Advancing Genetic Alphabet Expansion: Synthesis of 7-(2-Thienyl)-Imidazo[4,5-b]pyridine (Ds) and 4-(4-Pentyne-1,2-diol)-1-Propynyl-2-Nitropyrrole (Diol-Px) for Use in Replicable Unnatural Base Pairs for PCR Applications. H.P. Tan, M. Kimoto, I. Hirao, Curr. Protoc., 4, 2024, e1009 (2024).

Systematic mutation and unnatural base pair incorporation improve riboswitch-based biosensor response time. S. Manna, M. Kimoto, J. Truong, P. Bommisetti, A. Peitz, I. Hirao, M. C. Hammond, ACS Sensors, 8, 4468-4472 (2023).

Strict interactions of fifth letters, hydrophobic unnatural bases, in XenoAptamers with target proteins. M. Kimoto, H.P. Tan, K. Matsunaga, N.A.B.M. Mislan, G. Kawai, I. Hirao. J. Am. Chem. Soc., 145, 20432-441 (2023).

Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase. J. Oh, M. Kimoto, H. Xu, J. Chong, I. Hirao, D. Wang, Nat. Commun., 14, 195 (2023).

Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion. M. Kimoto, H.P. Tan, Y.S. Tan, N.A.B.M. Mislan, I. Hirao, Philos. Trans. R. Soc. Lond. B Biol. Sci., 378, 20220031 (2023).

Genetic code engineering by natural and unnatural base pair systems for the site-specific incorporation of non-standard amino acids into protein. M. Kimoto, I. Hirao, Front. Mol. Biosci., 9, 851646 (2022).

Dye-conjugated spinach RNA by genetic alphabet expansion. K.H. Lee, M. Kimoto, G. Kawai, I. Okamoto, A. Fin, I. Hirao, Chem. Eur. J., 28, e202104396 (2022).

Competitive ELISA for a serologic test to detect dengue serotype-specific anti-NS1 IgGs using high-affinity UB-DNA aptamers. Matsunaga, M. Kimoto, V.W. Lim, T.-L. Thein, S. Vasoo, Y.S. Leo, W. Sun. I. Hirao, Sci. Rep., 11, 18000 (2021).

Uptake mechanisms of cell-internalizing nucleic acid aptamers for applications as pharmacological agents. J. Alamudi, M. Kimoto, I. Hirao, RSC Med. Chem., 12, 1640-1649 (2021).

High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification. K. Matsunaga, M. Kimoto, V.W. Lim, H.P. Tan, Y.Q. Wong, W. Sun, S. Vasoo, Y.S. Leo, I. Hirao, Nucleic Acids Res., 49, 11407-11424 (2021). [Selected as a Breakthrough Article.]

Cognate base-pair selectivity of hydrophobic unnatural bases in DNA ligation by T4 DNA ligase. M. Kimoto, S.H.G. Soh, H.P. Tan, I. Okamoto, I. Hirao, Biopolymers, 112, e23407 (2021).

Genetic Alphabet Expansion Technology by Creating Unnatural Base Pairs. M. Kimoto, I. Hirao, Chem. Soc. Rev., 49, 7602-7626 (2020).

Sanger Gap Sequencing for Genetic Alphabet Expansion of DNA. M. Kimoto, S.H.G. Soh, and I. Hirao, Chembiochem., 21, 2287-2296 (2020).

Molecular affinity rulers: systematic evaluation of DNA aptamers for their applicabilities in ELISA. M. Kimoto, Y.W.S. Lim, I. Hirao, Nucleic Acids Res., 47, 8362-8374 (2019).

DNA sequencing method including unnatural bases for DNA aptamer generation by genetic alphabet expansion. K. Hamashima, Y.T. Soong, K. Matsunaga, M. Kimoto, I. Hirao, ACS Synthetic Biology, 8, 1401-1410 (2019).

Genetic Alphabet Expansion Provides Versatile Specificities and Activities of Unnatural-base DNA Aptamers Targeting Cancer Cells. K. Futami, M. Kimoto, Y.W.S. Lim, I. Hirao, Mol. Ther. Nucleic Acids, 14, 158-170 (2019).

Visual Detection of Amplified DNA by PCR using a Genetic Alphabet Expansion System. R. Yamashige, M. Kimoto, R. Okumura, I. Hirao, J. Am. Chem. Soc., 140, 14038-14041 (2018).

