various sources of randomness accounted for by averaging over ensembles of modeled constructs. Fits to the spectra suggest near-ideal behavior when the photonic wires have two sequential acceptor dyes (Cy3 and Cy3.5) and exciton transfer efficiencies approaching 100% are seen when the dye spacings are 0.5 × R0. However, as additional dyes are included in each wire, strong nonidealities appear that are suspected to arise predominantly from the poor photophysical performance of the last two acceptor dyes (Cy5 and Cy5.5). The results are discussed in the context of improving exciton transfer efficiency along photonic wires and the contributions these architectures can make to understanding multistep FRET processes.
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Affiliation(s)
- Christopher M Spillmann
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
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Hobert EM, Doerner AE, Walker AS, Schepartz A. Effective molarity redux: Proximity as a guiding force in chemistry and biology. Isr J Chem 2013; 53:567-576. [PMID: 25418998 PMCID: PMC4238305 DOI: 10.1002/ijch.201300063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The cell interior is a complex and demanding environment. An incredible variety of molecules jockey to identify the correct position-the specific interactions that promote biology that are hidden among countless unproductive options. Ensuring that the business of the cell is successful requires sophisticated mechanisms to impose temporal and spatial specificity-both on transient interactions and their eventual outcomes. Two strategies employed to regulate macromolecular interactions in a cellular context are co-localization and compartmentalization. Macromolecular interactions can be promoted and specified by localizing the partners within the same subcellular compartment, or by holding them in proximity through covalent or non-covalent interactions with proteins, lipids, or DNA- themes that are familiar to any biologist. The net result of these strategies is an increase in effective molarity: the local concentration of a reactive molecule near its reaction partners. We will focus on this general mechanism, employed by Nature and adapted in the lab, which allows delicate control in complex environments: the power of proximity to accelerate, guide, or otherwise influence the reactivity of signaling proteins and the information that they encode.
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Nucleic acids for the rational design of reaction circuits. Curr Opin Biotechnol 2013; 24:575-80. [DOI: 10.1016/j.copbio.2012.11.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/08/2012] [Accepted: 11/29/2012] [Indexed: 11/18/2022]
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Gorska K, Winssinger N. Reactions templated by nucleic acids: more ways to translate oligonucleotide-based instructions into emerging function. Angew Chem Int Ed Engl 2013; 52:6820-43. [PMID: 23794204 DOI: 10.1002/anie.201208460] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Indexed: 12/30/2022]
Abstract
The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.
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Affiliation(s)
- Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Universite de Strasbourg-CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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Gorska K, Winssinger N. Reaktionen an Nucleinsäuretemplaten: mehr Methoden zur Übersetzung Oligonucleotid-basierter Informationen in neue Funktionen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208460] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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