* Corresponding Author

2025

Takeda, Y., Onoguchi, M., Ito, F., Yamamoto, I., Sumi, S., Yoshii, T., Ishida, M., Kajikawa, E., Zhang, J., Nishimura, O., Kadota, M., Tagami, S., Kondo, T., Saito, H., Hamada, M., & Shibuya, H. (2025). Nematode telomerase RNA hitchhikes on introns of germline–up-regulated genes. Science, 390(6771). https://doi.org/10.1126/science.ads7778

Sahoo, B. R., Deng, X., Wong, E. L., Clark, N., Yang, H. J., Kovalenko, A., Subramanian, V., Guzman, B. B., Harris, S. E., Dehury, B., Miyashita, E., Damon Hoff, J., Kocman, V., Saito, H., Dominguez, D., Plavec, J., & Bardwell, J. C. A. (2025). Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-63597-7

Abe, I., Ohno, H., Mochizuki, M., Hayashi, K., & Saito, H. (2025). Split RNA switch orchestrates pre- and post-translational control to enable cell type-specific gene expression. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-60392-2

Masaki, K., Fujita, Y., & Saito, H. (2025). MicroRNA-responsive ON-OFF hybrid mRNA switch for precise protein expression control. Molecular Therapy Nucleic Acids, 36(3), 102609. https://doi.org/10.1016/j.omtn.2025.102609

Pardi, M. L., Takayama, K., & Saito, H. (2025). SARS-CoV-2 Nsp1-Resistant Modified RNA for the Creation of Nsp1-Responsive Systems. ACS Synthetic Biology, 14(6), 2386–2392. https://doi.org/10.1021/acssynbio.5c00075

2024

Nagasawa, R., Onizuka, K., Komatsu, K. R., Miyashita, E., Murase, H., Ojima, K., Ishikawa, S., Ozawa, M., Saito, H., & Nagatsugi, F. (2024). Large-scale analysis of small molecule-RNA interactions using multiplexed RNA structure libraries. Communications Chemistry, 7(1). https://doi.org/10.1038/s42004-024-01181-8

Sumi, S., Hamada, M., & Saito, H. (2024). Deep generative design of RNA family sequences. Nature Methods. https://doi.org/10.1038/s41592-023-02148-8

2023

Komatsu, S., Ohno, H., Saito, H. (2023). Target-dependent RNA polymerase as universal platform for gene expression control in response to intracellular molecules. Nature Communications14(1). https://doi.org/10.1038/s41467-023-42802-5

Kawasaki S*, Ono H, Hirosawa M, Kuwabara T, Sumi S, Lee S, Woltjen K, Saito H.*, Programmable mammalian translational modulators by CRISPR-associated proteins., Nature Communications., 2023 Apr 19;14(1):2243. 

Ohno H*, Akamine S, Mochizuki M, Hayashi K, Akichika S, Suzuki T, Saito H.*, Versatile strategy using vaccinia virus-capping enzyme to synthesize functional 5′ cap-modified mRNAs., Nucleic Acids Res., 2023 Feb 3; 51(6): e34

Kameda S, Ohno H, Saito H*., Synthetic circular RNA switches and circuits that control protein expression in mammalian cells., Nucleic Acids Res., 2023 Jan 16; 51(4): e24

2022

Nakanishi H*, Yoshii T, Tsukiji S, Saito H.*, A protocol to construct RNA-protein devices for photochemical translational regulation of synthetic mRNAs in mammalian cells., STAR Protocols, 2022 Jun 10;3(2):101451. doi: 10.1016/j.xpro.2022.101451.

Tsujisaka Y, Hatani T, Okubo C, Ito R, Kimura A, Narita M, Chonabayashi K, Funakoshi S, Lucena-Cacace A, Toyoda T, Osafune K, Kimura T, Saito H*, Yoshida Y*., Purification of human iPSC-derived cells at large scale using microRNA switch and magnetic-activated cell sorting., Stem Cell Reports, 2022 May 30:S2213-6711(22)00255-7.

