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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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2
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Design of photofunctional oligonucleotides by copolymerization of natural nucleobases with base surrogates prepared from acyclic scaffolds. Polym J 2016. [DOI: 10.1038/pj.2016.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Kundu R. G-Tetraplex-Induced FRET within Telomeric Repeat Sequences Using (Py) A-(Per) A as Energy Donor-Acceptor Pair. Chem Asian J 2015; 11:198-201. [PMID: 26490798 DOI: 10.1002/asia.201500996] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 01/08/2023]
Abstract
G-tetraplex induced fluorescence resonance energy transfer (FRET) within telomeric repeat sequences has been studied using a nucleoside-tethered FRET pair embedded in the human telomeric G-quadruplex forming sequence (5'-A GGG TT(Py) A GGG TT(Per) A GGG TTA GGG-3', Py=pyrene, Per=perylene). Conformational change from a single strand to an anti-parallel G-quadruplex leads to FRET from energy donor ((Py) A) to acceptor ((Per) A). The distance between the FRET donor/acceptor partners was controlled by changing the number of G-quartet spacer units. The FRET efficiency decreases with increase in G-quartet units. Overall findings indicate that this could be further used for the development of FRET-based sensing and measurement techniques.
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Affiliation(s)
- Rajen Kundu
- Department of Chemistry, Pohang University of Science and Technology, Pohang, 790784, South Korea. .,Department of Chemistry and Biochemistry, University of Colorado, Boulder, 80303, USA.
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Li J, Wang X, Liang X. Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology. Chem Asian J 2014; 9:3344-58. [DOI: 10.1002/asia.201402758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 01/29/2023]
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Asanuma H, Kashida H, Kamiya Y. De novo design of functional oligonucleotides with acyclic scaffolds. CHEM REC 2014; 14:1055-69. [PMID: 25171046 DOI: 10.1002/tcr.201402040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Indexed: 01/20/2023]
Abstract
In this account, we demonstrate a new methodology for the de novo design of functional oligonucleotides with the acyclic scaffolds threoninol and serinol. Four functional motifs-wedge, interstrand-wedge, dimer, and cluster-have been prepared from natural DNA or RNA and functional base surrogates prepared from d-threoninol. The following applications of these motifs are described: (1) photoregulation of formation and dissociation of a DNA duplex modified with azobenzene, (2) sequence-specific detection of DNA using a fluorescent probe, (3) formation of fluorophore assemblies that mimic quantum dots, (4) improved strand selectivity of siRNA modified with a base surrogate, and (5) in vivo tracing of the RNAi pathway. Finally, we introduce artificial nucleic acids (XNAs) prepared from d-threoninol and serinol functionalized with each of the four nucleobases, which have unique properties compared with other acyclic XNAs. Functional oligonucleotides designed from acyclic scaffolds will be powerful tools for both DNA nanotechnology and biotechnology.
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Affiliation(s)
- Hiroyuki Asanuma
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
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Kamiya Y, Asanuma H. Light-driven DNA nanomachine with a photoresponsive molecular engine. Acc Chem Res 2014; 47:1663-72. [PMID: 24617966 DOI: 10.1021/ar400308f] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CONSPECTUS: DNA is regarded as an excellent nanomaterial due to its supramolecular property of duplex formation through A-T and G-C complementary pairs. By simply designing sequences, we can create any desired 2D or 3D nanoarchitecture with DNA. Based on these nanoarchitectures, motional DNA-based nanomachines have also been developed. Most of the nanomachines require molecular fuels to drive them. Typically, a toehold exchange reaction is applied with a complementary DNA strand as a fuel. However, repetitive operation of the machines accumulates waste DNA duplexes in the solution that gradually deteriorate the motional efficiency. Hence, we are facing an "environmental problem" even in the nanoworld. One of the direct solutions to this problem is to use clean energy, such as light. Since light does not contaminate the reaction system, a DNA nanomachine run by a photon engine can overcome the drawback of waste that is a problem with molecular-fueled engines. There are several photoresponsive molecules that convert light energy to mechanical motion through the change of geometry of the molecules; these include spiropyran, diarylethene, stilbene, and azobenzene. Although each molecule has both advantages and drawbacks, azobenzene derivatives are widely used as "molecular photon engines". In this Account, we review light-driven DNA nanomachines mainly focusing on the photoresponsive DNAs that we have developed for the past decade. The basis of our method is installation of an azobenzene into a DNA sequence through a d-threoninol scaffold. Reversible hybridization of the DNA duplex, triggered by trans-cis isomerization of azobenzene in the DNA sequences by irradiation with light, induces mechanical motion of the DNA nanomachine. Moreover we have successfully developed azobenzene derivatives that improve its photoisomerizaition properties. Use of these derivatives and techniques have allowed us to design various DNA machines that demonstrate sophisticated motion in response to lights of different wavelengths without a drop in photoregulatory efficiency. In this Account, we emphasize the advantages of our methods including (1) ease of preparation, (2) comprehensive sequence design of azobenzene-tethered DNA, (3) efficient photoisomerization, and (4) reversible photocontrol of hybridization by irradiation with appropriate wavelengths of light. We believe that photon-fueled DNA nanomachines driven by azobenzene-derivative molecular photon-fueled engines will be soon science rather than "science fiction".