Creation of unnatural base pairs for genetic alphabet expansion toward synthetic xenobiology. K. Hamashima, M. Kimoto, I. Hirao, Curr. Opin. Chem. Biol., 46, 108-114 (2018).

DNA aptamer generation by ExSELEX using genetic alphabet expansion with a mini-hairpin DNA stabilization method. I. Hirao, M. Kimoto, K.H. Lee, Biochimie, 145, 15-21 (2018).

Genetic alphabet expansion biotechnology by creating unnatural base pairs. K.H. Lee, K. Hamashima, M. Kimoto, I. Hirao, Curr. Opin. Biotechnol., 51, 8-15 (2018).

Genetic alphabet expansion transcription generating functional RNA molecules containing a five-letter alphabet including modified unnatural and natural base nucleotides by thermostable T7 RNA polymerase variants. M. Kimoto, A.J. Meyer, I. Hirao, A.D. Ellington, Chem. Comm., 53, 12309-12312 (2017).

Evolving aptamers with unnatural base pairs. M. Kimoto, K. Matsunaga, I. Hirao, Curr. Protoc. Chem. Biol., 9, 315-339 (2017).

Unique Thermal Stability of Unnatural Hydrophobic Ds Bases in Double-Stranded DNAs. M. Kimoto, I. Hirao, ACS Synth. Biol., 6, 1944-1951 (2017).

Structural basis for expansion of the genetic alphabet with an artificial nucleobase pair. K. Betz, M. Kimoto, K. Diederichs, I, Hirao, A. Marx, Angew. Chem. Int. Ed. Engl., 56, 12000-12003 (2017).

Crystal structure of Deep Vent DNA polymerase. Y. Hikida, M. Kimoto, I. Hirao, S. Yokoyama, Biochem. Biophys. Res. Commun., 483, 52-57 (2017).

High-Affinity DNA Aptamer Generation Targeting von Willebrand Factor A1-Domain by Genetic Alphabet Expansion SELEX (ExSELEX) using Two Types of Libraries Composed of Five Different Bases. K. Matsunaga, M. Kimoto and I. Hirao, J. Am. Chem. Soc., 139, 324-334 (2017).

Post-ExSELEX Stabilization of an Unnatural-Base DNA Aptamer Targeting VEGF165 toward Pharmaceutical Applications. M. Kimoto, M. Nakamura, I. Hirao, Nucleic Acids Res., 44, 7487-7494 (2016).

High Fidelity, Efficiency and Functionalization of Ds-Px Unnatural Base Pairs in PCR Amplification for a Genetic Alphabet Expansion System. I. Okamoto, Y. Miyatake, M. Kimoto, I. Hirao, ACS Synthetic Biology, 5, 1220-1230 (2016).

DNA aptamer generation by genetic alphabet expansion SELEX (EXSELEX) using an unnatural base pair system. M. Kimoto, K. Matsunaga, I. Hirao, Methods Mol. Biol., 1380, 47-60 (2016).

Architecture of high-affinity unnatural-base DNA aptamers toward pharmaceutical applications. K. Matsunaga, M. Kimoto, C. Hanson, M. Sanford, H.A. Young, I. Hirao, Sci. Rep., 5, 18478 (2015).

Site-specific labeling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry. T. Someya, A. Ando, M. Kimoto, I. Hirao, Nucleic Acids Res., 43, 6665-6676 (2015).

Chemical fidelity of an RNA polymerase ribozyme. J. Attwater, S. Tagami, M. Kimoto, K. Butler, E. Kool, J. Wengel, P. Herdewijn, I. Hirao, P. Holliger, Chem. Sci., 4, 2804-2814 (2013).

Generation of high-affinity DNA aptamers using an expanded genetic alphabet. M. Kimoto, R. Yamashige, K. Matsunaga, S. Yokoyama, I. Hirao, Nat. Biotechnol., 31, 453-457 (2013).

Site-specific functional labeling of nucleic acids by in vitro replication and transcription using unnatural base pair systems. M. Kimoto, Y. Hikida, I. Hirao, Israel J. Chem., 53, 450-468 (2013).