Fujita Y, Kameda T, Singh CR, Pepper W, Cecil A, Hilgers M, Thornton M, Asano I, Moravek C, Togashi Y*, Saito H*, Asano K*., Translational recoding by chemical modification of non-AUG start codon ribonucleotide bases., Sci Adv., 2022 Apr 8;8(14): eabm8501.

Pardi ML, Wu J, Kawasaki S, Saito H*., Synthetic RNA-based post-transcriptional expression control methods and genetic circuits., Advanced Drug Delivery Reviews, 2022 Mar 184:114196. (Review)

Nakanishi H, Saito H, Itaka K*., Versatile Design of Intracellular Protein-Responsive Translational Regulation System for Synthetic mRNA., ACS Synth Biol., 2022 Mar 18;11(3):1077-1085.

Fujita Y*, Hirosawa M, Hayashi K, Hatani T, Yoshida Y, Yamamoto T, Saito H*., A versatile and robust cell purification system with an RNA-only circuit composed of microRNA-responsive ON and OFF switches., Sci Adv., 2022 Jan 7;8(1):eabj1793.

2021

Nakanishi H, Saito H*. Purification of Specific Cell Populations Differentiated from Stem Cells Using MicroRNA-Responsive Synthetic Messenger RNAs. Methods Mol Biol., 2021 2312:73-86. 

Minegishi K, Rothé B, Komatsu KR, Ono H, Ikawa Y, Nishimura H, Katoh TA, Kajikawa E, Sai X, Miyashita E, Takaoka K, Bando K, Kiyonari H, Yamamoto T, Saito H*, Constam DB*, Hamada H*. Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex. Nat Commun., 2021 Jul 1;12(1):4071.

Nakanishi H, Yoshii T, Kawasaki S, Hayashi K, Tsutsui K, Oki C, Tsukiji S, Saito H.*, ‘Light-controllable RNA-protein devices for translational regulation of synthetic mRNAs in mammalian cells’, Cell Chem Biol., 2021 Jan 20:S2451-9456(21)00002-7. doi: 10.1016/j.chembiol.2021.01.002.

2020

Komatsu K. R., Taya T., Matsumoto S., Miyashita E., Kashida S.*, & Saito H.*, ‘RNA structure-wide discovery of functional interactions with multiplexed RNA motif library’, Nature Communications, 2020 Dec 8;11(1):6275. doi: 10.1038/s41467-020-19699-5.

Nakanishi H & Saito H.*, ‘Caliciviral Protein-Based Artificial Translational Activator for Mammalian Gene Circuits With RNA-only Delivery’, Nature Communications, 2020 Mar 10;11(1):1297.doi: 10.1038/s41467-020-15061-x.

Ohno H, Akamine S, Saito H.*, ‘Synthetic mRNA-Based Systems in Mammalian Cells ’, Advanced Biosystems, 4(5):e1900247. doi: 10.1002/adbi.201900247. Epub 2020 Mar 2. (Review)

Parr CJC, Wada S, Kotake K, Kameda S, Matsuura S, Sakashita S, Park S, Sugiyama H, Kuang Y*, Saito H.*, ‘N1-Methylpseudouridine substitution enhances the performance of synthetic mRNA switches in cells. ’, Nucleic Acids Res.,  doi: 10.1093/nar/gkaa070, (2020)

Kawasaki S, Ono H, Hirosawa M, Saito H.*, ‘RNA and protein-based nanodevices for mammalian post-transcriptional circuits. ’, Curr Opin Biotechnol., doi: 10.1016/j.copbio.2019. (2020) (Review)

Ono H, Kawasaki S, Saito H.*, ‘Orthogonal Protein-Responsive mRNA Switches for Mammalian Synthetic Biology. ’, ACS Synth Biol. Jan 17;9(1):169-174. (2020) (Selected as a front cover)

2019

Endo, K., Hayashi, K., Saito H.*, ‘Numerical operations in living cells by programmable RNA devices’, Science Advances, 2019 Aug 21;5(8):eaax0835. doi: 10.1126/sciadv.aax0835.

