Faculty Profiles - MURAYAMA Keiji

Papers - MURAYAMA Keiji

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Nonenzymatic polymerase-like template-directed synthesis of acyclic l-threoninol nucleic acid Reviewed Open Access

Murayama Keiji, Okita Hikari, Kuriki Takumi, Asanuma Hiroyuki

NATURE COMMUNICATIONS Vol. 12 ( 1 ) 2021.2

Omega Nucleic Acids (ΩNA), Ultimate Nucleic Acids for Future Technology Reviewed Open Access

Hamada, S; Murayama, K; Takezawa, Y; Toyoda, R; Kuzuya, A

MOLECULES Vol. 31 ( 3 ) 2026.2

Membrane-Penetrating Molecular Device Based on a Triplex Containing Acyclic L-Threoninol Nucleic Acid Functionalized with Cholesterol Reviewed Open Access

Liu, KF; Asanuma, H; Murayama, K

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 2025.11

Reversible photocycloaddition of 8-pyrenylvinylguanine for photoreactive serinol nucleic acid (SNA) Reviewed

Murayama, K; Ikeda, A; Sato, F; Asanuma, H

ORGANIC & BIOMOLECULAR CHEMISTRY 2025.7

Highly Effective Chemical Ligation of DNA and l-aTNA. Reviewed International journal

Hikari Okita, Keiji Murayama, Hiroyuki Asanuma

Current protocols Vol. 5 ( 5 ) page： e70140 2025.5

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

Chemical ligation of nucleic acids is a significant strategy for the establishment of a variety of functional biological tools and other applications. However, the conventional methodology has been suffering from low reaction efficiency or generation of unnatural structures at the ligation site. This article describes an effective chemical ligation method that connects the hydroxyl group and the monophosphate group at the nick site on the template, generating a natural phosphodiester bond. The method uses only N-cyanoimidazole (CNIm) and divalent metal cations to achieve chemical ligation in a template-directed manner, which can be applied to the ligations of not only DNA but also artificial nucleic acids such as acyclic l-threoninol nucleic acid (l-aTNA). Quantitative ligation is available within 10 min for l-aTNA fragments on an l-aTNA template, and within 2 hr for DNA fragments on a DNA template under optimized conditions. The effective chemical ligation system reported here will enable the development of biotechnology and nanotechnology, including exploration of l-aTNA aptamer via in vitro selection, chemical synthesis of genome-sized DNA and l-aTNA, functionalization of nanostructure, and creation of an l-aTNA-based artificial life in the future. © 2025 Wiley Periodicals LLC. Basic Protocol 1: Chemical ligation using CNIm and divalent metal cation Basic Protocol 2: Imaging analysis of ligation reaction Basic Protocol 3: Mass spectrometry of ligation products Support Protocol: Kinetic analysis.

DOI： 10.1002/cpz1.70140

Web of Science

PubMed

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Chirality-Promoted Chemical Ligation and Reverse Transcription of Acyclic Threoninol Nucleic Acid. Reviewed International journal

Hikari Okita, Keiji Murayama, Hiroyuki Asanuma

Journal of the American Chemical Society Vol. 147 ( 21 ) page： 17967 - 17974 2025.4

Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)

The building blocks of current life on Earth are chiral compounds, such as 2'-deoxy-D-ribose of DNA and L-amino acids with homochirality, which play an important role in various biological reactions. We investigated the effect of chirality on the template-directed chemical synthesis of nucleic acids as a model for primitive replication of genetic materials in the absence of enzymes. The efficiency of the template-directed chemical ligation of two acyclic nucleic acids, achiral serinol nucleic acid (SNA) and chiral acyclic l-threoninol nucleic acid (L-aTNA), induced by N-cyanoimidazole and a divalent metal cation, was evaluated. The chemical ligation of SNA fragments on an SNA template was much slower than the ligation of L-aTNA fragments on an L-aTNA template. Examination of L-aTNA and SNA heteroligation and the effects of chimeric template strands revealed the crucial importance of L-aTNA chirality, which induces helical propagation and fixes the local conformation of the reactive phosphate group for effective chemical ligation. DNA and RNA templates also enhanced the ligation of SNA and L-aTNA fragments. "Reverse transcription" from template RNA to L-aTNA was also demonstrated. Our findings show that scaffold chirality is crucial for chemical replication and reverse transcription in XNA-based systems. Furthermore, the reverse transcription from RNA to L-aTNA will find applications in XNA-based in vitro selection, the creation of artificial life, and nanotechnologies.