Site-specific functionalization of RNA molecules by an unnatural base pair transcription system via click chemistry. T. Ishizuka, M. Kimoto, A. Sato, I. Hirao, Chem. Comm. 45, 10835-10837 (2012).

Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma. I. Hirao, M. Kimoto, Proc. Jpn. Acad. Ser. B Phys. Biol. Sci., 88, 345-367 (2012).

PCR Amplification and Transcription for Site-Specific Labeling of Large RNA Molecules by a Two-Unnatural Base Pair System. M. Kimoto, R. Yamashige, S. Yokoyama, I. Hirao, J. Nucleic Acids, 2012, 230943 (2012).

Natural vs artificial creation of base pairs in DNA: origin of nucleobases from the perspectives of unnatural base pair studies. I. Hirao, M. Kimoto, R. Yamashige, Acc. Chem. Res.,45, 2055-2065 (2012).

Site-specific incorporation of functional components into RNA by an unnatural base pair transcription system. N. Morohashi, M. Kimoto, A. Sato, R. Kawai, I. Hirao, Molecules, 17, 2833-2854 (2012).

Highly specific unnatural base pair systems as a third base pair for PCR amplification. R. Yamashige, M. Kimoto, Y. Takezawa, A. Sato, T. Mitsui, S. Yokoyama, I. Hirao, Nucleic Acids Res., 40, 2793-2806 (2012).

Exploring the roles of nucleobase desolvation and shape complementarity during the misreplication of O(6)-methylguanine. D. Chavarria, A. Ramos-Serrano, I. Hirao, A.J. Berdis, J. Mol. Biol., 9, 7504-7509 (2011).

Monitoring the site-specific incorporation of dual fluorophore-quencher base analogues for target DNA detection by an unnatural base pair system. R. Yamashige, M. Kimoto, T. Mitsui, S. Yokoyama, I. Hirao, Org. Biomol. Chem., 412, 325-339 (2011).

Unnatural base pair systems for sensing and diagnostic applications. M. Kimoto, R. S. Cox 3rd, I. Hirao, Expert Rev. Mol. Diagn., 11, 321-331 (2011).

A new unnatural base pair system between fluorophore and quencher base analogues for nucleic acid-based imaging technology. M. Kimoto, T. Mitsui, R. Yamashige, A. Sato, S. Yokoyama, I. Hirao, J. Am. Chem. Soc., 132, 15418-15426 (2010).

Site-specific incorporation of extra components into RNA by transcription using unnatural base pair systems. M. Kimoto, I. Hirao, Methods, Mol. Biol., 634, 355-369 (2010).

Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis. Y. Hikida, M. Kimoto, S. Yokoyama, I. Hirao, Nature Protocols, 5, 1312-1323 (2010).

A unique fluorescent base analogue for the expansion of the genetic alphabet. M. Kimoto, T. Mitsui, S. Yokoyama, I. Hirao, J. Am. Chem. Soc., 132, 4988-4989 (2010).

An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules. M. Kimoto, R. Kawai, T. Mitsui, S. Yokoyama, I. Hirao, Nucleic Acids Res., 37, e14 (2009).

Phosphoserine aminoacylation of tRNA bearing an unnatural base anticodon. R. Fukunaga, Y. Harada, I. Hirao, S. Yokoyama, Biochem. Biophys. Res. Commun. 372, 480-485 (2008).

An efficient unnatural base pair for PCR amplification. I. Hirao, T. Mitsui, M. Kimoto, S. Yokoyama, J. Am. Chem. Soc., 129, 15549-15555 (2007).

Fluorescent probing for RNA molecules by an unnatural base-pair system. M. Kimoto, T. Mitsui, Y. Harada, A. Sato, S. Yokoyama, I. Hirao, Nucleic Acids Res., 35, 5360-5369 (2007).

Cytostatic evaluations of nucleoside analogs related to unnatural base pairs for a genetic expansion system. M. Kimoto, K. Moriyama, S. Yokoyama, I. Hirao, Bioorg. Med. Chem. Lett., 17, 5582-5585 (2007).

Characterization of fluorescent, unnatural base pairs. T. Mitsui, M. Kimoto, R. Kawai, S. Yokoyama, and I. Hirao, Tetrahedron, 63, 3528-3537 (2007).

Unnatural base pair systems for DNA/RNA-based biotechnology. I. Hirao, Curr. Op. Chem. Biol., 10, 622-627 (2006).