Sunohara T, Morizane A, Matsuura S, Miyamoto S, Saito H, Takahashi J. ‘MicroRNA-Based Separation of Cortico-Fugal Projection Neuron-Like Cells Derived From Embryonic Stem Cells.’, Front Neurosci. 2019 Oct 23;13:1141. doi: 10.3389/fnins.2019.01141. eCollection 2019.

Hirosawa, M., Fujita, Y., Saito H.*, ‘Cell-Type-Specific CRISPR Activation with MicroRNA-Responsive AcrllA4 Switch’, ACS Synthetic Biology, 2019 8(7): 1575-1582 

Saito H.*, Yokobayashi Y*. ‘Editorial overview: Mammalian synthetic biology: from devices to multicellular systems.’, Curr Opin Chem Biol. 2019 Oct;52:A1-A2. doi: 10.1016/j.cbpa.2019.07.010

Nakanishi H and Saito H.*,. ‘Mammalian gene circuits with biomolecule-responsive RNA devices.’, Curr Opin Chem Biol. Oct;52:16-22. doi: 10.1016/j.cbpa.2019.04.013 (Review)

Kashida S, Wang DO, Saito H, Gueroui Z. ‘Nanoparticle-based local translation reveals mRNA as a translation-coupled scaffold with anchoring function.’, Proc Natl Acad Sci U S A. 2019 Jul 2;116(27):13346-13351. doi: 10.1073/pnas.1900310116

Ohno H, Akamine S, and Saito H.*,. ‘RNA nanostructures and scaffolds for biotechnology applications.’, Curr Opin Biotechnol. 2019 Aug;58:53-61. doi: 10.1016/j.copbio.2018.11.006 (Review)

2018

Matsuura S., Ono H., Kuang Y., Kawasaki S., Fujita Y., Saito H.*, ‘Synthetic RNA-based logic computation in mammalian cells’, Nature Communications, 9(1):4847, doi: 10.1038/s41467-018-07181-2.

Zhitnyuk Y, Gee P, Lung MSY, Sasakawa N, Xu H, Saito H, Hotta A ‘Efficient mRNA delivery system utilizing chimeric VSVG-L7Ae virus-like particles.’, Biochem Biophys Res Commun. 2018 Nov 10;505(4):1097-1102. doi: 10.1016/j.bbrc.2018.09.113.

Kashida, Shunnichi, and Hirohide Saito., "Design of Ligand‐Controlled Genetic Switches Based on RNA Interference." 

Synthetic Biology: Parts, Devices and Applications 8 (2018).

Endo, Kei, and Hirohide Saito.,  "mRNA Engineering for the Control of Mammalian Cells in Medical Applications."

 Applied RNA Bioscience. Springer, Singapore, 2018. 95-114.

2017

Shibata, T., Fujita, Y., Ohno, H., Suzuki, Y., Hayashi, K., Komatsu, K.R., Kawasaki, S., Hidaka, K., Yonehara, S., Sugiyama, H., Endo, M., Saito H.*, ‘Protein-Driven RNA Nanostructured Devices That Function in Vitro and Control Mammalian Cell Fate’, Nature Communications, 8, 1, 540.

Hirosawa, M., Fujita, Y., Parr, C.J.C., Hayashi, K., Kashida, S., Hotta, A., Woltjen, K., Saito H.*, ‘Cell-Type-Specific Genome Editing with a microRNA-Responsive CRISPR-Cas9 Switch’, Nucleic Acids Research, 45, 13, e118.

Kawasaki, S., Fujita, Y., Nagaike, T., Tomita, K., Saito H.*, ‘Synthetic mRNA Devices That Detect Endogenous Proteins and Distinguish Mammalian Cells’, Nucleic Acids Research, 45, 12, e117.

Nakanishi, H., Miki, K., Komatsu, K.R., Umeda, M., Mochizuki, M., Inagaki, A., Yoshida, Y., Saito H.*, ‘Monitoring and Visualizing microRNA Dynamics during Live Cell Differentiation Using microRNA-Responsive Non-Viral Reporter Vectors’, Biomaterials, 128, 121-35. 