DOI： 10.1021/jacs.5c03128

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Reversible Optical Control of Receptor Tyrosine Kinase Activity and ERK Dynamics Using Azobenzene-Carrying DNA Aptamer Agonist

Masahiro Wakano, Masaya Tsunoda, Keiji Murayama, Jumpei Morimoto, Ryosuke Ueki, Saeko Aoyama-Ishiwatari, Yusuke Hirabayashi, Hiroyuki Asanuma, Shinsuke Sando

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Vol. 147 ( 13 ) page： 11477 - 11484 2025.3

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Receptor tyrosine kinases (RTKs) play a pivotal role in cell signaling through their activation via dimerization. Recent studies have demonstrated the importance of the temporal dynamics of RTK activity and downstream signals, such as ERK, in determining the cell fate. To better understand these dynamics, it is essential to develop methods capable of controlling the RTK activity with high temporal resolution. However, techniques for precisely modulating the activity of endogenous RTKs without requiring genetic modification remain insufficiently established. In this study, we developed a DNA aptamer agonist, Met-azo-aptamer, which enables reversible optical control of the activity of the c-Met receptor, a member of the RTK family. This was achieved by incorporating azobenzene, a photoisomerizable molecule, into a DNA aptamer that binds to c-Met. This design allows light-induced switching between the active and inactive structures of the aptamer. When the aptamer was applied to HeLa cells and exposed to ultraviolet or blue light, phosphorylation signals within the cells were activated in response to the light patterns. Furthermore, by variation of the light patterns, the Met-azo-aptamer successfully controlled the timing, amplitude, and duration of downstream ERK activation. The Met-azo-aptamer developed in this study offers a high-resolution method for investigating the relationship between RTK activation patterns and cell function or fate.

DOI： 10.1021/jacs.5c01559

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A Light-Powered Single-Stranded DNA Molecular Motor with Colour-Selective Single-Step Control Reviewed International coauthorship Open Access

Anderson, T; Wu, W; Sirbu, O; Tong, KS; Siti, W; Liu, XR; Kou, B; Murayama, K; Asanuma, H; Wang, ZS

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Vol. 63 ( 32 ) 2024.8

DNA Reaction System That Acquires Classical Conditioning Reviewed International coauthorship

Nakakuki, T; Toyonari, M; Aso, K; Murayama, K; Asanuma, H; de Greef, TFA

ACS SYNTHETIC BIOLOGY Vol. 13 ( 2 ) page： 521 - 529 2024.1

Highly Functional Acyclic Xeno Nucleic Acids Invited Reviewed

Murayama, K; Okita, H; Asanuma, H

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN Vol. 96 ( 10 ) page： 1179 - 1187 2023.10

Rapid Chemical Ligation of DNA and Acyclic Threoninol Nucleic Acid (aTNA) for Effective Nonenzymatic Primer Extension Reviewed Open Access

Hikari Okita, Shuto Kondo, Keiji Murayama, Hiroyuki Asanuma

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Vol. 145 ( 32 ) page： 17872 - 17880 2023.7

