Tokyo University of Technology School of Bioscience and Biotechnology Yoshida Lab

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Research Articles

[2018]

[49] Taka N., Karube I., Yoshida W.*
Direct detection of hemi-methylated DNA by SRA-fused luciferase based on bioluminescence resonance energy transfer.
Anal. Lett. (2018) in press (*Corresponding author)

[48] Baba Y., Karube I., Yoshida W.*
Global DNA methylation level monitoring by methyl-CpG binding domain-fused luciferase.
Anal. Lett. (2018) in press (*Corresponding author)

[47] Tsukakoshi K.#, Yoshida W.#, Kobayashi M., Kobayashi N., Kim J., Kaku T., Iguchi T., Nagasawa K., Asano R., Ikebukuro K., Sode K.
Esterification of PQQ enhances blood-brain barrier permeability and inhibitory activity against amyloidogenic protein fibril formation.
ACS Chem. Neurosci. (2018) in press (#co-first authors)

[46] Yoshida W.*, Terasaka M., Laddachote S., Karube I.
Stabilization of G-quadruplex structure on vascular endothelial growth factor gene promoter depends on CpG methylation site and cation type.
BBA General Subjects (2018) 1862, 1933 (*Corresponding author)

[45] Tsukakoshi K.#, Saito S.#, Yoshida W.#, Goto S., Ikebukuro K.
CpG methylation changes G-quadruplex structures derived from gene promoters and interaction with VEGF and SP1.
Molecules (2018) 23, 944 (#co-first authors)

[44] Yoshida W.*, Saikyo H., Nakabayashi K., Yoshioka H., Bay D.H., Iida K., Kawai T., Hata K., Ikebukuro K., Nagasawa K., Karube I.
Identification of G-quadruplex clusters by high-throughput sequencing of whole-genome amplified products with a G-quadruplex ligand.
Scientific Reports (2018) 8, 3116 (*Corresponding author)

 

[2017]

[43] Yoshida W.*, Baba Y., Banzawa K., Karube I.
A quantitative homogeneous assay for global DNA methylation levels using CpG-binding domain- and methyl-CpG-binding domain-fused luciferase
Anal. Chim. Acta (2017) 990, 168 (*Corresponding author)

[42] Bay D.H., Busch A., Lisdat F., Iida K., Ikebukuro K., Nagasawa K., Karube I., Yoshida W.*
Identification of G-quadruplex structures that possess transcriptional regulating functions in the Dele and Cdc6 CpG islands
BMC Molecular Biology (2017) 18, 17 (*Corresponding author)

[41] Yokoyama T., Tsukakoshi K., Yoshida W., Saito T., Teramoto K., Savory N., Abe K. Ikebukuro K.
Development of HGF-binding aptamers with the combination of G4 promoter-derived aptamer selection and in silico maturation
Biotechnol. Bioeng. (2017) 114, 2196

[40] Lee J., Yoshida W., Abe K., Nakabayashi K., Wakeda H., Hata K., Marquette C.A., Blum L.J., Sode K., Ikebukuro K.
Development of an electrochemical detection system for measuring DNA methylation levels using methyl CpG-binding protein and glucose dehydrogenase-fused zinc finger protein
Biosens. Bioelectron. (2017) 93, 118

 

[2016]

[39] Tsukakoshi K., Ikuta Y., Abe K., Yoshida W., Iida K., Ma Y., Nagasawa K., Sode K. Ikebukuro K.
Structural regulation by a G-quadruplex ligand increases binding abilities of G-quadruplex-forming aptamers
Chem. Commun. (2016) 52, 12646

[38] Yoshida W.*, Baba Y., Karube I.
Global DNA methylation detection system using MBD-fused luciferase based on bioluminescence resonance energy transfer assay
Anal. Chem. (2016) 88, 9264 (*Corresponding author)