Parr Callum, Shinya Yamanaka, Saito H.* ‘An update on stem cell biology and engineering for brain development. ’ Molecular Psychiatry. volume 22, pages 808-819 (2017), doi:10.1038/mp.2017.66. (Review)

Tang L, Morris J, Wan J, Moore C, Fujita Y, Gillaspie S, Aube E, Nanda J, Marques M, Jangal M, Anderson A, Cox C, Hiraishi H, Dong L, Saito H, Singh CR, Witcher M, Topisirovic I, Qian SB, Asano K., ‘Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide.’, Nucleic Acids Research, 2017 Nov 16;45(20):11941-11953. doi: 10.1093/nar/gkx808.

Kuang Y, Miki K, Parr CJC, Hayashi K, Takei I, Li J, Iwasaki M, Nakagawa M, Yoshida Y, Saito H*. ‘Efficient, Selective Removal of Human Pluripotent Stem Cells via Ecto-Alkaline Phosphatase-Mediated Aggregation of Synthetic Peptides.’, Cell Chem Biol. 2017 Jun 22;24(6):685-694.e4. doi: 10.1016/j.chembiol.2017.04.010.

2016

Karagiannis P, Fujita Y, Saito H*. ‘RNA-based gene circuits for cell regulation. ’Proc Jpn Acad Ser B Phys Biol Sci. 2016;92(9):412-422.PMID: 27840389 (Review)

Parr CJ, Katayama S, Miki K, Kuang Y, Yoshida Y, Morizane A, Takahashi J, Yamanaka S, Saito H*. ‘MicroRNA-302 switch to identify and eliminate undifferentiated human pluripotent stem cells. ’ Scientific Reports. 2016 Sep 9;6:32532. doi: 10.1038/srep32532.

Ohno H, Saito H*. ‘RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology. ’ Prog Mol Biol Transl Sci. 2016;139:165-85. doi: 10.1016/bs.pmbts.2015.12.004. (Review)

Endo K, Hayashi K, Saito H*. ‘High-resolution Identification and Separation of Living Cell Types by Multiple microRNA-responsive Synthetic mRNAs’ Scientific Reports. 2016 Feb 23;6:21991. 

2015

Wroblewska L, Kitada T, Endo K, Siciliano V, Stillo B, Saito H*, and Weiss R.* ‘Mammalian synthetic circuits with RNA binding proteins for RNA-only delivery. ’ Nature Biotechnology, 2015, 33(8):839-41. doi: 10.1038/nbt.3301. 

Miki K, Endo K, Takahashi S, Funakoshi S, Takei I, Katayama S, Toyoda T, Kotaka M, Takaki T, Umeda M, Okubo C, Nishikawa M, Oishi A, Narita M, Miyashita I, Asano K, Hayashi K, Osafune K, Yamanaka S, Saito H*, Yoshida Y*. ‘Efficient Detection and Purification of Cell Populations Using Synthetic MicroRNA Switches. ’ Cell Stem Cell. 2015 May 20. pii: S1934-5909(15)00163-0. doi: 10.1016/j.stem.2015.04.005.

Shibata T, Suzuki Y, Sugiyama H, Endo M, Saito H*. ‘Folding RNA-Protein Complex into Designed Nanostructures.’ Methods Mol Biol. 2015;1316:169-79. doi: 10.1007/978-1-4939-2730-2_14.

Ohno H, Osada E, Saito H*.  ‘Design, Assembly, and Evaluation of RNA-Protein Nanostructures. ’ Methods Mol Biol. 2015;1297:197-211. doi: 10.1007/978-1-4939-2562-9_14. 

