【Labs spotlight】 Ohkubo Laboratory

Sugar-, nucleic acid-, & photo-based biomolecules

May 1, 2017

The Department has a variety of laboratories for Life Science and Technology, in which cutting-edge innovative research is being undertaken not only in basic science and engineering but also in the areas of medicine, pharmacy, agriculture, and multidisciplinary sciences.

This "Spotlight" series features a laboratory from the Department and introduces you to the laboratory's research projects and outcomes. This time we focus on Ohkubo Laboratory.

Associate Professor Akihiro Ohkubo

Life Science and Technology
Associate Professor Akihiro Ohkubo

Degree	PhD 2004, Tokyo Institute of Technology
Areas of Research	Organic Chemistry, Bioorganic Chemistry, Nucleic Acid Chemistry.
Keywords	Nucleic Acid Drug, Gene Therapy, Chemical Synthesis of Modified Oligonucleotide.
Website	Yuasa and Ohkubo Laboratory (Japanese)

Research interest

New strategy for gene therapy.

Development of a new method of splicing correction using chemically modified U1 snRNA.

New nucleic acid drug.

Design and synthesis of triplex forming oligonucleotides that can bind to the corresponding DNA duplexes strongly and accurately.

U1 snRNA

Triplex forming oligonucleotide

Selected publications

[1] A new modified cytosine base capable of base pairing with guanine using four hydrogen bonds. K. Yamada, Y. Masaki, H. Tsunoda, A. Ohkubo, K. Seio, M. Sekine, Org Biomol Chem., 12, 2255-2262 (2014).
[2] 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. Y. Masaki, R. Miyasaka, K. Hirai, T. Kanamori, H. Tsunoda, A. Ohkubo, K. Seio, M. Sekine, Org Biomol Chem., 12, 1157-1162 (2014)
[3] Assembly of pyrene-modified DNA/RNA duplexes incorporating a G-rich single strand region. K. Seio, M. Tokugawa, H. Tsunoda, A. Ohkubo, H. Arisaka, M. Sekine, Bioorg Med Chem Lett., 23, 6822-6824 (2013).
[4] Modified oligodeoxynucleotide primers for reverse-transcription of target RNAs that can discriminate among length variants at the 3′-terminus. Y. Iijima, S. Kojima, E. Kodama, S. Kurohagi, T. Kanamori, Y. Masaki, A. Ohkubo, M. Sekine, K. Seio, Org. Biomol. Chem., 11, 8276-8282 (2013).
[5] Chemical synthesis of U1 snRNA derivatives. A. Ohkubo, Y. Kondo, M. Suzuki, H. Kobayashi, T. Kanamori, Y. Masaki, K. Seio, K. Nagai, M. Sekine, Org. Lett., 15, 4386-4389 (2013).
[6] Fluorescent properties of oligonucleotides doubly modified with an indole-fused cytosine analog and 2-aminopurine. K. Seio, T. Kanamori, M. Tokugawa, H. Ohzeki, Y. Masaki, H. Tsunoda, A. Ohkubo, M. Sekine, Bioorg. Med. Chem., 21, 3197-3201 (2013).
[7] Base recognition of gap sites in DNA-DNA and DNA-RNA duplexes by short oligonucleotides. K. Yamada, A. Ohkubo, Y. Esaka, T. Kanamori, Y. Masaki, K. Seio, M. Sekine, Bioorg. Med. Chem. Lett., 23, 3448-3451 (2013).
[8] Remarkable stabilization of antiparallel DNA triplexes by strong stacking effects of consecutively modified nucleobases containing thiocarbonyl groups. K. Yamada, Y. Hattori, T. Inde, T. Kanamori, A. Ohkubo, K. Seio, and M. Sekine, Bioorg. Med. Chem. Lett., 23, 776-778 (2013).
[9] Prediction of the stability of modified RNA duplexes based on deformability analysis: oligoribonucleotide derivatives modified with 2'-O-cyanoethyl-5-propynyl-2-thiouridine as a promising component. Y. Masaki, R. Miyasaka, K. Hirai, H. Tsunoda, A. Ohkubo, K. Seio, M. Sekine, Chem. Comm., 48, 7313-7315 (2012).
