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Research Output 1998 2019

  • 1007 Citations
  • 13 h-Index
  • 36 Article
  • 4 Review article
  • 3 Conference contribution
  • 1 Chapter
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Article
2019

Comparison between effects of retroactivity and resource competition upon change in downstream reporter genes of synthetic genetic circuits

Moriya, T., Yamaoka, T., Wakayama, Y., Ayukawa, S., Zhang, Z., Yamamura, M., Wakao, S. & Kiga, D., 2019 Mar 1, In : Life. 9, 1, 30.

Research output: Contribution to journalArticle

Open Access
Reporter Genes
reporter genes
genes
Computer Simulation
resources

Enhancement of binding affinity of folate to its receptor by peptide conjugation

Dharmatti, R., Miyatake, H., Nandakumar, A., Ueda, M., Kobayashi, K., Kiga, D., Yamamura, M. & Ito, Y., 2019 May 1, In : International journal of molecular sciences. 20, 9, 2152.

Research output: Contribution to journalArticle

Open Access
Peptide Receptors
conjugation
Folic Acid
Peptides
peptides
2018

A Highly Bioactive Lys-Deficient IFN Leads to a Site-Specific Di-PEGylated IFN with Equivalent Bioactivity to That of Unmodified IFN-α2b

Imada, T., Moriya, K., Uchiyama, M., Inukai, N., Hitotsuyanagi, M., Masuda, A., Suzuki, T., Ayukawa, S., Tagawa, Y. I., Dohmae, N., Kohara, M., Yamamura, M. & Kiga, D., 2018 Jan 1, (Accepted/In press) In : ACS Synthetic Biology.

Research output: Contribution to journalArticle

Interferons
Bioactivity
Proteins
Antiviral Agents
Pharmacokinetics
1 Citation (Scopus)

Escherichia coli expression, purification, and refolding of human folate receptor α (hFRα) and β (hFRβ)

Dharmatti, R., Miyatake, H., Zhang, C., Ren, X., Yumoto, A., Kiga, D., Yamamura, M. & Ito, Y., 2018 Sep 1, In : Protein Expression and Purification. 149, p. 17-22 6 p.

Research output: Contribution to journalArticle

Folic Acid
Escherichia coli
Inclusion Bodies
Disulfides
Prokaryotic Cells
2 Citations (Scopus)

Horizontal transfer of code fragments between protocells can explain the origins of the genetic code without vertical descent

Froese, T., Campos, J. I., Fujishima, K., Kiga, D. & Virgo, N., 2018 Dec 1, In : Scientific Reports. 8, 1, 3532.

Research output: Contribution to journalArticle

Artificial Cells
Aminoacylation
Genetic Code
Amino Acyl-tRNA Synthetases
Catalytic RNA
2017
1 Citation (Scopus)
irinotecan
Pharmacokinetics
Perturbation Analysis
Newton-Raphson method
Newton Methods
2016
1 Citation (Scopus)

A bacterial continuous culture system based on a microfluidic droplet open reactor

Ito, M., Sugiura, H., Ayukawa, S., Kiga, D. & Takinoue, M., 2016, In : Analytical Sciences. 32, 1, p. 61-66 6 p.

Research output: Contribution to journalArticle

Microfluidics
Fusion reactions
Metabolic engineering
Nutrients
Oils
14 Citations (Scopus)

Reproducibility of fluorescent expression from engineered biological constructs in E. coli

iGEM Interlab Study Contributors, 2016 Mar 1, In : PLoS One. 11, 3, e0150182.

Research output: Contribution to journalArticle

reproducibility
Escherichia coli
Fluorescence
promoter regions
fluorescence
2015
3 Citations (Scopus)

In vitro selection of a photoresponsive peptide aptamer to glutathione-immobilized microbeads

Tada, S., Zang, Q., Wang, W., Kawamoto, M., Liu, M., Iwashita, M., Uzawa, T., Kiga, D., Yamamura, M. & Ito, Y., 2015 Feb 1, In : Journal of Bioscience and Bioengineering. 119, 2, p. 137-139 3 p.