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Affiliation(s)
- Yukiko Kamiya
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
- Ecotopia
Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
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Liang X, Zhou M, Kato K, Asanuma H. Photoswitch nucleic acid catalytic activity by regulating topological structure with a universal supraphotoswitch. ACS Synth Biol 2013; 2:194-202. [PMID: 23656478 DOI: 10.1021/sb300120n] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We demonstrated the generality of a strategy for photoswitching the activity of functional oligonucleotides by modulating their topological structure. Our strategy was proved to be versatile because it can be used to photoregulate functional oligonucleotides, e.g., ribozymes and DNAzymes, which have two binding arms and a catalytic loop. Repeated reversible photoregulation of RNA cleavage by a ribozyme or a DNAzyme was achieved by attaching two photoresponsive strands, artificial oligomers involving azobenzene moieties and nucleobases capable of forming a duplex as the supraphotoswitch. Individual strands were attached to the 3' and 5' ends of a RNA-cleavage oligonucleotide. Thus, the topological structure of the ribozyme or DNAzyme was constrained, and RNA cleavage was greatly suppressed when the supraphotoswitch duplex formed (OFF state). In contrast, RNA cleavage resumed when the supraphotoswitch duplex dissociated (ON state). Light irradiation was used to repeatedly switch the supraphotoswitch between the ON and OFF states so that RNA cleavage activity could be efficiently photoregulated. Analysis of the regulatory mechanism showed that topological constraints suppressed the RNA cleavage by causing both structural changes at the catalytic site and lower binding affinity between the RNA substrates and the functional oligonucleotides.
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Affiliation(s)
- Xingguo Liang
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603,
Japan
- College of Food Science
and
Engineering, Ocean University of China,
Qingdao 266003, China
| | - Mengguang Zhou
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603,
Japan
| | - Kenjiro Kato
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603,
Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603,
Japan
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Kato T, Kashida H, Kishida H, Yada H, Okamoto H, Asanuma H. Development of a Robust Model System of FRET using Base Surrogates Tethering Fluorophores for Strict Control of Their Position and Orientation within DNA Duplex. J Am Chem Soc 2013; 135:741-50. [DOI: 10.1021/ja309279w] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tomohiro Kato
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603,
Japan
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603,
Japan
| | - Hideo Kishida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603,
Japan
| | - Hiroyuki Yada
- Department of Advanced
Materials
Science, The University of Tokyo, 5-1-5
Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Hiroshi Okamoto
- Department of Advanced
Materials
Science, The University of Tokyo, 5-1-5
Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603,
Japan
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Kashida H, Asanuma H. Preparation of supramolecular chromophoric assemblies using a DNA duplex. Phys Chem Chem Phys 2012; 14:7196-204. [DOI: 10.1039/c2cp40520b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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10
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Nishioka H, Liang X, Kato T, Asanuma H. A Photon-Fueled DNA Nanodevice that Contains Two Different Photoswitches. Angew Chem Int Ed Engl 2011; 51:1165-8. [DOI: 10.1002/anie.201106093] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 10/31/2011] [Indexed: 12/19/2022]
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11
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Nishioka H, Liang X, Kato T, Asanuma H. A Photon-Fueled DNA Nanodevice that Contains Two Different Photoswitches. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106093] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Asanuma H, Nishioka H, Ishikawa T, Liang X. Preparation of photoresponsive DNA tethering ortho-methylated azobenzene as a supra-photoswitch. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2011; Chapter 4:Unit 4.45.1-18. [PMID: 21901671 DOI: 10.1002/0471142700.nc0445s46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This unit describes synthetic procedures of photoresponsive DNA via a phosphoramidite monomer composed of D-threoninol as a scaffold and 4-carboxy-2',6'-dimethylazobenzene or 4-carboxy-2'-methylazobenzene that works as a photoswitch more efficiently than previous nonmodified azobenzene (4-phenylazobenzoic acid). With these newly modified-azobenzenes, photoregulatory efficiency of DNA hybridization can be greatly improved. Furthermore, thermal stability of cis-azobenzene of 4-carboxy-2',6'-dimethylazobenzene remarkably increases compared with the previous non-modified azobenzene.
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Ke YZ, Lee SL, Chen CH, Luh TY. Unsymmetrical polymeric ladderphanes by sequential polymerization: a new approach for the template synthesis of polymers with well-defined chain length and narrow polydispersity. Chem Asian J 2011; 6:1748-51. [PMID: 21341375 DOI: 10.1002/asia.201000877] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Indexed: 11/07/2022]
Affiliation(s)
- Yuan-Zhen Ke
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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14
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Design of a Functional Nanomaterial with Recognition Ability for Constructing Light-Driven Nanodevices. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-3-642-18305-8_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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Zhou M, Liang X, Mochizuki T, Asanuma H. A light-driven DNA nanomachine for the efficient photoswitching of RNA digestion. Angew Chem Int Ed Engl 2010; 49:2167-70. [PMID: 20175178 DOI: 10.1002/anie.200907082] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mengguang Zhou
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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16
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Kashida H, Sekiguchi K, Liang X, Asanuma H. Accumulation of Fluorophores into DNA Duplexes To Mimic the Properties of Quantum Dots. J Am Chem Soc 2010; 132:6223-30. [DOI: 10.1021/ja101007d] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Koji Sekiguchi
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Xingguo Liang
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
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Zhou M, Liang X, Mochizuki T, Asanuma H. A Light-Driven DNA Nanomachine for the Efficient Photoswitching of RNA Digestion. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907082] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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