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Wang X, Wang F, Zhang C, Wang Q. Regulating the proton conductivity of metal organic framework materials through solvent control. NEW J CHEM 2022. [DOI: 10.1039/d2nj00342b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MOFs were used as probes through changes in the proton conductivity caused by changes in solvent molecules.
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Affiliation(s)
- Xinxin Wang
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Fengdong Wang
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chenxi Zhang
- College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Qinglun Wang
- College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Nankai University, Tianjin 300071, P. R. China
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2
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Directly Arylated Oligonucleotides as Fluorescent Molecular Rotors for Probing DNA Single-Nucleotide Polymorphisms. Bioorg Med Chem 2022; 56:116617. [DOI: 10.1016/j.bmc.2022.116617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 11/18/2022]
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3
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Kashida H, Asanuma H. Pseudo Base Pairs that Exhibit High Duplex Stability and Orthogonality through Covalent and Non-covalent Interactions. J SYN ORG CHEM JPN 2021. [DOI: 10.5059/yukigoseikyokaishi.79.1013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University
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Ravi Kumara GS, Seo YJ. Polymerase-mediated synthesis of p-vinylaniline-coupled fluorescent DNA for the sensing of nucleolin protein- c-myc G-quadruplex interactions. Org Biomol Chem 2021; 19:5788-5793. [PMID: 34085078 DOI: 10.1039/d1ob00863c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this paper we report the synthesis of two deoxyuridine derivatives (dUCN2, dUPy)-featuring p-vinylaniline-based fluorophores linked through a propargyl unit at the 5' position-that function as molecular rotors. This probing system proved to be useful for the sensing of gene regulation arising from interactions between this G-quadruplex and nucleolin.
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Affiliation(s)
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea.
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Asanuma H, Murayama K, Kamiya Y, Kashida H. The DNA Duplex as an Aqueous One-Dimensional Soft Crystal Scaffold for Photochemistry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180278] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Keiji Murayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Yukiko Kamiya
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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Kashida H, Asanuma H. Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20160371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hiromu Kashida
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012
| | - Hiroyuki Asanuma
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603
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KASHIDA H, ASANUMA H. Development of Pseudo Base Pairs Which Show High DNA Duplex Stabilities and Orthogonality. KOBUNSHI RONBUNSHU 2017. [DOI: 10.1295/koron.2017-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hiromu KASHIDA
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University
- PRESTO, Japan Science and Technology Agency
| | - Hiroyuki ASANUMA
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University
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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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Esposito V, Russo A, Amato T, Varra M, Vellecco V, Bucci M, Russo G, Virgilio A, Galeone A. Backbone modified TBA analogues endowed with antiproliferative activity. Biochim Biophys Acta Gen Subj 2016; 1861:1213-1221. [PMID: 27663232 DOI: 10.1016/j.bbagen.2016.09.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/13/2016] [Accepted: 09/16/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND The thrombin binding aptamer (TBA) is endowed with antiproliferative properties but its potential development is counteracted by the concomitant anticoagulant activity. METHODS Five oligonucleotides (ODNs) based on TBA sequence (GGTTGGTGTGGTTGG) and containing l-residues or both l-residues and inversion of polarity sites have been investigated by NMR and CD techniques for their ability to form G-quadruplex structures. Furthermore, their anticoagulant (PT assay) and antiproliferative properties (MTT assay), and their resistance in fetal bovine serum have been tested. RESULTS CD and NMR data suggest that the investigated ODNs are able to form right- and left-handed G-quadruplex structures. All ODNs do not retain the anticoagulant activity characteristic of TBA but are endowed with a significant antiproliferative activity against two cancerous cell lines. Their resistance in biological environment after six days is variable, depending on the ODN. CONCLUSIONS A comparison between results and literature data suggests that the antiproliferative activity of the TBA analogues investigated could depends on two factors: a) biological pathways and targets different from those already identified or proposed for other antiproliferative G-quadruplex aptamers, and b) the contribution of the guanine-based degradation products. GENERAL SIGNIFICANCE Modified TBA analogues containing l-residues and inversion of polarity sites lose the anticoagulant activity but gain antiproliferative properties against two cancer cell lines. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Annapina Russo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Teresa Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Michela Varra
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Giulia Russo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy.
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy.