[37] Yoshida W.*, Yoshioka H., Bay D.H., Iida K., Ikebukuro K., Nagasawa K., Karube I.
Detection of DNA methylation of G-quadruplex and i-motif-forming sequences by measuring the initial elongation efficiency of polymerase chain reaction
Anal. Chem. (2016) 88, 7101 (*Corresponding author)

[36] Matsumoto D., Nishio M., Kato Y., Yoshida W., Abe K., Fukazawa K., Ishihara K., Iwata F., Ikebukuro K., Nakamura C.
ATP-mediated Release of a DNA-binding Protein from a Silicon Nanoneedle Array
Electrochemistry (2016) 84, 305

 

[2015]

[35] Saito T.#, Yoshida W.#, Yokoyama T., Abe K., Ikebukuro K.
Identification of RNA oligonucleotides binding to several proteins from potential G-quadruplex forming regions in transcribed pre-mRNA
Molecules (2015) 20, 20832 (#co-first authors)

[34] Fukaya T., Abe K., Savory N., Tsukakoshi K., Yoshida W., Ferri S., Sode K., Ikebukuro K.
Improvement of the VEGF binding ability of DNA aptamers through in silico maturation and multimerization strategy
J. Biotechnol. (2015) 212, 99

[33] Ogihara K., Savory N., Abe K., Yoshida W., Arakawa M., Asahi M., Kamohara S., Ikebukuro K.
Inhibition of an allergen–antibody reaction related to Japanese cedar pollinosis using DNA aptamers against the Cry j 2 allergen
Nucleic Acid Ther. (2015) 25, 311

[32] Yoshida W.*, Tomikawa J., Inaki M., Kimura H., Onodera M., Hata K., Nakabayashi K.*
An insulator element located at the cyclin B1 interacting protein 1 gene locus is highly conserved among mammalian species
PLOS ONE (2015) 10, e0131204 (*Corresponding authors)

[31] Ogihara K., Savory N., Abe K., Yoshida W., Asahi M., Kamohara S., Ikebukuro K.
DNA aptamers against the Cry j 2 allergen of Japanese cedar pollen for biosensing applications
Biosens. Bioelectron. (2015) 63, 159

 

[2014]

[30] Savory N., Nzakizwanayo J., Abe K., Yoshida W., Ferri S., Dedi C., Jones B.V., Ikebukuro K.
Selection of DNA aptamers against uropathogenic Escherichia coli NSM59 by quantitative PCR controlled Cell-SELEX
J. Microbiol. Methods (2014) 104, 94

[29] Lee J., Tatsumi A., Abe K., Yoshida W., Sode K., Ikebukuro K.
Electrochemical detection of pathogenic bacteria by using a glucose dehydrogenase fused zinc finger protein
Anal. Methods (2014) 6, 4991

[28] Miyake K., Abe K., Ferri S., Nakajima M., Nakamura M., Yoshida W., Kojima K., Ikebukuro K. Sode K.
A green-light-inducible lytic system for cyanobacterial cells
Biotechnology for Biofuels (2014) 7, 56

[27] Sakai Y., Abe K., Nakashima S., Yoshida W., Ferri S., Sode K., Ikebukuro K.
Improving gene regulation ability of small RNAs by scaffold engineering in Escherichia coli
ACS Synthetic Biology (2014) 3, 152

[26] Abe K., Sakai Y., Nakashima S., Araki M., Yoshida W., Sode K., Ikebukuro K.
Design of riboregulators for control of cyanobacterial (Synechocystis) protein expression
Biotechnol. Lett. (2014) 36, 287

[25] Savory N., Takahashi Y., Tsukakoshi K., Hasegawa H., Takase M., Abe K., Yoshida W., Ferri S., Kumazawa S., Sode K., Ikebukuro K.
Simultaneous improvement of specificity and affinity of aptamers against Streptococcus mutans by in silico maturation for biosensor development
Biotechnol. Bioeng. (2014) 111, 454