[10] Synthesis and properties of cationic 2'-O-[N-(4-aminobutyl)carbamoyl] modified oligonucleotides. K. Seio, M. Tokugawa, T. Kanamori, H. Tsunoda, A. Ohkubo, M. Sekine, Bioorg. Med. Chem. Lett., 22, 2470-2473 (2012).
[11] Formation of new base pairs between inosine and 5-methyl-2-thiocytidine derivatives. A. Ohkubo, Y. Nishino, Y. Ito, H. Tsunoda, K. Seio, and M. Sekine, Org. Biomol. Chem., 10, 2008-2010 (2012).
[12] Development of an efficient method for phosphorodiamidate bond formation by using inorganic salts. T. Harakawa, H. Tsunoda, A. Ohkubo, K. Seio, and M. Sekine, Bioorg. Med. Chem. Lett., 22, 1445-1447 (2012).
[13] Synthesis of 5'-terminal capped oligonucleotide using O-N phosphoryl migration of phosphoramidite derivatives. A. Ohkubo, N. Tago, A. Yokouchi, Y. Nishino, K. Yamada, H. Tsunoda, K. Seio, M. Sekine, Org. Lett., 14, 10-13 (2012).
[14] Short-RNA selective binding of oligonucleotides modified using adenosine and guanosine derivatives that possess cyclohexyl phosphates as substituents. K. Seio, S. Kurohagi, E. Kodama, H. Tsunoda, A. Ohkubo and M. Sekine, Org. Biomol. Chem., 10, 994-1006 (2012).
[15] DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes. T. Kanamori, Y. Masaki, M. Mizuta, H. Tsunoda, A. Ohkubo, M. Sekine, K. Seio, Org. Biomol. Chem., 10, 1007-1013 (2012).
[16] Stable triplex formation using the strong stacking effect of consecutive thionucleoside moieties. A. Ohkubo, Y. Nishino, A. Yokouchi, Y. Ito, Y. Noma, Y. Kakishima, Y. Masaki, H. Tsunoda, K. Seio, M. Sekine, Chem. Comm., 47, 12556-12558 (2011).
[17] Biochemical behavior of N-oxidized cytosine and adenine bases in DNA polymerase-mediated primer extension reactions. H. Tsunoda, T. Kudo, Y. Masaki, A. Ohkubo, K. Seio, M. Sekine, Nucleic Acids Res., 39, 2995-3004 (2011).
[18] Synthesis of 2'-O-[2-(N-Methylcarbamoyl)ethyl]ribonucleosides Using Oxa-Michael Reaction and Chemical and Biological Properties of Oligonucleotide Derivatives Incorporating These Modified Ribonucleosides. Y. Takeshi, N. Okaniwa, H. Saneyoshi, A. Ohkubo, K. Seio, T. Nagata, Y. Aoki, S. Takeda, M. Sekine, J. Org. Chem., 76, 3042-3053 (2011).
[19] Synthesis and triplex-forming properties of oligonucleotides containing thio-substituted C-nucleoside 4-thiopseudoisocytidine. S. Cao, I. Okamoto, H. Tsunoda, A. Ohkubo, K. Seio, M. Sekine, Tetrahedron Lett., 52, 407-410 (2011).
[20] Synthesis and hybridization properties of 2'-O-methylated oligoribonucleotides incorporating 2'-O-naphthyluridines. M. Sekine, Y. Oeda, Y. Iijima, H. Taguchi, A. Ohkubo, K. Seio, Org. Biomol. Chem., 9, 210-218 (2011).
[21] Synthesis of oligodeoxynucleotides using fully protected deoxynucleoside 3'-phosphoramidite building blocks and base recognition of oligodeoxynucleotides incorporating N3-cyano-ethylthymine. H. Tsunoda, T. Kudo, A. Ohkubo, K. Seio, M. Sekine, Molecules, 15, 7509-7531 (2010).
[22] Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one. E. C. M. Juan, S. Shimizu, X. Ma, T. Kurose, T. Haraguchi, F. Zhang, M. Tsunoda, A. Ohkubo, M. Sekine, T. Shibata, C. L. Millington, D. M. Williams, A. Takénaka, Nucleic Acids Res., 38, 6737-6745 (2010).
[23] Synthesis and hybridization properties of oligonucleotides incorporating Bi- and Tri-cyclic cytosine derivatives. A. Ohkubo, T. Sakaue, H. Tsunoda, K. Seio, M. Sekine, Chem. Lett., 39, 726-727 (2010).
