Shinsuke Sando

Summary

Affiliation: Kyoto University
Country: Japan

Publications

  1. ncbi Unexpected preference of the E. coli translation system for the ester bond during incorporation of backbone-elongated substrates
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    J Am Chem Soc 129:6180-6. 2007
  2. ncbi Amplified nucleic acid sensing using programmed self-cleaving DNAzyme
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    J Am Chem Soc 125:15720-1. 2003
  3. ncbi A small-molecule-based approach to sense codon-templated natural-unnatural hybrid peptides. Selective silencing and reassignment of the sense codon by orthogonal reacylation stalling at the single-codon level
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    J Am Chem Soc 127:7998-9. 2005
  4. ncbi Light-up Hoechst-DNA aptamer pair: generation of an aptamer-selective fluorophore from a conventional DNA-staining dye
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Chembiochem 8:1795-803. 2007
  5. doi Enzymatic N-methylaminoacylation of tRNA using chemically misacylated AMP as a substrate
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
    Org Biomol Chem 6:2666-8. 2008
  6. ncbi In vitro selection of RNA aptamer against Escherichia coli release factor 1
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Bioorg Med Chem Lett 17:1216-20. 2007
  7. ncbi RNAi silencing of exogenous and endogenous reporter genes using a macrocyclic octaamine as a "compact" siRNA carrier. Studies on the nonsilenced residual activity
    Kazuki Matsui
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Bioconjug Chem 17:132-8. 2006
  8. ncbi Termination-free prokaryotic protein translation by using anticodon-adjusted E. coli tRNASer as unified suppressors of the UAA/UGA/UAG stop codons. Read-through ribosome display of full-length DHFR with translated UTR as a buried spacer arm
    Atsushi Ogawa
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Chembiochem 7:249-52. 2006
  9. ncbi Cis-regulatory hairpin-shaped mRNA encoding a reporter protein: catalytic sensing of nucleic acid sequence at single nucleotide resolution
    Atsushi Narita
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Nat Protoc 2:1105-16. 2007
  10. ncbi Locked TASC probes for homogeneous sensing of nucleic acids and imaging of fixed E. coli cells
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto, 615 8510, Japan
    Org Biomol Chem 3:1002-7. 2005