Research output: Contribution to journalArticle

Peptide Aptamers
Amino Acid-Specific Transfer RNA
Azobenzene
Transfer RNA
Microspheres
4 Citations (Scopus)

Two site genetic incorporation of varying length polyethylene glycol into the backbone of one peptide

Zang, Q., Tada, S., Uzawa, T., Kiga, D., Yamamura, M. & Ito, Y., 2015 Jul 31, In : Chemical Communications. 51, 76, p. 14385-14388 4 p.

Research output: Contribution to journalArticle

Anticodon
Peptides
Polyethylene glycols
Polypeptides
Transfer RNA
2014

An observation method for autonomous signaling- mediated synthetic diversification in escherichia coli

Sekine, R., Ayukawa, S. & Kiga, D., 2014, In : Methods in Molecular Biology. 1151, p. 69-74 6 p.

Research output: Contribution to journalArticle

Observation
Escherichia coli
Artificial Cells
Calcium Carbonate
Regeneration
4 Citations (Scopus)

Effects of downstream genes on synthetic genetic circuits

Moriya, T., Yamamura, M. & Kiga, D., 2014 Dec 8, In : BMC Systems Biology. 8, 4, S4.

Research output: Contribution to journalArticle

Synthetic Genes
Synthetic Biology
Genes
Gene
Networks (circuits)

Experimental Evolution of a Green Fluorescent Protein Composed of 19 Unique Amino Acids without Tryptophan

Kawahara-Kobayashi, A., Hitotsuyanagi, M., Amikura, K. & Kiga, D., 2014 Dec 11, In : Origins of Life and Evolution of the Biosphere. 44, 2, p. 75-86 12 p.

Research output: Contribution to journalArticle

tryptophan
Green Fluorescent Proteins
green fluorescent protein
Tryptophan
amino acids
5 Citations (Scopus)

General Applicability of Synthetic Gene-Overexpression for Cell-Type Ratio Control via Reprogramming

Ishimatsu, K., Hata, T., Mochizuki, A., Sekine, R., Yamamura, M. & Kiga, D., 2014 Sep 19, In : ACS Synthetic Biology. 3, 9, p. 638-644 7 p.

Research output: Contribution to journalArticle

Synthetic Genes
Genes
Escherichia coli
Switches
Molecules
5 Citations (Scopus)

Multiple amino acid-excluded genetic codes for protein engineering using multiple sets of tRNA variants

Amikura, K., Sakai, Y., Asami, S. & Kiga, D., 2014 Mar 21, In : ACS Synthetic Biology. 3, 3, p. 140-144 5 p.

Research output: Contribution to journalArticle

Genetic Code
Protein Engineering
Transfer RNA
Amino acids
Proteins

Why 20 amino acids?

Amikura, K. & Kiga, D., 2014, In : Kobunshi. 63, 6, p. 392-393 2 p.

Research output: Contribution to journalArticle

Amino acids
Amino Acids
Proteins
Biochemistry
Alanine
2012
13 Citations (Scopus)

An aptazyme-based molecular device that converts a small-molecule input into an RNA output

Ayukawa, S., Sakai, Y. & Kiga, D., 2012 Aug 7, In : Chemical Communications. 48, 61, p. 7556-7558 3 p.

Research output: Contribution to journalArticle

RNA
Molecules
Nucleic acids
Nucleic Acids
14 Citations (Scopus)

Simplification of the genetic code: Restricted diversity of genetically encoded amino acids

Kawahara-Kobayashi, A., Masuda, A., Araiso, Y., Sakai, Y., Kohda, A., Uchiyama, M., Asami, S., Matsuda, T., Ishitani, R., Dohmae, N., Yokoyama, S., Kigawa, T., Nureki, O. & Kiga, D., 2012 Nov, In : Nucleic Acids Research. 40, 20, p. 10576-10584 9 p.