[24] Synthesis of oligodeoxynucleotides using the oxidatively cleavable 4-methoxytritylthio (MMTrS) group for protection of the 5'-hydroxyl group. K. Seio, M. Shiraishi, E. Utagawa, A. Ohkubo, M. Sekine, New J. Chem., 34, 984-992 (2010).
[25] Oligonucleotide synthesis involving deprotection of amidine-type protecting groups for nucleobases under acidic conditions. A. Ohkubo, Y. Kuwayama, Y. Nishino, H. Tsunoda, K. Seio, M. Sekine, Org. Lett., 12, 2496-2499 (2010).
[26] Linear relationship between deformability and thermal stability of 2'-O-modified RNA hetero duplexes. Y. Masaki, H. A. Ohkubo, K. Seio, M. Sekine, J. Phys. Chem. B., 114, 2517-2524 (2010).
[27] Synthesis of 6-N-(benzothiazol-2-yl)deoxyadenosine and its exciton-coupled circular dichroism. Y. Masaki, H. A. Ohkubo, K. Seio, M. Sekine, Bioorg. Med. Chem., 18, 567-572 (2010).
[28] Microwave-assisted synthesis of 2'-O-aryluridine derivatives. Y. Oeda, Y. Iijima, H. Taguchi, A. Ohkubo, K. Seio, M. Sekine, Org. Lett., 11, 5682-5585 (2009).
[29] Synthesis and hybridization of 2'-O-methyl-RNAs incorporating 2'-O-carbamoyluridine and unique participation of the carbamoyl group in U-G base pair. K. Seio, R. Tawarada, T. Sasami, M. Serizawa, M. Ise, A. Ohkubo, M. Sekine, Bioorg. Med. Chem., 17, 7275-7280 (2009).
[30] Synthesis and properties of nucleoside derivatives acylated by chemically stable 2-(trimethylsilyl)benzoyl group. K. Yamada, H. Taguchi, A. Ohkubo, K. Seio, M. Sekine, Bioorg. Med. Chem., 17, 5928-5932 (2009).
[31] Fluorescence properties of pyrimidopyrimidoindole nucleoside dC(PPI) incorporated into oligodeoxynucleotides. M. Mizuta, K. Seio, A. Ohkubo, M. Sekine, J. Phys. Chem. B., 113, 9562-9569 (2009).
[32] Efficient solid-phase synthesis of oligodeoxynucleotides having a 5'-terminal 2,2,7-trimethylguanosine pyrophosphate linkage. A. Ohkubo, R. Kasuya, K. Aoki, A. Kobori, H. Taguchi, K. Seio, M. Sekine, Bioorg. Med. Chem., 17, 4819-4824 (2009).
[33] Synthesis of terminally modified oligonucleotides and their hybridization dependence on the size of the target RNAs. K. Seio, Y. Takaku, K. Miyazaki, S. kurohagi, Y. Masaki, A. Ohkubo, M. Sekine, Org. Biomol. Chem., 7, 2440-2451 (2009).
[34] Computational evaluation of the stability of 2'-O-methyl-RNA/RNA duplexes incorporating 3-deazaguanine derivatives by ab initio calculations and a molecular dynamics simulation. T. Sasami, R. Tawarada, A. Ohkubo, M. Sekine, K. Seio, J. Mol. Struct. (Theochem), 899, 54-60 (2009).
[35] Introduction of 3'-terminal nucleosides having a silyl-type linker into polymer supports without base protection. A. Ohkubo, Y. Noma, K. Aoki, H. Tsunoda, K. Seio, M. Sekine, J. Org. Chem., 74, 2817-2823 (2009).
[36] Synthesis and triplex formation of oligonucleotides containing 8-thioxodeoxyadenosine. K. Miyata, R. tamamushi, H. Tsunoda, A. Ohkubo, K. Seio, M. Sekine, Org. Lett., 11, 605-608 (2009).
[37] New thermolytic carbamoyl groups for the protection of nucleobases. A. Ohkubo, R. Kasuya, K. Miyata, H. Tsunoda, K. Seio, M. Sekine, Org. Biomol. Chem., 7, 687-694 (2009).
[38] Synthesis of oligodeoxynucleotides incorporating 2-N-carbamoylguanine and evaluation of the hybridization properties. T. Sasami, Y. Odawara, A. Ohkubo, K. Seio, M. Sekine; Bioorg. Med. Chem., 16, 8287-8293 (2008).