Collaborators

Detail Information

Publications28

  1. ncbi Unexpected preference of the E. coli translation system for the ester bond during incorporation of backbone-elongated substrates
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    J Am Chem Soc 129:6180-6. 2007
    ..These results indicate that the E. coli translation machinery can utilize main-chain-elongated substrates if the pKa of the substrate is appropriately chosen...
  2. ncbi Amplified nucleic acid sensing using programmed self-cleaving DNAzyme
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    J Am Chem Soc 125:15720-1. 2003
    ..e., isothermal and enzyme/reagent-free, conditions. A fluorescence-reporting TASC probe having a fluorescein/dabsyl FRET pair across the cleavage site allows a mix-and-read discrimination of single-nucleotide differences in the target...
  3. ncbi A small-molecule-based approach to sense codon-templated natural-unnatural hybrid peptides. Selective silencing and reassignment of the sense codon by orthogonal reacylation stalling at the single-codon level
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    J Am Chem Soc 127:7998-9. 2005
    ..We discuss the significance of the present small-molecule-based approach to sense-codon templated natural-unnatural peptides...
  4. ncbi Light-up Hoechst-DNA aptamer pair: generation of an aptamer-selective fluorophore from a conventional DNA-staining dye
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Chembiochem 8:1795-803. 2007
    ..The 25-mer sequence was split into binary aptamer probes, thus enabling us to detect a target nucleic acid sequence with a single-nucleotide resolution by use of unmodified DNA as a probe...
  5. doi Enzymatic N-methylaminoacylation of tRNA using chemically misacylated AMP as a substrate
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
    Org Biomol Chem 6:2666-8. 2008
    ..Using "chemically misacylated AMP" which is photogeneratable, tRNA can be enzymatically acylated with N-methylamino acids in an efficiency comparable to that of the corresponding natural aminoacylation process with amino acids...
  6. ncbi In vitro selection of RNA aptamer against Escherichia coli release factor 1
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Bioorg Med Chem Lett 17:1216-20. 2007
    ..coli, as confirmed by the translation of amber-mutated (gfp(amber141) or gfp(amber178)) and wild-type (gfp(wild)) genes of GFP...
  7. ncbi RNAi silencing of exogenous and endogenous reporter genes using a macrocyclic octaamine as a "compact" siRNA carrier. Studies on the nonsilenced residual activity
    Kazuki Matsui
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Bioconjug Chem 17:132-8. 2006
    ..Implication of item 2 is briefly discussed...
  8. ncbi Termination-free prokaryotic protein translation by using anticodon-adjusted E. coli tRNASer as unified suppressors of the UAA/UGA/UAG stop codons. Read-through ribosome display of full-length DHFR with translated UTR as a buried spacer arm
    Atsushi Ogawa
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Chembiochem 7:249-52. 2006
  9. ncbi Cis-regulatory hairpin-shaped mRNA encoding a reporter protein: catalytic sensing of nucleic acid sequence at single nucleotide resolution
    Atsushi Narita
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Nat Protoc 2:1105-16. 2007
    ..Preparation of a probe takes 1-3 d and gene sensing using the probe takes 1-3 h...
  10. ncbi Locked TASC probes for homogeneous sensing of nucleic acids and imaging of fixed E. coli cells
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto, 615 8510, Japan
    Org Biomol Chem 3:1002-7. 2005
    ..Preliminary experiments with fixed E. coli cells show that the locked TASC probe with a FRET pair can be used to image fixed E. coli cells...
  11. ncbi A quantum dot conjugated sugar ball and its cellular uptake. On the size effects of endocytosis in the subviral region
    Fumio Osaki
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    J Am Chem Soc 126:6520-1. 2004
    ..The work thus suggests an utmost importance of size control at the viral size when designing molecular (gene, drug, probe, etc.) delivery machines...
  12. ncbi Cerasome as an infusible, cell-friendly, and serum-compatible transfection agent in a viral size
    Kazuki Matsui
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    J Am Chem Soc 128:3114-5. 2006
    ..The silicon strategy thus provides a simple and widely applicable tool to overcome general problems associated with current technology of artificial gene delivery...
  13. ncbi Remarkably size-regulated cell invasion by artificial viruses. Saccharide-dependent self-aggregation of glycoviruses and its consequences in glycoviral gene delivery
    Takashi Nakai
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida, Sakyo ku, Kyoto 606 8501, Japan
    J Am Chem Soc 125:8465-75. 2003
    ..The scope and prospect of artificial glycoviruses are discussed...
  14. ncbi Visible sensing of nucleic acid sequences with a genetically encodable unmodified RNA probe
    Atsushi Narita
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Angew Chem Int Ed Engl 45:2879-83. 2006