Morita M, Onoe H, Yanagisawa M, Ito H, Ichikawa M, Fujiwara K, Saito H, Takinoue M. ‘Droplet-Shooting and Size-Filtration (DSSF) Method for Synthesis of Cell-Sized Liposomes with Controlled Lipid Compositions. ’ Chembiochem. 2015 Sep 21;16(14):2029-35. doi: 10.1002/cbic.201500354

Saito H*. ‘Synthetic RNA technologies to control functions of mammalian cells.‘ Yakugaku Zasshi. 2015;135(3):399-404. (Review)

2014

Endo K, Callum P, Saito H.*. ‘Expanding the synthetic ribonucleoprotein world in cells.‘ Nature Methods. 11:1105-06 (2014) (News and Views)

Eriko Osada, Yuki Suzuki, Kumi Hidaka, Hirohisa Ohno, Hiroshi Sugiyama, Masayuki Endo, Hirohide Saito*. ‘Engineering RNA-Protein Complexes with Different Shapes for Imaging and Therapeutic Applications.‘ ACS Nano. 2014 Aug 26;8(8):8130-40.

Masami Hagiya*, Akihiko Konagaya, Satoshi Kobayashi, Hirohide Saito, Satoshi Murata. Molecular robots with sensors and intelligence. ‘ Acc Chem Res. 2014 Jun 17;47(6):1681-90. doi:10.1021/ar400318d. 

Shunnichi Kashida, Hirohide Saito*. ‘A three-dimensional design strategy for a protein-responsive shRNA switch.‘ Methods Mol Biol. 2014;1111:269-86. 

Kei Endo, Hirohide Saito*. ‘Engineering protein-responsive mRNA switch in mammalian cells.‘ Methods Mol Biol.  2014;1111:183-96.

2013

Endo K, Hayashi K, Inoue T*, Saito H*. ‘A versatile cis-acting inverter module for synthetic translational switches.‘ Nature Communications,  2013;4:2393. doi: 10.1038/ncomms3393.

Endo K, Stapleton JA, Hayashi K, Saito H*, Inoue T*. ‘Quantitative and stimulataneous translational control of distinct mammalian mRNAs.‘ Nucleic Acid Res., 41(13):e135 (2013)

Hara T, Saito H*, Inoue T*. ‘Directed evolution of a synthetic RNA-protein module to create a new translational switch.‘ Chem Commun (Camb). 2013 May 10;49(37):3833-5. (Selected as the front cover image)

Hirohisa Ohno, Eriko Osada, Tan Inoue, and Saito H*. ‘Synthetic RNA-Protein Nanostructures and Their Potential Applications. ‘ RNA Nanotechnology and Therapeutics, (ed. Guo, P., CRC press), (Book)

2012

Kashida S, Inoue T*, Saito H*. ‘Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation.‘ Nucleic Acids Research, 40(18):9369-9378 (Selected as Featured Articles) 

James A. Stapleton, Kei Endo, Yoshihiko Fujita, Karin Hayashi, Masahiro Takinoue, Saito H*, Inoue T*  ‘Feedback Control of Protein Expression in Mammalian Cells by Tunable Synthetic Translational Inhibition.‘  ACS Synthetic Biology, 1(3): 83-88 (2012) (Selected as a front cover)

2011

Saito H*, Fujita Y, Kashida S, Hayashi K, Inoue T. ‘Synthetic human cell fate regulation by protein-driven RNA switches.‘ Nature Communications 2011 Jan 18;2:160.

Ohno H, Kobayashi T, Kabata R, Endo K, Iwasa T, Yoshimura SH, Takeyasu K, Inoue T*, Saito H*. ‘Synthetic RNA-protein complex shaped like an equilateral triangle. ‘ Nature Nanotechnology 2011 Feb;6(2):116-20. 