[39] Hybridization-dependent fluorescence of oligodeoxynucleotides incorporating new pyrene-modified adenosine residues. K. Seio, M. Mizuta, K. Tasaki, K. Tamaki, A. Ohkubo, M. Sekine. Bioorg. Med. Chem., 16, 8287-8293 (2008).
[40] New nucleotide pairs for stable DNA triplexes stabilized by stacking interaction. M. Mizuta, J. Banba, T. Kanamori, R. Tawarada, A. Ohkubo, M. Sekine, K. Seio, J. Am. Chem. Soc., 130, 9622-9623 (2008).
[41] O-selective condensation using P-N bond cleavage in RNA synthesis without base protection. A. Ohkubo, Y. Kuwayama, T. Kudo, H. Tsunoda, K. Seio, M. Sekine, Org. Lett., 10, 2793-2796 (2008).
[42] Synthesis and hybridization properties of 2'-O-(tetrazol-5-yl)ethyl-modified oligonucleotides. H. Saneyoshi, K. Tamaki, A. Ohkubo, K. Seio, M. Sekine, Tetrahedron, 64, 4370-4376. (2008)
[43] Efficient synthesis of functionalized oligodeoxyribonucleotides with base-labile groups using a new silyl linker. A. Ohkubo, R. Kasuya, K. Aoki, A. Kobori, H. Taguchi, K. Seio, M. Sekine, Bioorg. Med. Chem., 16, 5345-5351 (2008).
[44] "Protected DNA Probes (PDP)" capable of strong hybridization without removal of base protecting groups. A. Ohkubo, R. Kasuya, K. Sakamoto, K. Miyata, H. Taguchi, H. Nagasawa, T. Tsukahara, T. Watanobe, Y. Maki, K. Seio, M. Sekine, Nucleic Acids Res., 36, 1952-1964 (2008).
[45] Synthesis and properties of DNA oligomers containing 2'-deoxynucleoside-N-oxide derivatives. H. Tsunoda, A. Ohkubo, H. Taguchi, K. Seio, M. Sekine, J. Org. Chem., 73, 1217-1224 (2008).
[46] Synthesis and properties of oligodeoxynucleotides containing 5-carboxy-2'-deoxycytidines: M. Sumino, A. Ohkubo, H. Taguchi, K. Seio, M. Sekine, Bioorg. Med. Chem. Lett., 18, 274-277 (2008).
[47] A pyrimidopyrimidoindole nucleoside (dC(PPI)): Photophysical properties and thermal stability of the modified DNA duplexes. M. Mizuta, K. Seio, K. Miyata, A. Ohkubo, H. Taguchi, M. Sekine, Nucleosides, Nucleotides, Nucleic Acids, 26, 1335-1338 (2007).
[48] Facile synthesis of 2'-O-cyanoethyluridine by ring-opening reaction of 2,2'-anhydrouridine with cyanoethyl trimethylsilyl ether in the presence of BF3 center dot Et2O. H. Saneyoshi, I, Okamoto, Y. Masaki, A. Ohkubo, K. Seio, M. Sekine, Tetrahedron. Lett., 48, 8554-8557 (2007).
[49] Synthesis and hybridization properties of oligodeoxynucleotides with long-chain linker. K. Seio, T. Terada, M. Mizuta, A. Ohkubo, H. Taguchi, M. Sekine, Helvetica Chemica. Acta., 90, 1946-1965 (2007).
[50] Synthesis of branched oligonucleotides with three different sequences using an oxidatively removable tritylthio group. E. Utagawa, A. Ohkubo, M. Sekine, K. Seio, J. Org. Chem., 72, 8259-8266 (2007).
[51] An effective method for the in situ synthesis of DNA-CPG conjugates using chemical ligation technology as tools for SNP analysis. A. Ohkubo, H. Taguchi, K. Seio, H. Nagasawa, T. Tsukahara, M. Sekine, Bioorg. Med. Chem. Lett., 17, 5969-5973 (2007).
[52] Synthesis and hybridization properties of oligodeoxynucleotides incorporating 2-N-carbamoylguanine derivatives as guanine analogs. T. Sasami, Y, Odawara, A. Ohkubo, M. Sekine, K. Seio, Tetrahedron. Lett., 48, 5325-5329 (2007).
[53] A new hydrophobic linker effective for the in situ synthesis of DNA-CPG conjugates as tools for SNP analysis. A. Ohkubo, H. Taguchi, K. Seio, H. Nagasawa, T. Tsukahara, M. Sekine, Tetrahedron. Lett., 48, 5147-5150 (2007).
