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WPI-iCeMs Kyoto University

Sugiyama Laboratory, Kyoto University

Publications :2014 - 2010

2014 (Highlighted Articles Representing International Collaboration Project)

297. Locating the Uracil-5-yl Radical Formed Upon Photoirradiation of 5-Bromouracil-substituted DNA
Hashiya, F.; Saha, A.; Kizaki, S.; Li, Y.; Sugiyama, H.
Nucleic Acids Res. 2014, 42, 13469-13473.

296. Identification of a Small Molecule that Turns `ON` the Pluripotency Gene Circuitry in Human Fibroblasts
Pandian, G. N.; Sato, S.; Chandran, A.; Taniguchi, J.; Takashima, K.; Syed, J.; Han, L.; Saha, A.; Bando, T.; Nagase, H.; Sugiyama, H.
ACS Chem. Biol. 2014, 9, 2729-2736.

295. Direct Quantification of Loop Interaction and - Stacking for G-quadruplex Stability at the Submolecular Level
Ghimire, C.; Park, S.; Iida, K.; Yangyuoru, P.; Otomo, H.; Yu, Z.; Nagasawa, K.; Sugiyama, H.; Mao, H.
J. Am. Chem. Soc. 2014, 136, 15537-15544.

294. Preparation of Chemically Modified RNA Origami Nanostructures
Endo, M.; Takeuchi, Y.; Emura, T.; Hidaka, K.; Sugiyama, H.
Chem. Eur. J. 2014, 20, 15330-15333.

293. Development of DNA-Based Hybrid Catalysts through Direct Ligand Incorpororation: Toward Understanding of DNA-Based Asymmetric Catalysis
Park, S.; Zheng, L. J.; Kumakiri, S.; Sakashita, S.; Otomo, H.; Ikehata, K.; Sugiyama, H.
ACS Catalysis. 2014, 4, 4070-4073.

292. Next-Generation Sequencing Studies Guide the Design of Pyrrole-Imidazole Polyamides with Improved Binding Specifictiy by the Addition of -alanine
Chandran, A.; Li, Y.; Kizaki, S.; Pandian, G. N.; Hashiya, K.; Bando, T.; Sugiyama, H.
ChemBioChem. 2014, 15, 2647-2651.

291. Photoresponsive DNA Nanocapsule Having an Open/Close System for Capture and Release of Nanomaterials
Takenaka, T.; Endo, M.; Suzuki, Y.; Yang, Y.; Emura, T.; Hidaka, K.; Kato, T.; Mitata, T.; Namba, K.; Sugiyama, H.
Chem. Eur. J. 2014, 20, 14951-14954.

290. NanoScript: A Nanoparticle-Based Artificial Transcription Factor for Effective Gene Regulation
Patel, S.; Jung, D.; Yin, P.; Carlton, P.; Yamamoto, M.; Bando, T.; Sugiyama, H.; Lee, K. B.
ACS Nano. 2014, 8, 8959-8967.

289. Engineering RNA-Protein Complexes with Different Shapes for Imaging and Therapeutic Applications
Osada, E.; Suzuki, Y.; Hidaka, K.; Ohno, H.; Sugiyama, H.; Endo, M.; Saito, H.
ACS Nano. 2014, 8, 8130-8140.

288. Structure Evaluation of Tandem Hairpin Pyrrole-Imidazole Polyamides Recognizing Human Telomeres
Hirata, A.; Nokihara, K.; Kawamoto, Y.; Bando, T.; Sasaki, A.; Ide, S.; Maeshima, K.; Kasama, T.; Sugiyama, H.
J. Am. Chem. Soc. 2014, 136, 11546-11554.

287. Targeted Suppression of EVI1 Oncogene Expression by Sequence-specific Pyrrole-imidazole Polyamide
Junetha, S.; Pandian, G. N.; Sato, S.; Taniguchi, J.; Chandran, A.; Hashiya, K.; Bando, T.; Sugiyama, H.
Chem. Biol. 2014, 23, 1370-1380.