An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA. I. Hirao, M. Kimoto, T. Mitsui, T. Fujiwara, R. Kawai, A. Sato, Y. Harada, S. Yokoyama, Nature Methods, 3, 729-735 (2006).

Placing extra components into RNA by specific transcription using unnatural base pair system.Hirao, BioTechniques, 40, 711-717 (2006).

Site-specific fluorescent labeling of RNA molecules by specific transcription using unnatural base pairs. R. Kawai, M. Kimoto, S. Ikeda, T. Mitsui, M. Endo, S. Yokoyama, I. Hirao, J. Am. Chem. Soc., 127, 17286-17295 (2005).

Interaction analysis between tmRNA and SmpB from Thermus thermophilus. N. Nameki, T. Someya, S. Okano, R. Suemasa, M. Kimoto, K. Hanawa-Suetsugu, T. Terada, M. Shirouzu, I. Hirao, H. Takaku, H. Himeno, A. Muto, S. Kuramitsu, S. Yokoyama, G. Kawai, J. Biochem., 138, 729-739 (2005).

Site-specific biotinylation of RNA molecules by transcription using unnatural base pairs. K. Moriyama, M. Kimoto, T. Mitsui, S. Yokoyama, I. Hirao, Nucleic Acids Res., 33, e129 (2005).

An efficient unnatural base pair for a base-pair-expanded transcription system. T. Mitsui, M. Kimoto, Y. Harada, S. Yokoyama, I. Hirao, J. Am. Chem. Soc., 127, 8652-8658 (2005).

A two-unnatural-base-pair system toward the expansion of the genetic code. I. Hirao, Y. Harada, M. Kimoto, T. Mitsui, T. Fujiwara, S. Yokoyama, J. Am. Chem. Soc., 126, 13298-13305 (2004).

Unnatural base pairs between 2- and 6-substituted purines and 2-oxo(1H)pyridine for expansion of the genetic alphabet. I. Hirao, T. Fujiwara, M. Kimoto, S. Yokoyama, Bioorg. Med. Chem. Lett., 14, 4887-4890 (2004).

A quantitative, non-radioactive single-nucleotide insertion assay for analysis of DNA replication fidelity by using an automated DNA sequencer. M. Kimoto, S. Yokoyama, I. Hirao, Biotechnology Lett., 26, 999-1005 (2004).

Unnatural base pairs mediate the site-specific incorporation of an unnatural hydrophobic component into RNA transcripts. M. Endo, T. Mitsui, T. Okuni, M. Kimoto, I. Hirao, S. Yokoyama, Bioorg. Med. Chem. Lett., 14, 2593-2596 (2004).

In vitro selection of RNA aptamers that bind to colicin E3 and structurally resemble the decoding site of 16S ribosomal RNA. I. Hirao, Y. Harada, T. Nojima, Y. Osawa, H. Masaki, S. Yokoyama, Biochemistry, 43, 3214-3221 (2004).

Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs. M. Kimoto, M. Endo, T. Mitsui, T. Okuni, I. Hirao, S. Yokoyama, Chem. & Biol., 11, 47-55 (2004).

Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing. T. Sunami, J. Kondo, I. Hirao, K. Watanabe, K. Miura, A. Takenaka, Acta Crystallograph. Sec. D60, 422-431 (2004).

Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure. T. Sunami, J. Kondo, I. Hirao, K. Watanabe, K. Miura, A. Takenaka, Acta Crystallograph. Sec. D60, 90-96 (2004).

An unnatural hydrophobic base, 4-propynylpyrrole-2-carbaldehyde, as an efficient pairing partner of 9-methylimidazo[(4,5)-b]pyridine.Mitsui, M. Kimoto, A. Sato, S. Yokoyama, I. Hirao, Bioorg. Med. Chem. Lett., 13, 4515-4518 (2003).

An Unnatural Hydrophobic Base Pair with Shape Complementarity between Pyrrole-2-carbaldehyde and 9-Methylimidazo[(4,5)-b]pyridine.Mitsui, A. Kitamura, M. Kimoto, T. To, A. Sato, I. Hirao, S. Yokoyama, J. Am. Chem. Soc., 125, 5298-5307 (2003).

Crystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Duplex with Homo Base Pairs and Anti-Parallel Duplex with Watson-Crick Base Pairs.Sunami, J. Kondo, T. Kobuna, I. Hirao, K. Watanabe, K. Miura, A. Takenaka, Nucleic Acids Res., 30, 5253-5260 (2002).

Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells.Sakamoto, A. Hayashi, A. Sakamoto, D. Kiga, H. Nakayama, A. Soma, T. Kobayash, M. Kitabatake, K. Takio, K. Saito, M. Shirouzu, I. Hirao, S. Yokoyama, Nucleic Acids Res., 30, 4692-4699 (2002).

An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system.Kiga, K. Sakamoto, K. Kodama, T. Kigawa, T. Matsuda, T. Yabuki, M. Shirouzu, Y. Harada, H. Nakayama, K. Takio, Y. Hasegawa, Y. Endo, I. Hirao, S. Yokoyama, Proc. Natl. Acad. Sci. USA, 99, 9715-9720 (2002).

A unique unnatural base pair between a C analogue, pseudoisocytosine, and an A analogue, 6-methoxypurine, in replication.Hirao, M. Kimoto, S. Yamakage, M. Ishikawa, J. Kikuchi, S. Yokoyama, Bioorg Med Chem Lett., 12, 1391-1393 (2002).

An unnatural base pair for incorporating amino acid analogs into proteins.Hirao, T. Ohtsuki, T. Fujiwara, T. Mitsui, T. Yokogawa, T. Okuni, H. Nakayama, K. Takio, T. Yabuki, T. Kigawa, K. Kodama, T. Yokogawa, K. Nishikawa, S. Yokoyama, Nature Biotechnology, 20, 177-182 (2002).

Anti-(Raf-1) RNA aptamers that inhibit Ras-induced Raf-1 activation.Kimoto, M. Shirouzu, S. Mizutani, H. Koide, Y. Kaziro, I. Hirao, S.Yokoyama, Eur. J. Biochem., 269, 697-704 (2002).

Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase.Kiga, K. Sakamoto, S. Sato, I. Hirao, S. Yokoyama, Eur. J. Biochem. 268, 6207－6213 (2001).

Synthesis of DNA templates containing the fifth base, 2-amino-6-(N,N-dimethylamino)purine, for specific transcription involving unnatural base pairs. I. Hirao, T. Nojima, T. Mitsui, S. Yokoyama, Chem. Lett., 914-915 (2001).

Synthesis of 6-(2-thienyl)purine nucleoside derivatives that form unnatural base pairs with pyridin-2-one nucleosides. Fujiwara, M. Kimoto, H. Sugiyama, I. Hirao, S. Yokoyama, Bioorg. Med. Chem. Lett., 11, 2221-2223 (2001).

Unnatural base pairs for specific transcription. Ohtsuki, M. Kimoto, M. Ishikawa, T. Mitsui, I. Hirao, S. Yokoyama, Proc. Natl. Acad. Sci. USA, 98, 4922-4925 (2001)

Synthesis of 3-(2-Deoxy-β-D-ribofuranosyl)pyridin-2-one and 2-Amino-6-(N,N-dimethylamino)-9-(2-deoxy-β-D-ribofuranosyl)purine Derivatives for an Unnatural Base Pair. M. Ishikawa, I. Hirao, S. Yokoyama, Tetrahedron Lett., 41, 3931-3934 (2000).

Dual Specificity of the Pyrimidine Analog, 4-Methylpyridin-2-one, in DNA Replication, I.Hirao, T. Ohtsuki, T. Mitsui, S. Yokoyama, J. Am. Chem. Soc., 122, 6118-6119 (2000).

The Effect of Hairpin DNA Fragments on E. coli Poly(U)-Dependent Poly(Phe) Synthesis. S. Yoshizawa, K. Watanabe, K. Miura, I. Hirao, Chem. Lett., 154-155 (2000).

RNA aptamers that bind to and inhibit the ribosome-inactivating protein, pepocin. I. Hirao, K. Madin, Y. Endo, S. Yokoyama, A. D. Ellington, J. Biol. Chem. 275, 4943-4948 (2000).

The limits of specificity: An experimental analysis with RNA aptamers to MS2 coat protein variants. I.Hirao, M. Spingola, D. Peabody, A. D. Ellington, Molecular Diversity, 4, 75-89 (1999).