  15. doi Synthesis of puromycin derivatives with backbone-elongated substrates and associated translation inhibitory activities
    Keigo Mizusawa
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Bioorg Med Chem 17:2381-7. 2009
    ..All the synthesized puromycin derivatives showed good solubility in water and were applied to translation inhibitory assay in a reconstituted Escherichia coli translation system...
  16. doi Modular blue fluorescent RNA sensors for label-free detection of target molecules
    Chika Furutani
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, 615 8510, Kyoto, Japan
    Mol Biosyst 6:1569-71. 2010
    ....
  17. ncbi Doubly catalytic sensing of HIV-1-related CCR5 sequence in prokaryotic cell-free translation system using riboregulator-controlled luciferase activity
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    J Am Chem Soc 127:5300-1. 2005
    ..5 fmol (1 ng/muL) of probe and a single nucleotide resolution...
  18. ncbi Aptamer selection for the inhibition of cell adhesion with fibronectin as target
    Atsushi Ogawa
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Bioorg Med Chem Lett 14:4001-4. 2004
    ..coli and sequenced to give a couple of highly homologous ODNs, which indeed inhibited fibronectin-integrin mediated cell adhesion...
  19. ncbi Facile preparation of DNA-tagged carbohydrates
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 606 8501, Japan
    Bioorg Med Chem Lett 13:2633-6. 2003
    ..0, NaBH(3)CN, 60 degrees C) without notable side reactions. Quadruplex-forming G-rich oligonucleotide, 5'-aminoalkyl d(TGGGGT), is glycosylated with maltoheptaose to afford a novel DNA-assisted tetrasaccharide cluster motif...
  20. doi Substrate/Product-targeted NMR monitoring of pyrimidine catabolism and its inhibition by a clinical drug
    Hisatsugu Yamada
    Advanced Biomedical Engineering Research Unit, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    ACS Chem Biol 7:535-42. 2012
    ..The potentiality of triple-resonance NMR in the analysis of in vivo pharmaceutical activity of drugs targeting particular metabolic reactions is discussed...
  21. ncbi Artificial viruses and their application to gene delivery. Size-controlled gene coating with glycocluster nanoparticles
    Yasuhiro Aoyama
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida, Sakyo ku, Kyoto 606 8501, Japan
    J Am Chem Soc 125:3455-7. 2003
    ..The remarkable adhesion-manipulation ability of saccharide clusters also provides a strategy of bottom-up construction of nanometric or mesoscopic sizes...
  22. ncbi Macrocyclic glycoclusters. Self-aggregation and phosphate-induced agglutination behaviors of calix[4]resorcarene-based quadruple-chain amphiphiles with a huge oligosaccharide pool
    Osamu Hayashida
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Yoshida, Sakyo ku, Japan
    J Am Chem Soc 125:594-601. 2003
    ..The unique intermolecular binding properties of compound 22 and analogues so far reported are reviewed in light of the present finding...
  23. ncbi A facile route to dynamic glycopeptide libraries based on disulfide-linked sugar-peptide coupling
    Shinsuke Sando
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Bioorg Med Chem Lett 14:2835-8. 2004
    ..A preliminary SPR examination shows that the thiogalactose-derived library indeed contains active divalent galactoside species capable of cross-linking peanut lectin molecules...
  24. ncbi Macrocyclic proteoglycan mimics. Potent inhibition of cell adhesion by a bundle of chondroitin sulfate chains assembled on the calix[4]resorcarene platform
    Naotoshi Tomita
    Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo ku, Kyoto 615 8510, Japan
    Bioorg Med Chem Lett 14:2087-90. 2004
    ....
  25. ncbi Induction of a remarkable conformational change in a human telomeric sequence by the binding of naphthyridine dimer: inhibition of the elongation of a telomeric repeat by telomerase
    Kazuhiko Nakatani
    Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Japan
    J Am Chem Soc 125:662-6. 2003
    ..Telomeric repeat elongation assay showed that the binding of naphthyridine dimer to the telomeric sequence inhibits the elongation of the sequence by telomerase...
  26. ncbi Quenched auto-ligating DNAs: multicolor identification of nucleic acids at single nucleotide resolution
    Shinsuke Sando
    Department of Chemistry, Stanford University, Stanford, California 94305 5080, USA
    J Am Chem Soc 126:1081-7. 2004
    ..The results suggest that QUAL probes may be of general use in the detection and identification of sequences in solution, on microarrays, and in microorganisms...
  27. ncbi Imaging of RNA in bacteria with self-ligating quenched probes
    Shinsuke Sando
    Department of Chemistry, Stanford University, Stanford, California 94305 5080, USA
    J Am Chem Soc 124:9686-7. 2002
    ..The results demonstrate the use of QUAL probes to detect specific RNA sequences in bacterial cells without enzymes and without washing steps...
  28. ncbi Quencher as leaving group: efficient detection of DNA-joining reactions
    Shinsuke Sando
    Department of Chemistry, Stanford University, Stanford, California 94305 5080, USA
    J Am Chem Soc 124:2096-7. 2002
    ....