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Kanamori T, Masaki Y, Oda Y, Ohzeki H, Ohkubo A, Sekine M, Seio K. DNA triplex-based fluorescence turn-on sensors for adenosine using a fluorescent molecular rotor 5-(3-methylbenzofuran-2-yl) deoxyuridine. Org Biomol Chem 2019; 17:2077-2080. [DOI: 10.1039/c8ob02747a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence turn-on detection of adenosine based on microenvironmental and conformational changes of a fluorescent molecular rotor in the DNA triplex is reported.
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Affiliation(s)
- Takashi Kanamori
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Yoshiaki Masaki
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Yuki Oda
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Hiroki Ohzeki
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Akihiro Ohkubo
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Mitsuo Sekine
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Kohji Seio
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
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2
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Masaki Y, Yamamoto K, Inde T, Yoshida K, Maruyama A, Nagata T, Tanihata J, Takeda S, Sekine M, Seio K. Synthesis of 2'-O-(N-methylcarbamoylethyl) 5-methyl-2-thiouridine and its application to splice-switching oligonucleotides. Bioorg Med Chem Lett 2018; 29:160-163. [PMID: 30551900 DOI: 10.1016/j.bmcl.2018.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 01/16/2023]
Abstract
The effect of 2'-O-(N-methylcarbamoyl)ethyl (MCE) modification on splice-switching oligonucleotides (SSO) was systematically evaluated. The incorporation of five MCE nucleotides at the 5'-termini of SSOs effectively improved the splice switching effect. In addition, the incorporation of 2'-O-(N-methylcarbamoylethyl)-5-methyl-2-thiouridine (s2TMCE), a duplex-stabilizing nucleotide with an MCE modification, into SSOs further improved splice switching. These SSOs may be useful for the treatment of genetic diseases associated with splicing errors.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Keishi Yamamoto
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Takeshi Inde
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Keita Yoshida
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Atsuya Maruyama
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Jun Tanihata
- Department of Molecular Therapy, Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy, Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo 187-8502, Japan
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, 4259 J2-16, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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3
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Masaki Y, Ito H, Oda Y, Yamazaki K, Tago N, Ohno K, Ishii N, Tsunoda H, Kanamori T, Ohkubo A, Sekine M, Seio K. Enzymatic synthesis and reverse transcription of RNAs incorporating 2'-O-carbamoyl uridine triphosphate. Chem Commun (Camb) 2018; 52:12889-12892. [PMID: 27738673 DOI: 10.1039/c6cc05796a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Enzymatic synthesis and the reverse transcription of RNAs containing 2'-O-carbamoyl uridine were evaluated. A mild acidic deprotection procedure allowed the synthesis of 2'-O-carbamoyl uridine triphosphate (UcmTP). UcmTP was incorporated correctly into long RNAs, and its fidelity during reverse transcription using SuperScript III was sufficient for RNA aptamer selection.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Hyugo Ito
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Yuki Oda
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Kazufumi Yamazaki
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Nobuhiro Tago
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Kentaro Ohno
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Nozomi Ishii
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Hirosuke Tsunoda
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Takashi Kanamori
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Akihiro Ohkubo
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Japan.
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4
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Masaki Y, Sekine M, Seio K. Deformability Calculation for Estimation of the Relative Stability of Chemically Modified RNA Duplexes. ACTA ACUST UNITED AC 2017; 68:7.27.1-7.27.10. [PMID: 28252179 DOI: 10.1002/cpnc.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chemical modification of RNA duplexes alters their stability. We have attempted to develop a computational approach to estimate the thermal stability of chemically modified duplexes. These studies revealed that the deformability of chemically modified RNA duplexes, calculated from molecular dynamics simulations, could be used as a good indicator for estimating the effect of chemical modification on duplex thermal stability. This unit describes how deformability calculation can be applied to estimate the relative stability of chemically modified RNA duplexes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Mitsuo Sekine
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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5
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Izgu EC, Oh SS, Szostak JW. Synthesis of activated 3'-amino-3'-deoxy-2-thio-thymidine, a superior substrate for the nonenzymatic copying of nucleic acid templates. Chem Commun (Camb) 2016; 52:3684-6. [PMID: 26857159 DOI: 10.1039/c5cc10317g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a scalable synthesis of 3'-amino-3'-deoxy-2-thio-thymidine-5'-phosphoro-2-methylimidazolide, an activated monomer that can copy adenosine residues in nucleic acid templates rapidly without a polymerase. The sulfur atom substitution enhances the rate of template copying by 5-fold compared with the 3'-amino-3'-deoxy-T monomer, while the 3'-amino monomers exhibit a 2- to 30-fold enhancement compared with their ribonucleotide counterparts.