Research output: Contribution to journalArticle

Genetic Code
Amino Acids
RNA, Transfer, Ala
Anticodon
Protein Engineering

Tunability of the ratio of cell states after the synthetic diversification by the diversity generator

Sekine, R., Yamamura, M., Hagiya, M. & Kiga, D., 2012, In : Communicative and Integrative Biology. 5, 4, p. 393-394 2 p.

Research output: Contribution to journalArticle

generators (equipment)
Acyl-Butyrolactones
cells
homoserine
lactones
2011
18 Citations (Scopus)

RTRACS: A modularized RNA-dependent RNA transcription system with high programmability

Ayukawa, S., Takinoue, M. & Kiga, D., 2011 Dec 20, In : Accounts of Chemical Research. 44, 12, p. 1369-1379 11 p.

Research output: Contribution to journalArticle

Transcription
Biological systems
RNA
Large scale systems
Mathematical models
22 Citations (Scopus)

Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling

Sekine, R., Yamamura, M., Ayukawa, S., Ishimatsu, K., Akama, S., Takinoue, M., Hagiya, M. & Kiga, D., 2011 Nov 1, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 44, p. 17969-17973 5 p.

Research output: Contribution to journalArticle

Cell Count
Calcium Carbonate
Tissue Engineering
Cell Communication
Computer Simulation
2010
10 Citations (Scopus)

Construction of a genetic AND gate under a new standard for assembly of genetic parts

Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., Yamamura, M. & Kiga, D., 2010 Dec 2, In : BMC Genomics. 11, SUPPL. 4, S16.

Research output: Contribution to journalArticle

operator regions
Logic gates
Nucleic Acid Regulatory Sequences
Gene expression
Plasmids
2009
7 Citations (Scopus)

Rna oscillator: Limit cycle oscillations based on artificial biomolecular reactions

Takinoue, M., Kiga, D., Shohda, K. I. & Suyama, A., 2009 Feb, In : New Generation Computing. 27, 2, p. 107-127 21 p.

Research output: Contribution to journalArticle

Limit Cycle
RNA
DNA
Oscillation
Degradation
2008
1 Citation (Scopus)

A design and feasibility study of reactions comprising DNA molecular machine that walks autonomously by using a restriction enzyme

Sekiguchi, H., Komiya, K., Kiga, D. & Yamamura, M., 2008 Sep, In : Natural Computing. 7, 3, p. 303-315 13 p.

Research output: Contribution to journalArticle

DNA
Enzymes
Stators
Molecular biology
Computer simulation
34 Citations (Scopus)

Experiments and simulation models of a basic computation element of an autonomous molecular computing system

Takinoue, M., Kiga, D., Shohda, K. I. & Suyama, A., 2008 Oct 29, In : Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 78, 4, 041921.

Research output: Contribution to journalArticle

Molecular Computing
Transcription
Simulation Model
Experiment
Reverse
1 Citation (Scopus)

Synthetic biology

Kiga, D. & Yamamura, M., 2008 Aug, In : New Generation Computing. 26, 4, p. 347-364 18 p.

Research output: Contribution to journalArticle

Synthetic Biology
Molecular biology
Systems science
Molecular Biology
Biology
2007
2 Citations (Scopus)

SYANAC: SYnthetic biological Automaton for Noughts and Crosses

Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., Yamamura, M. & Kiga, D., 2007, In : IET Synthetic Biology. 1, 1-2, p. 64-67 4 p.

Research output: Contribution to journalArticle

Logic gates
Protein Binding
Binding sites
Genes
Binding Sites
2006
56 Citations (Scopus)

Cation-π interaction in the polyolefin cyclization cascade uncovered by incorporating unnatural amino acids into the catalytic sites of squalene cyclase

Morikubo, N., Fukuda, Y., Ohtake, K., Shinya, N., Kiga, D., Sakamoto, K., Asanuma, M., Hirota, H., Yokoyama, S. & Hoshino, T., 2006 Oct 11, In : Journal of the American Chemical Society. 128, 40, p. 13184-13194 11 p.