RNA aptamers that specifically bind to the Ras-binding domain of Raf-1. M.Kimoto, K. Sakamoto, M. Shirouzu, I. Hirao, S. Yokoyama, FEBS Lett., 441, 322-326 (1998).

Crystal structures of a series of RNA aptamers complexed to the same protein target. Rowsell, N. Stonehouse, M. A. Convery, C. J. Adams, A. D. Ellington, I. Hirao, D. S. Peabody, P. G. Stockley, S. E. V. Philips, Nature Structural Biol., 5, 970-975 (1998).

1,1,3,3-Tetraisopropyl-3-(2-(triphenylmethoxy)ethoxy)disiloxane-1-yl group, a potential 5’-O-protecting group for solid-phase RNA synthesis. I. Hirao, M. Koizumi, Y. Ishido, A. Andrus, Tetrahedron Lett., 39, 2989-2992 (1998).

Crystal structure of an RNA aptamer-protein complex at 2.8A resolution.A. Convery, S. Rowsell, N. Stonehouse, A. D. Ellington, I. Hirao, J. B. Murray, D. S. Peabody, S. E. V. Phillips, P. G. Stockley, Nature Structural Biol., 5, 133-139 (1998).

Landscapes for Molecular Evolution: Lessons from In Vitro Selection Experiments with Nucleic Acids.  S. D.  Jhaveri, I. Hirao, S. D. Bell, K. Uphoff, A. D. Ellington, Combinatorial Chemistry and Molecular Diversity, 1:169-191 (1997).

GNA-trinucleotide loop sequences producing extraordinarily stable DNA mini-hairpins. S. Yoshizawa, G. Kawai, K. Watanabe, K. Miura, I. Hirao, Biochemistry, 36, 4761-4767 (1997).

Re-creating the RNA world. I. Hirao, A. D. Ellington, Current Biol., 5, 1017-1022 (1995).

Human cystatin A is inactivated by engineered truncation. The NH2-terminal region of the cysteine proteinase inhibitor is essential of expression of its inhibitory activity. K. Shibuya, H. Kaji, T. Itoh, Y. Ohyama, A. Tsujikami, S. Tate, A. Takeda, I. Kumagai, I. Hirao, K. Miura, F. Inagaki, T. Samejima, Biochemistry, 34, 12185-12192 (1995).

Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat. I. Hirao, G. Kawai, S. Yoshizawa, Y. Nishimura, Y. Ishido, K. Watanabe, K. Miura, Nucleic Acids Res., 22, 576-582 (1994).

Nuclease resistance of an extraordinarily thermostable mini-hairpin DNA fragment, d(GCGAAGC) and its application to in vitro protein synthesis. S. Yoshizawa, T. Ueda, Y. Ishido, K. Miura, K. Watanabe, I. Hirao, Nucleic Acids Res., 22, 2217-2221 (1994).

Higher-order structure of bovine mitochondrial tRNA(Ser)UGA: chemical modification and computer modeling. Y. Watanabe, G. Kawai, T. Yokogawa, N. Hayashi, Y. Kumazawa, T. Ueda, K. Nishikawa, I. Hirao, K. Miura, K. Watanabe, Nucleic Acids Res., 22, 5378-5384 (1994).

Effect of tandem repeated AUG codons on translation efficiency of eukaryotic mRNA carrying a short leader sequence.Wakiyama, I. Hirao, I. Kumagai, K. Miura, Mol. Gen. Genet., 238, 59-64 (1993).

Stabilization of mRNA in an Escherichia coli cell-free translation system. I. Hirao, S. Yoshizawa, K. Miura, FEBS Lett., 321, 169-172 (1993).

Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing. I. Hirao, Y. Nishimura, Y. Tagawa, K. Watanabe, K. Miura, Nucleic Acids Res., 20, 3891-3896 (1992).

Gel electrophoresis using a fluorescence agent for analysis and purification of synthetic DNA fragments. I. Hirao, S. Yoshizawa, K. Miura, Nucleic Acids Res., 19, 4003 (1991).

Synthesis of fused oligoribonucleotides with trideoxyribo- nucleotide containing phosphor-thioate to stabilize against nuclease activity. M. Ishikawa, K. Ikebukuro, I. Hirao, K. Miura, Nucleosides & Nucleotides, 10, 1377-1390 (1991).