 

[2013]

[24] Abe K., Yoshida W., Terada K., Yagi-Ishii Y., Ferri S., Ikebukuro K., Sode K.
Screening of peptide ligands for pyrroloquinoline quinone glucose dehydrogenase using antagonistic template-based biopanning
Int. J. Mol. Sci. (2013) 14, 23244

[23] Iida K.#, Nakamura T.#, Yoshida W.#, Tera M., Nakabayashi K., Hata K., Ikebukuro K. Nagasawa K.
Fluorescent ligand-mediated screening of G-quadruplex structure using a DNA microarray
Angew. Chem. Int. Ed. Engl. (2013) 52, 12052 (#co-first authors) (highlighted as an inside cover picture)

[22] Yoshida W., Kezuka A., Murakami Y., Lee J., Abe K., Motoki H., Matsuo T., Shimura N., Noda M., Igimi S., Ikebukuro K.
Automatic polymerase chain reaction product detection system for food safety monitoring using zinc finger protein fused to luciferase
Anal. Chim. Acta (2013) 801, 78

[21] Savory N., Goto S., Yoshida W., Unuma Y., Nakamura M., Abe K., Ferri S., Ikebukuro K.
Two-dimensional electrophoresis based selection for aptamers against unidentified protein in tissue sample
Anal. Lett. (2013) 46, 2954

[20] Yoshida W., Kezuka A., Abe K., Wakeda H., Nakabayashi K., Hata K., Ikebukuro K.
Detection of histone modification by chromatin immunoprecipitation combined zinc finger luciferase-based bioluminescence resonance energy transfer assay
Anal. Chem. (2013) 85, 6485

[19] Yoshida W., Saito T., Yokoyama T., Ferri S., Ikebukuro K.
Aptamer selection based on G4-forming promoter region
PLOSONE (2013) 8, e65497

[18] Savory N., Lednor D., Tsukakoshi K., Abe K., Yoshida W., Ferri S., Jones B.V., Ikebukuro K.
In silico maturation of binding-specificity of DNA aptamers against Proteus mirabilis
Biotechnol. Bioeng. (2013) 110, 2573

[17] Yoshida W., Kobayashi N., Sasaki Y., Ikebukuro K., Sode K.
Partial peptide of α-synuclein modified with small-molecule inhibitors specifically inhibits amyloid fibrillation of α-synuclein
Int. J. Mol. Sci. (2013) 14, 2590

[16] Nonaka Y., Yoshida W., Abe K., Ferri S., Schulze H., Bachmann T., Ikebukuro K.
Affinity improvement of a VEGF aptamer by in silico maturation for a sensitive VEGF-detection system
Anal. Chem. (2013) 85, 1132

[15] Kim J., Sasaki Y., Yoshida W., Kobayashi N., Veloso A.J., Kerman K., Ikebukuro K., Sode K.
Rapid cytotoxicity screening platform for amyloid inhibitors using a membrane-potential sensitive fluorescent probe
Anal. Chem. (2013) 85, 185

[14] Yoshida W., Yamamoto H., Ikebukuro K.
An optical biosensing system based on interference-enhanced reflection with aptameric enzyme subunits of thrombin
Anal. Lett. (2013) 46, 242

 

[2012]

[13] Hiraoka D.#, Yoshida W.#, Abe K., Wakeda H., Hata K., Ikebukuro K.
Development of a method to measure DNA methylation levels by using methyl CpG-binding protein and luciferase-fused zinc finger protein
Anal. Chem. (2012) 84, 8259 (#co-first authors)

 

[2011]

[12] Morita Y.#, Yoshida W.#, Savory N., Han S., Tera M., Nagasawa K., Nakamura C., Sode K., Ikebukuro K.
Development of a novel biosensing system based on the structural change of a polymerized guanine-quadruplex DNA nanostructure
Biosens. Bioelectron. (2011) 26, 4837 (#co-first authors)