Ohmor R, Saito H, Ikawa Y, Fujita Y, Inoue T*. ‘Self-Replication Reactions Dependent on Tertiary Interaction Motifs in an RNA Ligase Ribozyme. ‘ J Mol Evol., 73:221-9 (2011)

Rudiuk S, Saito H, Hara T,Inoue T,Yoshikawa K, Baigl D. ‘Light-Regulated mRNA Condensation by a Photosensitive Surfactant Works as a Series Photoswitch of Translation Activity in the Presence of Small RNAs. ‘ Biomacromolecules, 12(11):3945-51 (2011)

2010

Saito H*, Kobayashi T, Hara T, Fujita Y, Hayashi K, Furushima R, Inoue T*.  ‘Synthetic Translational Regulation by an L7Ae-Kink-turn RNP Switch. ‘ Nature Chemical Biology, 6: 71-78 (2010)

2009

Shigeyoshi Matsumura, Rei Ohmori, Hirohide Saito, Yoshiya Ikawa, *Tan InoueCoordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction loop-receptor interaction

FEBS Letters, 583 (17): 2819-26

André Estévez-Torres, Cécile Crozatier, Antoine Diguet, Tomoaki Hara, Hirohide Saito, Kenichi Yoshikawa, *Damien BaiglSequence-independent and reversible photocontrol of transcription/expression systems using a photosensitive nucleic acid binder

PNAS, 106 (30): 12219-23

*Hirohide Saito, Yusho Kato, MAel Le Berre, Ayako Yamada, Tan Inoue, Kenichi Yoshikawa, and *Damien BaiglTime-resolved tracking of a minimum gene expression system reconstituted in giant liposomes

ChemBioChem. 10 (10): 1640-3

*Hirohide Saito and *Tan InoueSynthetic Biology with RNA motifs

Int. J. Biochem. Cell Biol., 41(2):398-404

Tomoaki Shiohara, *Hirohide Saito and *Tan InoueA,  'Designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions', 

Nucleic Acids Res. 37(3):e23

2008

Hirohide Saito, Tamiko Minamisawa, Takao Yamori, Kiyotaka Shiba, 'Motif-programmed artificial protein induces apoptosis in several cancer cells by disrupting mitochondria'

Cancer Science, 99 (2): 398-406.

2007

Hirohide Saito, Shunichi Kashida, Tan Inoue, *Kiyotaka Shiba, 'The role of peptide motifs in the evolution of a protein network'

Nucleic Acid. Res., 35 (19): 6357-6366.

Hirohide Saito, Tan Inoue, 'RNA and RNP as new molecular parts in synthetic biology'

J. Biotechnol., 132 (1): 1-7.

Hirohide Saito, Tamiko Minamisawa, Kiyotaka Shiba, 'Motif programming: a microgene-based method for creating synthetic proteins containing multiple functional motifs',

Nucleic Acid. Res., 35(6):e38

2004

Hirohide Saito, Takako Honma, Tamiko Minamisawa, Kanami Yamazaki, Tetsuo Noda, Takao Yamori, *Kiyotaka ShibaSynthesis of functional proteins by mixing peptide motifs

Chemistry & Biology 11(6): 765-773

Krishna Ramaswamy, Hirohide Saito, Hiroshi Murakami, Kiyotaka Shiba, *Hiroaki Suga, 'Designer Ribozymes: Programming the tRNA Specificity into Flexizyme'

J. Am. Chem. Soc., 126 (37) 11454 –11455

2003

Hiroshi Murakami, Hirohide Saito, Hiroaki Suga, 'A versatile tRNA aminoacylation catalyst based on RNA'

Chemistry & Biology 10(7): 655-662

2002

Hirohide Saito, Hiroaki Suga, 'Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme'

Nucleic Acid. Res., 30 (23): 5151-5159

2001

Hirohide Saito, *Hiroaki SugaA, 'Ribozyme exclusively aminoacylates the 3´- hydroxyl group of the tRNA terminal adenosine'

J. Am. Chem. Soc., 123 (29): 7178-7179

Hirohide Saito, Kimitsuna Watanabe, *Hiroaki Suga, 'Concurrent molecular recognition of both the amino acid and tRNA by a ribozyme'

RNA, 7 (12): 1867-1878

Hirohide Saito, Dimitrios Kourouklis, *Hiroaki Suga, 'An in vitro evolved precursor tRNA with aminoacylation activity'

The EMBO Journal, 20 (7): 1797-1806