286. Amplification of Fluorescent DNA through Enzymatic Incorporation of a Highly Emissive Deoxyguanosine Analogue
Otomo, H.; Park, S.; Yamamoto, S.; Sugiyama, H.
RSC Adv. 2014, 4, 31341-31344.

285. Sequence-Specific DNA Alkylation and Transcriptional Inhibition by Long-Chain Hairpin Pyrrole-Imidazole Polyamide-Chlorambucil Conjugates Targeting CAG/CTG Trinucleotide Repeats.
Asamitsu, S.; Kawamoto, Y.; Hashiya, F.; Hashiya, K.; Yamamoto, M.; Kizaki, S.; Bando, T.; Sugiyama, H.
Bioorg. Med. Chem 2014, 22, 4646-4657.

284. AFM Analysis of Changes in Nucleosome Wrapping Induced by DNA Epigenetic Modification
Kizaki, S.; Suzuki, Y.; Takenaka, T.; Endo, M.; Sugiyama, H.
Biomater. Sci. 2014, 2, 1399-1403.

283. Chemical Modification of a Synthetic Small Molecule Boosts its Biological Efficacy against Pluripotency Genes in Mouse Fibroblast
Saha, A.; Pandian, G. N.; Sato, S.; Taniguchi, J.; Kawamoto, Y.; Hashiya, K.; Bando, T.; Sugiyama, H.
ChemMedChem 2014, 9, 2374-2380.

282. Single-Molecule Mechanochemical Sensing Using DNA Origami Nanostructures
Koirala, D.; Shrestha, P.; Emura, T.; Hidaka, K.; Mandal, S.; Endo, M.; Sugiyama, H.; Mao, H.
Angew. Chem. Int. Ed. 2014, 126, 8275-8279.

281. Helical DNA Origami Tubular Structures with Various Sizes and Arrangements
Endo, M.; Yamamoto, S.; Emura, T; Hidaka, K.; Morone, N.; Heuser, J. E.; Sugiyama, H.
Angew. Chem. Int. Ed. 2014, 53, 7484-7490.

280. Sequence-specific DNA Alkylation by Tandem Py-Im Polyamide Conjugates
Taylor, R. D.; Kawamoto, Y.; Hashiya, K.; Bando, T.; Sugiyama, H.
Chem. Asian J. 2014, 9, 2527-2533.

279. A Lock-and-Key Mechanism for the Controllable Fabrication of DNA Origami Structures
Rajendran, A.; Endo, M.; Hidaka, K.; Shimada, N.; Maruyama, A.; Sugiyama, H.
Chem. Comm. 2014, 50, 8743-8746.

278. Alteration of Epigenetic Program to Recover Memory and Alleviate Neurodegeneration: Prospects of Multi-target Molecules
Pandian, G. N.; Taylor, R. D.; Junetha, S.; Saha, A.; Chandran, A.; Vaijayanthi, T.; Sugiyama, H.
Biomater. Sci. 2014, 2, 1043-1056.

277. Direct Analysis of Holliday Junction Resolving Enzyme in a DNA Origami Nanostructure
Suzuki, Y.; Endo, M.; Canas, C.; Ayora, S.; Alonso, J. C.; Sugiyama, H.; Takeyasu, K.
Nucleic Acids Res. 2014, 42, 7421-7428.

276. Single Molecule Visualization and Characterization of Sox2-Pax6 Complex Formation on a Regulatory DNA Element Using a DNA Origami Frame
Yamamoto, S.; De, D.; Hidaka, K.; Kim, K. K.; Endo, M.; Sugiyama, H.
Nano Lett. 2014, 14, 2286-2292.

275. The Origin of Enantioselectivity for Intramolecular Friedel-Crafts Reaction Catalyzed by Supramolecular Cu/DNA catalyst Complex
Petrova, G. P.; Ke, Z.; Park, S.; Sugiyama, H.; Morokuma, K.
Chem. Phys. Lett. 2014, 600, 87-95.

274. Cellular Reprogramming for Pancreatic -Cell Regeneration: Clinical Potential of Small Molecule Control
Pandian, G. N.; Taniguchi, J.; Sugiyama, H.
Clin. Transl. Med. 2014, 3: 6.