[11] Nakabayashi K., Trujillo A.M., Tayama C., Camprubi C., Yoshida W., Lapunzina P., Sanchez A., Soejima H., Aburatani H., Nagae G., Ogata T., Hata K., Monk D.
Methylation screening of reciprocal genome-wide UPDs identifies novel human specific imprinted genes
Hum. Mol. Genet. (2011) 20, 3188

[10] Sato S., Yoshida W., Soejima H., Nakabayashi K., Hata K.
Methylation dynamics of IG-DMR and Gtl2-DMR during murine embryonic and placental development
Genomics (2011) 98, 120

 [9] Abe K., Ogasawara D., Yoshida W., Sode K., Ikebukuro K.
Aptameric sensors based on structural change for diagnosis
Faraday Discuss. (2011) 149, 93

 

[2009]

[8] Fukasawa M., Yoshida W., Yamazaki H., Sode K., Ikebukuro K.
An aptamer-based bound/free separation system for protein detection
Electroanalysis (2009) 21, 1297

[7] Yoshida W., Mochizuki E., Takase M., Hasegawa H., Morita Y., Yamazaki H., Sode K., Ikebukuro K.
Selection of DNA aptamers against insulin and construction of an aptameric enzyme subunit for insulin sensing
Biosens. Bioelectron. (2009) 24, 1116

 

[2008]

[6] Yoshida W., Sode K., Ikebukuro K.
Label-free homogeneous detection of immunoglobulin E by an aptameric enzyme subunit
Biotechnol. Lett. (2008) 30, 421

[5] Ikebukuro K.#, Yoshida W.#, Sode K.
Aptameric enzyme subunit for homogeneous DNA sensing
Biotechnol. Lett. (2008) 30, 243 (#co-first authors)

 

[2007]

[4] Yoshida W., Yokobayashi Y.
Photonic Boolean logic gates based on DNA aptamers
Chem. Commun. (2007) 195 (highlighted by Nature Nanotechnology, 2006, 1, 160)

 

[2006]

[3] Ikebukuro K., Yoshida W., Noma T., Sode K.
Analysis of the evolution of the thrombin-inhibiting DNA aptamers using a genetic algorithm
Biotechnol. Lett. (2006) 28, 1933

[2] Yoshida W., Sode K., Ikebukuro K.
Homogeneous DNA sensing using enzyme-inhibiting DNA aptamers
Biochem. Biophys. Res. Commun. (2006) 348, 245

[1] Yoshida W., Sode K., Ikebukuro K.
Aptameric enzyme subunit for biosensing based on enzymatic activity measurement
Anal. Chem. (2006) 78, 3296

 

Review Articles

[2] Kumagai T., Abe K., Yoshida W., Ikebukuro K.
DNA detection technology using zinc finger protein
Journal of Microbial & Biochemical Technology (2015) 7, 278

[1] Yoshida W., Abe K., Ikebukuro K.,
Emerging techniques employed in aptamer-based diagnostic tests
Expert Rev. Mol. Diagn. (2014) 14, 143

 

Book Chapters

[4] Yoshida W., Karube I.
Determination of lactates
Flow Injection Analysis of Food Additives (2015) 273

[3] Savory N., Abe K., Yoshida W., Ikebukuro K.
In silico maturation: processing sequences to improve biopolymer functions based on genetic algorithms
Applications of Metaheuristics in Process Engineering (2014) 271

[2] Abe K., Yoshida W., Ikebukuro K
Electrochemical biosensors using aptamers for theranostics
Advances in Biochemical Engineering / Biotechnology (2014) 183

[1] Ikebukuro K., Yoshida W., Sode K.
Biosensors using the aptameric enzyme subunit: The use of aptamers in the allosteric control of enzymes
Aptamers in Bioanalysis (2009) 129

 

 

 

 

 

 

 

 

 

 

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