[54] Highly selective recognition of cytosine over uracil and adenine by a guanine analogue, 2-N-acetyl-3-deazaguanine, in 2'-O-methyl-RNA/RNA and DNA duplexes. K. Seio, T. Sasami, A. Ohkubo, K. Ando, M. Sekine, J. Am. Chem. Soc., 129, 1026-1027 (2007).
[55] Synthesis and fluorescent properties of bi- and tricyclic 4-N-carbamoyldeoxycytidine derivatives. K. Miyata, R. Mineo R. Tamamushi, M. Mizuta, A. Ohkubo, H. Taguchi, K. Seio, M. Sekine, J. Org. Chem., 72, 102-108 (2007).
[56] Conformational studies of 4-N-carbamoyldeoxycytidine derivatives and synthesis and hybridization properties of oligodeoxyribonucleotides incorporating these modified bases. K. Miyata, R. Tamamushi, A. Ohkubo, H. Taguchi, K. Seio, M. Sekine, Eur. J. Org. Chem., 16, 3626-3637 (2006).
[57] Synthesis and biological properties of new phosmidosine analogs having an N-acylsulfamate linkage. H. Taguchi, A, Ohkubo, K. Seio, H. Kakeya, H. Osada, T. Sasaki, M. Sekine, Nucleosides, Nucleotides, Nucleic Acids, 25, 647-654 (2006).
[58] Synthesis and properties of a new fluorescent bicyclic 4-N-carbamoyldeoxycytidine derivative. K. Miyata, R. Tamamushi, A. Ohkubo, H. Taguchi, K. Seio, T. Santa, M. Sekine, Org. Lett., 8, 1545-1548 (2006).
[59] Synthesis of oligodeoxyribonucleotides containing hydroxymethylphosphonate bonds in the phosphoramidite method and their hybridization properties. A. Ohkubo, K. Aoki, Y. Ezawa, Y. Sato, H. Taguchi, K. Seio, M. Sekine, Tetrahedron. Lett., 46, 8953-8957 (2005).
[60] Convenient synthesis of N-unprotected deoxynucleoside 3'-phosphoramidite building blocks by selective deacylation of N-acylated species and their facile conversion to other N-functionalized derivatives. A. Ohkubo, K. Sakamoto, K. Miyata, H. Taguchi, K. Seio, M. Sekine, Org. Lett., 7, 5389-5392 (2005).
[61] Chemically stabilized phenylboranylidene groups having a dimethoxytrityl group as a colorimetrically detectable protecting group designed for cis-1,2-diol functions of ribonucleosides in the Solid-Phase Synthesis of m22,2G5'ppT. M. Sekine, M. Aoyagi, M. Ushioda, A. Ohkubo, K, Seio, J. Org. Chem., 70, 8400-8408 (2005).
[62] Synthesis and hybridization affinity of oligodeoxyribonucleosides incorporating 4-N-(N-arylcarbamoyl)deoxycytidine derivatives. K. Miyata, R. Tamamushi, A. Ohkubo, H. Taguchi, K. Seio, M. Sekine, Tetrahedron Lett., 45, 9365-9368 (2004).
[63] O-Selectivity and utility of phosphorylation mediated by a phosphite intermediate in N-unprotected phosphoramidite method. A. Ohkubo, K. Seio, M. Sekine, J. Am. Chem. Soc., 126, 10884-10896 (2004).
[64] A new approach for pyrophosphate bond formation starting from phosphoramidite derivatives by use of 6-trifluoromethyl-1-hyroxybenzotriazole-mediated O-N phosphoryl migration. A. Ohkubo, K, Seio, M. Sekine, Tetrahedron Lett., 45, 979-982 (2004).
[65] A new strategy for the synthesis of oligodeoxynucleptides directed toward perfect O-selective internucleotidic bond formation without base protection. A. Ohkubo, K, Seio, M. Sekine, Tetrahedron Lett., 45, 363-366 (2004).
[66] Proton-Block strategy for the synthesis of oligodeoxynucleotides without base protection, capping reaction, and P-N bond cleavage reaction. M. Sekine, A. Ohkubo, K, Seio, J. Org. Chem., 68, 5478-5492 (2003).
[67] 2-(Azidomethyl)benzoyl as a new protecting group in nucleosides. T. Wada, A. Ohkubo, A. Mochizuki, M. Sekine, Tetrahedron Lett., 42, 1069-1072 (2001).