A novel cloverleaf structure found in mammalian mitochondrial tRNASer(UCN). T.Yokogawa, Y. Watanabe, Y. Kumazawa, T. Ueda, I. Hirao, K. Miura, K. Watanabe, Nucleic Acids Res., 19, 6101-6105 (1991).

Solid phase synthesis of oligoribonucleotides by the phosphoroamidite approach using 2′-O-1-(isopropoxy)ethyl protection. O. Sakatsume, T. Yamaguchi, M. Ishikawa, I. Hirao, K. Miura, H. Takaku, Tetrahedron, 47, 8717-8728 (1991).

Oligonucleotide synthesis in terms of a novel type of polymer- support; a cellulose acetate functionalized with 4-(2-hydroxyl- sulfonyl)dihydrocinnamoyl substituent. K. Kamaike, Y. Hasegawa, I. Masuda, Y. Ishido, K. Watanabe, I. Hirao, K. Miura, Tetrahedron, 46, 163-184 (1990).

Synthesis and properties of an initiation codon analog consisting of 2′-O-methyl nucleotides. I. Hirao, M. Okubo, M. Ishikawa, K. Miura, Nucleosides & Nucleotides, 9, 1113-1122 (1990).

Unique hairpin structures occurring at the replication origin of phage G4 DNA. I.  Hirao, M. Ishida, K. Watanabe, K. Miura, Biochim. Biophys. Acta, 1087, 199-204 (1990).

Extraordinary stable structure of short single-stranded DNA fragments containing a specific base sequence: d(GCGAAAGC). I. Hirao, Y. Nishimura, T. Naraoka, K. Watanabe, Y. Arata, K. Miura, Nucleic Acids Res., 17, 2223-2231 (1989).

Synthesis of nonadeca- and octadecaribonucleotides using the solid-phase phosphotriester with tetrahydropyranyl groups as the 2′-hydroxyl-protecting group. I. Hirao, M. Ishikawa, H. Hori, K. Watanabe, K. Miura, Bull. Chem. Soc. Jpn., 62, 1995-2001 (1989).

Synthesis of oligoribonucleotides by the hydroxybenzotriazole- activated phospho-triester/ dicyclohexylcarbodiimide system. I. Hirao, K. Miura, Chem. Lett., 1799-1802 (1989).

Synthetic oligodeoxyribonucleotides showing abnormal mobilities on polyacrylamide gel electrophoresis. I. Hirao, T. Naraoka, S. Kanamori, M. Nakamura, K. Miura, Biochem. Int., 16, 157-162 (1988).

Partial synthesis of leader sequence of phage f1 coat protein mRNA. I. Hirao, M. Ishikawa, K. Miura, Chem. Lett., 1929-1932 (1986).

Regioselective phenylcarbamoylation of purine and pyrimidine ribonucleosides through dibutyltin oxide – and tertiary amine – phenyl isocyanate systems. I. Hirao, K. Itoh, S. Nishino, Y. Araki, Y. Ishido, Carbohydrates Research, 152, 159-172 (1986).

Chemical conversion of some ribonucleosides into the corresponding β-D-arabinofuranosyl derivatives. N. Sakairi, I. Hirao, Y. Zama, Y. Ishido, Nucleosides & Nucleotides, 2, 221-229 (1983).

Ion selectivities of some extracellular viscous polysaccharides from red algae. T. Akahane, S. Kawashima, I. Hirao, T. Shimizu, A. Minakata, Polymer J., 14, 181-188 (1982).

Bis(tributyltin) oxide – phenyl isocyanate system for regio-selective (phenylcarbamoyl)ation of purine and pyrimidine ribonucleosides. I. Hirao, K. Itoh, N. Sakairi, Y. Araki, Y. Ishido, Carbohydr. Res., 109, 181-205 (1982).

Photocyclization of 2′-hydroxychalcones to 4-flavanones. R. Matsushima, I. Hirao, Bull. Chem. Soc. Jpn., 53, 518-522 (1980).

Regioselective phenylcarbamoylation of the hydroxyl groups of purine and pyrimidine ribo-nucleosides with bis(tributyltin) oxide – phenyl isocyanate.Ishido, I. Hirao, N. Sakairi, Y. Araki, Heterocycles, 13, 181-185 (1979).