273. Investigation of B-Z Transitions with DNA Oligonucleotides Containing 8-Methylguanine
Chen, Y-H.; Park, S.; Otomo, H.; Sakashita, S.; Sugiyama, H.
Artificial DNA: PNA & XNA. 2014, 5, e28226-1-e28226-7.

272. Direct Observation of the Dual-Switching Behaviors Corresponding to the State Transition in a DNA Nanoframe
Yang, Y.; Endo, M.; Suzuki, Y.; Hidaka, K.; Sugiyama, H.
Chem. Comm. 2014, 50, 4211-4213.

271. Targeted Editing of Therapeutic Genes using DNA-Based Transcriptional Activators: Scope and Challenges
Pandian, G. N.; Sugiyama, H.
Chemical Biology of Nucleic Acids:Fundamentals and Clinical Applications (Springer Book) 2014, 347-365.

270. Direct and Single-Molecule Visualization of the Solution-State Structures of G-Hairpin and G-Triplex Intermediates
Rajendran, A.; Endo, M.; Hidaka, K.; Sugiyama, H.
Angew. Chem. Int. Ed. 2014, 126, 4191-4196.

269. Single-Molecule Imaging of Dynamic Motions of Biomolecules in DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy
Endo, M.; Sugiyama, H.
Acc. Chem. Res. 2014, 47, 1645-1653.

268. Specific Alkylation of Human Telomere Repeat Sequences by a Tandem-Hairpin Motif of Pyrrole-Imidazole Polyamides with Indole-Seco-CBI
Yamamoto, M.; Bando, T.; Kawamoto, Y.; Taylor, R. D.; Hashiya, K.; Sugiyama, H.
Bioconjugate Chem. 2014, 25, 552-559.

267. Direct Observation of G-Quadruplexes using DNA Origami Nanoscaffold
Rajendran, A.; Li, Y.; Endo,M. ; Sugiyama, H.
E. Book Chapter:DNA G-quadruplexes as new anticancer targets, (Ed. Ryan De Vooght-Johnson), Future Science Ltd, London. 2014

266. Dynamic Assembly/Disassembly Processes of Photoresponsive DNA Origami Nanostructures Directly Visualized on a Lipid Membrane Surface
Suzuki, Y.; Endo, M.; Yang, Y.; Sugiyama, H.
J. Am. Chem. Soc. 2014, 136, 1714-1717.

265. Distinct DNA-based Epigenetic Switches Trigger Transcriptional Activation of Silent Genes in Human Dermal Fibroblasts
Pandian, G. N.; Taniguchi, J.; Junetha, S.; Sato, S.; Han, L.; Saha, A.; Chandran, A.; Bando, T.; Nagase, H.; Thangavel, V.; Taylor, R. D.; Sugiyama, H.
Sci. Rep. 2014, 4, 3843.

264. G-quadruplex-binding Ligand-induced DNA Synapsis Inside a DNA Origami Frame
Rajendran, A.; Endo, M.; Hidaka, K.;Tran, P. L. T.; Teulade-Fichou, M-P.; Mergny, J-L.; Sugiyama, H.
RSC Adv. 2014, 4, 6346-6355.

263. DNA Origami Based Visualization System for Studying Site-Specific Recombination Events
Suzuki, Y.; Endo, M.; Katsuda, Y.;Ou, K.; Hidaka, K.; Sugiyama, H.
J. Am. Chem. Soc. 2014, 136, 211-218.

262. Highly Emissive Deoxyguanosine Analogue Capable of Direct Visualization of B-Z Transition
Park, S.; Otomo, H.; Zheng, L.; Sugiyama, H.
Chem. Comm. 2014, 50, 1573-1575.

261. Sequence-specific DNA Alkylation Targeting for Kras Codon 13 Mutation by Pyrrole-Imidazole Polyamide seco-CBI Conjugates
Taylor, R. D.; Asamitsu, S.; Takenaka, T.; Yamamoto, M.; Hashiya, K.; Kawamoto, Y.; Bando, T.; Nagase, H.; Sugiyama, H.
Chem. Eur. J. 2014, 20, 1310-1317.