Research output: Contribution to journalArticle

Cyclization
Polyolefins
Cations
Amino acids
Catalytic Domain
18 Citations (Scopus)

DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing

Komiya, K., Sakamoto, K., Kameda, A., Yamamoto, M., Ohuchi, A., Kiga, D., Yokoyama, S. & Hagiya, M., 2006 Jan, In : BioSystems. 83, 1, p. 18-25 8 p.

Research output: Contribution to journalArticle

Molecular Computing
DNA-directed DNA polymerase
DNA-Directed DNA Polymerase
Hamiltonians
DNA
22 Citations (Scopus)

Translation of 'rare' codons in a cell-free protein synthesis system from Escherichia coli

Chumpolkulwong, N., Sakamoto, K., Hayashi, A., Iraha, F., Shinya, N., Matsuda, N., Kiga, D., Urushibata, A., Shirouzu, M., Oki, K., Kigawa, T. & Yokoyama, S., 2006 Mar, In : Journal of Structural and Functional Genomics. 7, 1, p. 31-36 6 p.

Research output: Contribution to journalArticle

Codon
Escherichia coli
Bearings (structural)
Genes
Proteins
2002
134 Citations (Scopus)

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, D., Sakamoto, K., Kodama, K., Kigawa, T., Matsuda, T., Yabuki, T., Shirouzu, M., Harada, Y., Nakayama, H., Takio, K., Hasegawa, Y., Endo, Y., Hirao, I. & Yokoyama, S., 2002 Jul 23, In : Proceedings of the National Academy of Sciences of the United States of America. 99, 15, p. 9715-9720 6 p.

Research output: Contribution to journalArticle

Tyrosine-tRNA Ligase
Cell-Free System
Germ Cells
Triticum
Escherichia coli
164 Citations (Scopus)

Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells

Sakamoto, K., Hayashi, A., Sakamoto, A., Kiga, D., Nakayama, H., Soma, A., Kobayashi, T., Kitabatake, M., Takio, K., Saito, K., Shirouzu, M., Hirao, I. & Yokoyama, S., 2002 Nov 1, In : Nucleic Acids Research. 30, 21, p. 4692-4699 8 p.

Research output: Contribution to journalArticle

Tyrosine-tRNA Ligase
RNA, Transfer, Tyr
Amino Acids
Transfer RNA
Amber
2001
6 Citations (Scopus)

Shifted positioning of the anticodon nucleotide residues of amber suppressor tRNA species by Escherichia coli arginyl-tRNA synthetase

Kiga, D., Sakamoto, K., Sato, S., Hirao, I. & Yokoyama, S., 2001, In : European Journal of Biochemistry. 268, 23, p. 6207-6213 7 p.

Research output: Contribution to journalArticle

Arginine-tRNA Ligase
Anticodon
Transfer RNA
Escherichia coli
RNA, Transfer, Arg
2000
312 Citations (Scopus)

Molecular computation by DNA hairpin formation

Sakamoto, K., Gouzu, H., Komiya, K., Kiga, D., Yokoyama, S., Yokomori, T. & Hagiya, M., 2000 May 19, In : Science. 288, 5469, p. 1223-1226 4 p.

Research output: Contribution to journalArticle

Molecular Computers
Single-Stranded DNA
Molecular Biology
DNA
1999
68 Citations (Scopus)

State transitions by molecules

Sakamoto, K., Kiga, D., Komiya, K., Gouzu, H., Yokoyama, S., Ikeda, S., Sugiyama, H. & Hagiya, M., 1999 Oct, In : BioSystems. 52, 1-3, p. 81-91 11 p.

Research output: Contribution to journalArticle

State Transition
State Machine
DNA
Molecules
Single-Stranded DNA
1998
59 Citations (Scopus)

An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition

Kiga, D., Futamura, Y., Sakamoto, K. & Yokoyama, S., 1998 Apr 1, In : Nucleic Acids Research. 26, 7, p. 1755-1760 6 p.

Research output: Contribution to journalArticle

Nucleotide Aptamers
Xanthine
Guanine
RNA
Consensus Sequence