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Affiliation(s)
- Enver Cagri Izgu
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA. and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Seung Soo Oh
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA. and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, USA. and Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA and Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Cambridge, Massachusetts 02138, USA
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6
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Tokugawa M, Masaki Y, Canggadibrata JC, Kaneko K, Shiozawa T, Kanamori T, Grøtli M, Wilhelmsson LM, Sekine M, Seio K. 7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein. Chem Commun (Camb) 2016; 52:3809-12. [DOI: 10.1039/c5cc09700b] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
7-(Benzofuran-2-yl)-7-deazadeoxyguanosine (BFdG) was synthesized and incorporated into an oligodeoxynucleotide (ODN).
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Affiliation(s)
- Munefumi Tokugawa
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Yoshiaki Masaki
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | | | - Kazuhei Kaneko
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takashi Shiozawa
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takashi Kanamori
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- S-41296 Gothenburg
- Sweden
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry
- Chalmers University of Technology
- S-41296 Gothenburg
- Sweden
| | - Mitsuo Sekine
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Kohji Seio
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
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Yamada T, Masaki Y, Okaniwa N, Kanamori T, Ohkubo A, Tsunoda H, Seio K, Sekine M. Synthesis and properties of oligonucleotides modified with 2'-O-(2-carboxyethyl)nucleotides and their carbamoyl derivatives. Org Biomol Chem 2015; 12:6457-64. [PMID: 25019462 DOI: 10.1039/c4ob01260g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
2'-O-Methyl oligoribonucleotides with four kinds of 2'-O-modified uridine derivatives were synthesised. Their duplex stability, hydration behavior and exonuclease resistance were studied by spectroscopic analyses and molecular dynamics simulations. Consequently, 2'-O-modification of the uridine residue with 2-carbamoylethyl or 2-(N-methylcarbamoyl)ethyl groups resulted in a significant improvement of the exonuclease resistance without the loss of duplex stability.
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Affiliation(s)
- Takeshi Yamada
- Department of Life Science, Tokyo Institute of Technology, J2-12, 4259 Nagatsuta-cho, Midoriku, Yokohama, Japan.
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Masaki Y, Inde T, Nagata T, Tanihata J, Kanamori T, Seio K, Takeda S, Sekine M. Enhancement of exon skipping in mdx52 mice by 2′-O-methyl-2-thioribothymidine incorporation into phosphorothioate oligonucleotides. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00468j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Incorporation of 2′-O-methyl-2-thioribothymidine (s2Tm) into antisense oligoribonucleotides significantly enhanced the exon skipping activity in Duchenne muscular dystrophy model mice.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Takeshi Inde
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Tetsuya Nagata
- Department of Molecular Therapy
- Institute of Neuroscience
- National Center of Neurology and Psychiatry
- Kodaira
- Japan
| | - Jun Tanihata
- Department of Molecular Therapy
- Institute of Neuroscience
- National Center of Neurology and Psychiatry
- Kodaira
- Japan
| | - Takashi Kanamori
- Education Academy of Computational Life Sciences
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Kohji Seio
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Shin'ichi Takeda
- Department of Molecular Therapy
- Institute of Neuroscience
- National Center of Neurology and Psychiatry
- Kodaira
- Japan
| | - Mitsuo Sekine
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama
- Japan
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Yamada K, Masaki Y, Tsunoda H, Ohkubo A, Seio K, Sekine M. A new modified cytosine base capable of base pairing with guanine using four hydrogen bonds. Org Biomol Chem 2014; 12:2255-62. [PMID: 24569493 DOI: 10.1039/c3ob42420k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides, containing 4-N-(1H-pyrrol-2-ylcarbonyl)deoxycytidine (dC(Pyc)) and related derivatives, were synthesized via deprotection using 1.5 M NaOMe/MeOH. Among them, oligodeoxynucleotides containing dC(Pyc) exhibited a higher hybridization affinity for DNA and RNA than the unmodified oligodeoxynucleotides. Comparative analysis between dC(Pyc) and its derivatives by molecular dynamic simulation indicated that the C(Pyc) residue could form four hydrogen bonds with the opposite G nucleobase keeping a more planar structure than the C(Inc) residue where the Pyc group was replaced with a 1H-indol-2-ylcarbonyl group.
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Affiliation(s)
- Ken Yamada
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501 Japan.
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Masaki Y, Miyasaka R, Hirai K, Kanamori T, Tsunoda H, Ohkubo A, Seio K, Sekine M. Properties of 5- and/or 2-modified 2′-O-cyanoethyl uridine residue: 2′-O-cyanoethyl-5-propynyl-2-thiouridine as an efficient duplex stabilizing component. Org Biomol Chem 2014; 12:1157-62. [DOI: 10.1039/c3ob41983e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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