Authorship：Lead author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Previously, nonenzymatic primer extension reaction of acyclic l-threoninol nucleic acid (L-aTNA) wasachieved in the presence of N-cyanoimidazole (CNIm)and Mn2+; however, the reaction conditions were not optimizedand a mechanistic insight was not sufficient. Herein, we report investigationof the kinetics and reaction mechanism of the chemical ligation ofL-aTNA to L-aTNA and of DNA to DNA.We found that Cd2+, Ni2+, and Co2+ accelerated ligation of both L-aTNA and DNA and that the rate-determining step was activationof the phosphate group. The activation was enhanced by duplex formationbetween a phosphorylated L-aTNA fragment and template,resulting in unexpectedly more effective L-aTNA ligationthan DNA ligation. Under optimized conditions, an 8-mer L-aTNA primer could be elongated by ligation to L-aTNA trimers to produce a 29-mer full-length oligomer with60% yield within 2 h at 4 & DEG;C. This highly effective chemicalligation system will allow construction of artificial genomes, robustDNA nanostructures, and xeno nucleic acids for use in selection methods.Our findings also shed light on the possible pre-RNA world.

DOI： 10.1021/jacs.3c04979

Open Access

Web of Science

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Functionalization of acyclic xenonucleic acid with modified nucleobases Invited Reviewed Open Access

Keiji Murayama, Yuuhei Yamano, Hiroyuki Asanuma

Polymer Journal Vol. 55 ( 7 ) page： 743 - 752 2023.7

Authorship：Lead author,　Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Science and Business Media LLC

DOI： 10.1038/s41428-023-00776-7

Open Access

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Other Link： https://www.nature.com/articles/s41428-023-00776-7

Kinesin motors driven microtubule swarming triggered by UV light Reviewed

Ishii Satsuki, Akter Mousumi, Murayama Keiji, Kabir Arif Md Rashedul, Asanuma Hiroyuki, Sada Kazuki, Kakugo Akira

POLYMER JOURNAL Vol. 54 ( 12 ) page： 1501 - 1507 2022.12

DNA Concentration Regulator That can be Driven for a Long Time Reviewed Open Access

Nakakuki Takashi, Murayama Keiji, Asanuma Hiroyuki

NEW GENERATION COMPUTING Vol. 40 ( 2 ) page： 681 - 702 2022.7

Orthogonal Amplification Circuits Composed of Acyclic NucleicAcids Enable RNA Detection br Reviewed Open Access

Chen Yanglingzhi, Nagao Ryuya, Murayama Keiji, Asanuma Hiroyuki

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Vol. 144 ( 13 ) page： 5887 - 5892 2022.4

Methyl group configuration on acyclic threoninol nucleic acids (aTNAs) impacts supramolecular properties Reviewed

Murayama Keiji, Kashida Hiromu, Asanuma Hiroyuki

ORGANIC & BIOMOLECULAR CHEMISTRY 2022.3

Unexpected Dissociation of Photoresponsive UV-ON DNA Carrying p-tert-Butyl Azobenzene under UV Light Irradiation Reviewed

Ishii Satsuki, Murayama Keiji, Sada Kazuki, Asanuma Hiroyuki, Kakugo Akira

CHEMISTRY LETTERS Vol. 51 ( 3 ) page： 292 - 295 2022.3

Signal Amplification Circuit Composed of Serinol Nucleic Acid for RNA Detection Reviewed

Chen Yanglingzhi, Murayama Keiji, Asanuma Hiroyuki

CHEMISTRY LETTERS Vol. 51 ( 3 ) page： 330 - 333 2022.3

Renewable DNA Proportional-Integral Controller with Photoresponsive Molecules Open Access

Tamba Masaaki, Murayama Keiji, Asanuma Hiroyuki, Nakakuki Takashi

MICROMACHINES Vol. 13 ( 2 ) 2022.2

Xeno nucleic acids (XNAs) having non-ribose scaffolds with unique supramolecular properties Invited Reviewed

Asanuma Hiroyuki, Kamiya Yukiko, Kashida Hiromu, Murayama Keiji

CHEMICAL COMMUNICATIONS 2022.1

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Papers - MURAYAMA Keiji