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Doi T, Sakakibara T, Kashida H, Araki Y, Wada T, Asanuma H. Hetero-Selective DNA-Like Duplex Stabilized by Donor-Acceptor Interactions. Chemistry 2015; 21:15974-80. [PMID: 26404181 DOI: 10.1002/chem.201502653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/20/2023]
Abstract
We report on the characterization of a novel hetero-selective DNA-like duplex of pyrene and anthraquinone pseudo base pairs. The pyrene/anthraquinone pairs showed excellent selectivity in hetero-recognition and even trimers were found to form a hetero-duplex. Pyrene and anthraquinone moieties were tethered on acyclic D-threoninol linkers and linked to adjacent residues by using standard phosphoramidite chemistry. When pyrene and anthraquinone were incorporated at pairing positions in complementary strands of natural DNA oligonucleotides, the duplex was stabilized significantly. Moreover, a pyrene hexamer and an anthraquinone hexamer formed a stable artificial hetero-duplex without the assistance of natural base pairs. The pyrene/anthraquinone pair was so stable that even trimers formed a hetero-duplex under conditions in which natural DNA strands of three residues do not.
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Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
| | - Takumi Sakakibara
- 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).,PRESTO (Japan) Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan)
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577 (Japan)
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577 (Japan)
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan).
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Kashida H, Osawa T, Morimoto K, Kamiya Y, Asanuma H. Molecular design of Cy3 derivative for highly sensitive in-stem molecular beacon and its application to the wash-free FISH. Bioorg Med Chem 2015; 23:1758-62. [DOI: 10.1016/j.bmc.2015.02.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 02/13/2015] [Accepted: 02/17/2015] [Indexed: 10/23/2022]
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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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Kashida H, Doi T, Sakakibara T, Hayashi T, Asanuma H. p-Stilbazole Moieties As Artificial Base Pairs for Photo-Cross-Linking of DNA Duplex. J Am Chem Soc 2013; 135:7960-6. [DOI: 10.1021/ja401835j] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiromu Kashida
- Graduate School
of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Tetsuya Doi
- Graduate School
of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Takumi Sakakibara
- Graduate School
of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Takamitsu Hayashi
- Graduate School
of Engineering, 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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Kole GK, Chin CK, Tan GK, Vittal JJ. Silver(I) macrocycles and coordination polymers containing pyridyl carboxylate and phosphine ligands. Polyhedron 2013. [DOI: 10.1016/j.poly.2012.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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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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Kashida H, Hayashi T, Fujii T, Asanuma H. A cationic dye triplet as a unique "glue" that can connect fully matched termini of DNA duplexes. Chemistry 2011; 17:2614-22. [PMID: 21305625 DOI: 10.1002/chem.201003059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Indexed: 11/08/2022]
Abstract
In this study, we propose that three consecutive cationic p-methylstilbazoles tethered on D-threoninols (Z residues) at 5' termini act as a unique "glue" connecting DNA duplexes by their interstrand cluster formation. Interstrand clustering of p-methylstilbazoles (ZZZ triplets) induces narrowing and hypsochromic shift of bands at 350 nm, which can be assigned to the absorption of p-methylstilbazole. However, single-stranded DNA conjugates involving a ZZZ triplet at the 5' terminus of 8-mer native nucleotides is found not to induce such large spectral changes, which implies that the intrinsic self-assembling property of ZZZ triplets is weak. Interestingly, when this conjugate is hybridized with a complementary 8-mer native oligonucleotide, a remarkable spectral change is observed, indicating the dimerization of a duplex through the interstrand clustering of ZZZ triplets. Dimerization of the duplex is also evidenced by cold-spray ionization mass spectrometry. This interstrand clustering is observed only when a ZZZ triplet is tethered to a 5' rather than 3' terminus. Furthermore, the stability of the interstrand cluster increases by increasing the number of nucleobases of the DNA portion, and when mismatched base pairs are incorporated or when a base next to the Z residue is deleted, the stability substantially drops. When we apply the ZZZ triplet to the formation of a nanowire using two complementary DNA conjugates, each of which has a ZZZ triplet at the 5' termini as overhang, we demonstrate the successful formation of a nanowire by native PAGE analysis. Since native sticky ends that have three nucleotides do not serve as "glue", ZZZ triplets with their unique glue-like properties are prime candidates for constructing DNA-based nanoarchitectures.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan
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Kashida H, Sekiguchi K, Higashiyama N, Kato T, Asanuma H. Cyclohexyl “base pairs” stabilize duplexes and intensify pyrene fluorescence by shielding it from natural base pairs. Org Biomol Chem 2011; 9:8313-20. [DOI: 10.1039/c1ob06325a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Ishikawa K, Yamamoto T, Asakawa M, Tezuka Y. Effective Synthesis of Polymer Catenanes by Cooperative Electrostatic/Hydrogen-Bonding Self-Assembly and Covalent Fixation. Macromolecules 2009. [DOI: 10.1021/ma902031j] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kazuyuki Ishikawa
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Takuya Yamamoto
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
| | - Masumi Asakawa
- Nanotube Research Center, National Instutute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Yasuyuki Tezuka
- Department of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8552, Japan
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