260. Controlling Electron Rebound Within Four-Base -Stacks in Z-DNA by Changing the Sugar Moiety from Deoxy- to Ribonucleotide
Sannohe, Y.; Kizaki, S.; Kanesato, S.; Fujiwara, A.; Morinaga, H.; Tashiro, R.; Sugiyama, H.
Chem. Eur. J. 2014, 20, 1223-1225.

259. Sequence-Specific DNA Recognition by Cyclic Pyrrole-Imidazole Cysteine-Derived Polyamide Dimers
Yamamoto, M.; Bando, T.; Morinaga, N.; Kawamoto, Y.; Hashiya, K.; Sugiyama, H.
Chem. Eur. J. 2014, 20, 752-759.

258. Construction and Characterization of Cy3- or Cy5-Conjugated Hairpin Pyrrole-Imidazole Polyamides Binding to DNA in the Nucleosome
Han, Y-W.; Tsunaka, Y.; Yokota, H.; Matsumoto, T.; Kashiwazaki, G.; Morinaga, H.; Hashiya, K.; Bando, T.; Sugiyama, H.; Harada, Y.
Biomater. Sci. 2014, 2, 297-307.

257. State-of-the Art High-Speed Atomic Force Microscopy for Investigation of Single-Molecular Dynamics of Proteins
Rajendran, A.; Endo, M.; Sugiyama, H.
Chem. Rev. 2014, 114, 1493-1520.

256. CGmCGCG is a Versatile Substrate with which to Evaluate Tet Protein Activity
Kizaki, S.; Sugiyama, H.
Org. Biomol. Chem. 2014, 12, 104-107.


2013

255. Conjugation of Peptide Nucleic Acid with a Pyrrole-Imidazole Polyamide to Specifically Recognize and Cleave DNA
Kameshima, W.; Ishizuka, T.; Minoshima, M.; Yamamoto, M.; Sugiyama, H.; Xu, Y.; Komiyama, M.
Angew. Chem. Int. Ed. 2013, 52, 13681-13684.

254. HIV-1 Nucleocapsid Proteins as Molecular Chaperones for Tetramolecular Antiparallel G-Quadruplex Formation
Rajendran, A.; Endo, M.; Hidaka, K.; Tran, P. L. T.; Mergny, J-L.; Gorelick, R. J.; Sugiyama, H.
J. Am. Chem. Soc. 2013, 135, 18575-18585.

253. Regulation of B-Z Conformational Transition and Complex Formation with a Z-form Binding Protein by Introduction of Constraint to Double-stranded DNA using DNA Nanoscaffold
Endo, M.; Inoue, M.; Suzuki, Y.; Masui, C.; Morinaga, H.; Hidaka, K.; Sugiyama, H.
Chem. Eur. J. 2013, 19, 16887-16890.

252. Clinical Grade iPS Cells: Need For Versatile Small Molecules and Optimal Cell Sources
Wu, Y-L.; Pandian, G. N.; Ding, Y-P.; Zhang, W.; Tanaka, Y.; Sugiyama, H.
Chem. Biol. 2013, 20, 1311-1322.

251. Development of a New Method for Synthesis of Tandem Hairpin Pyrrole-Imidazole Polyamide Probes Targeting Human Telomeres
Kawamoto, Y.; Bando, T.; Kamada, F.; Li, Y.; Hashiya, K.; Maeshima, K.; Sugiyama, H.
J. Am. Chem. Soc. 2013, 135, 16468-16477.

250. A Synthetic Small Molecule for Targeted Transcriptional Activation of Germ Cell Genes in a Human Somatic Cell
Han, L.; Pandian, G. N.; Junetha, S.; Sato, S.; Chandran, A.; Taniguchi, J.; Saha, A.; Bando, T.; Nagase, H.; Sugiyama, H.
Angew. Chem. Int. Ed. 2013, 52, 13410-13413.
(Hot Paper)

249. Chemically Induced Pluripotent Stem Cells (CiPSCs): A Transgene-Free Approach
Masuda, S.; Wu, J.; Hishida, T.; Pandian, G. N.; Sugiyama, H.; Belmonte, J. C. I.
J. Mol. Cell Biol. 2013, 5, 354-355.

