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Yamaoka K, Oikawa R, Abe N, Nakamoto K, Tomoike F, Hashiya F, Kimura Y, Abe H. Completely Chemically Synthesized Long DNA Can be Transcribed in Human Cells. Chembiochem 2021; 22:3273-3276. [PMID: 34519401 DOI: 10.1002/cbic.202100312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/11/2021] [Indexed: 11/10/2022]
Abstract
Chemical ligation reaction of DNA is useful for the construction of long functional DNA using oligonucleotide fragments that are prepared by solid phase chemical synthesis. However, the unnatural linkage structure formed by the ligation reaction generally impairs the biological function of the resulting ligated DNA. We achieved the complete chemical synthesis of 78 and 258 bp synthetic DNAs via multiple chemical ligation reactions with phosphorothioate and haloacyl-modified DNA fragments. The latter synthetic DNA, coding shRNA for luciferase genes with a designed truncated SV promoter sequence, successfully induced the expected gene silencing effect in HeLa cells.
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Affiliation(s)
- Kazuki Yamaoka
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ryota Oikawa
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kosuke Nakamoto
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Hiroshi Abe
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST, Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.,Institute for Glyco-core Research, Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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Prinzen AL, Saliba D, Hennecker C, Trinh T, Mittermaier A, Sleiman HF. Amplified Self‐Immolative Release of Small Molecules by Spatial Isolation of Reactive Groups on DNA‐Minimal Architectures. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alexander L. Prinzen
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Daniel Saliba
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Christopher Hennecker
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Anthony Mittermaier
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
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3
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Prinzen AL, Saliba D, Hennecker C, Trinh T, Mittermaier A, Sleiman HF. Amplified Self‐Immolative Release of Small Molecules by Spatial Isolation of Reactive Groups on DNA‐Minimal Architectures. Angew Chem Int Ed Engl 2020; 59:12900-12908. [PMID: 32277788 DOI: 10.1002/anie.202001123] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/24/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Alexander L. Prinzen
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Daniel Saliba
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Christopher Hennecker
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Anthony Mittermaier
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 rue Sherbrooke West Montreal QC, H3A 0B8 Canada
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Gauthier F, Beltran F, Biscans A, Debart F, Dupouy C, Vasseur JJ. A 2',2'-disulfide-bridged dinucleotide conformationally locks RNA hairpins. Org Biomol Chem 2019; 16:3181-3188. [PMID: 29645048 DOI: 10.1039/c8ob00328a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The synthesis and the impact of a disulfide bridge between 2'-O-positions of two adjacent nucleotides in an RNA duplex and in the loop of RNA hairpins are reported. The incorporation of this 2',2'-disulfide (S-S) bridge enabled thermal and enzymatic stabilization of the hairpin depending on its position in the loop. The influence of the disulfide bridge on RNA folding was studied at the HIV Dimerization Initiation Site (DIS) as an RNA sequence model. We have shown that this S-S bridge locked the hairpin form, whereas the extended duplex form was generated after the reduction of the disulfide bond in the presence of tris(2-carboxyethyl)phosphine or glutathione. Thus, the S-S bridge can be useful for understanding RNA folding; an RNA molecular beacon locked by an S-S bridge was also investigated as a sensor for the detection of glutathione.
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Affiliation(s)
- Florian Gauthier
- IBMM, UMR 5247, Univ. Montpellier, CNRS, ENSCM, Montpellier, France.
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Meyer A, Vasseur JJ, Dumy P, Morvan F. Phthalimide-Oxy Derivatives for 3′- or 5′-Conjugation of Oligonucleotides by Oxime Ligation and Circularization of DNA by “Bis- or Tris-Click” Oxime Ligation. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Albert Meyer
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
| | - François Morvan
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
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6
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Ali Shah MI, Xu ZY, Liu L, Jiang YY, Shi J. Mechanism for the enhanced reactivity of 4-mercaptoprolyl thioesters in native chemical ligation. RSC Adv 2016. [DOI: 10.1039/c6ra13793h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Ring-strain-precluded strategy benefiting from entropy effects and n → π* orbital interaction, enhances the reactivity of C-terminal prolyl thioesters in NCL.
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Affiliation(s)
| | - Zhe-Yuan Xu
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
| | - Lei Liu
- Department of Chemistry
- Tsinghua University
- Beijing 100084
- China
| | - Yuan-Ye Jiang
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
| | - Jing Shi
- Collaborative Innovation Center of Chemistry for Energy Materials
- CAS Key Laboratory of Urban Pollutant Conversion
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
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Barbeyron R, Martin AR, Jean-Jacques Vasseur JJV, Michael Smietana MS. DNA-templated borononucleic acid self assembly: a study of minimal complexity. RSC Adv 2015. [DOI: 10.1039/c5ra20767c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The minimal degree of sequence complexity needed for DNA-templated self-assembly of bifunctional oligonucleotides able to form internucleosidic boronate linkages has been studied.
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Affiliation(s)
- Renaud Barbeyron
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
| | - Anthony R. Martin
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
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Feng J, Lv MF, Lu GP, Cai C. Direct oxidative coupling of thiols and benzylic ethers via C(sp3)–H activation and C–O cleavage to lead thioesters. Org Biomol Chem 2015; 13:677-81. [DOI: 10.1039/c4ob02250e] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
An unprecedented protocol for the synthesis of thioesters via C–H thioesterification and C–O cleavage was developed. This CDC protocol was found convenient and easy-to-handle involving the use of DTBP as the only green oxidant.
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Affiliation(s)
- J. Feng
- Chemical Engineering College
- Nanjing University of Science & Technology
- Nanjing 210094
- P. R. China
| | - M.-F. Lv
- Chemical Engineering College
- Nanjing University of Science & Technology
- Nanjing 210094
- P. R. China
| | - G.-P. Lu
- Chemical Engineering College
- Nanjing University of Science & Technology
- Nanjing 210094
- P. R. China
| | - C. Cai
- Chemical Engineering College
- Nanjing University of Science & Technology
- Nanjing 210094
- P. R. China
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