248. Guided Assembly of Tetramolecular G-Quadruplexes
Yatsunyk, L. A.; Pietrement, O.; Albrecht, D.; Tran, P. L. T., Renciiuk, D.; Sugiyama, H.; Arbona, J-M.; Aime, J-P.; Mergny, J-L.
ACS Nano. 2013, 7, 5701-5710.

247. Controlling the Stoichiometry and Strand Polarity of a Tetramolecular G-Quadruplex Structure by Using a DNA Origami Frame
Rajendran, A.; Endo, M.; Hidaka, K.; Thao, P. L. T.; Mergny, J-L.; Sugiyama, H.
Nucleic Acids Res. 2013, 41, 8738-8747.

246. Solid-Supported DNA for Asymmetric Synthesis: a Stepping-Stone toward Practical Applications
Park, S.; Ikehata, K.; Sugiyama, H.
Biomater. Sci. 2013, 1, 1034-1036.

245. Effect of Single Pyrrole Replacement with -Alanine on DNA Binding Affinity and Sequence Specificity of Hairpin Pyrrole/Imidazole Polyamides Targeting 5L-GCGC-3L
Han, Y-W.; Kashiwazaki, G. ;Morinaga, H.; Matsumoto, T.; Hashiya, K.; Bando, T.; Sugiyama, H.
Bioorg. Med. Chem.2013, 21, 5436-5441.

244. The C-Kit Receptor-Mediated Signal Transduction and Tumor-Related Diseases
Liang, J.; Wu, Y.; Chen, B.; Zhang, W.; Tanaka, Y.; Sugiyama, H.
Int. J. Biol. Sci. 2013, 9, 435-443.

243. Synthesis and Biological Evaluation of a Targeted DNA-binding Transcriptional Activator with HDAC8 Inhibitory Activity
Saha, A.; Pandian, G. N.; Sato, S.; Taniguchi, J.; Hashiya, K.; Bando, T.; Sugiyama, H.
Bioorg. Med. Chem. 2013, 21, 4201-4209.

242. RNA Binding Properties of Novel Gene Silencing Pyrrole-Imidazole Polyamides
Iguchi, A.; Fukuda, N.; Takahashi, T.; Watanabe, T.; Matsuda, H.; Nagase, H.; Bando, T.; Sugiyama, H.; Shimizu, K.
Biol. Pharm. Bull. 2013, 36, 1152-1158.

241. RNA-templated DNA Origami Structures
Endo, M.; Yamamoto, S.; Tatsumi, K.; Emura, T.; Hidaka, K.; Sugiyama, H.
Chem. Comm. 2013, 49, 2879-2881.

240. Sequence-Specific Electron Injection into DNA from an Intermolecular Electron Donor
Morinaga, H.; Takenaka, T.; Hashiya, F.; Kizaki, S.; Hashiya, K.; Bando, T.; Sugiyama, H.
Nucleic Acids Res. 2013, 41, 4724-4728.

239. Hydrochlorothiazide Enhances UVA-induced DNA Damage
Kunisada, M.; Masaki, T.; Ono, R.; Morinaga, H.; Nakano, E.; Yogianti, F.; Okunishi, K.; Sugiyama, H.; Nishigori, C.
Photochemistry and Photobiology. 2013, 39, 649-652.

238. Long-loop G-Quadruplexes are Misfolded Population Minorities with Fast Transition Kinetics in Human Telomeric Sequences
Koirala, D.; Ghimire, C.; Bohrer, C.; Sannohe, Y.; Sugiyama, H.; Mao, H.
J. Am. Chem. Soc. 2013, 135, 2235-2241.

237. Direct and Real-Time Observation of Rotary Movement of a DNA Nanomechanical Device
Rajendran, A.; Endo, M.; Hidaka, K.; Sugiyama, H.
J. Am. Chem. Soc. 2013, 135, 1117-1123.

236. Design of a New Fluorescent Probe: Pyrrole/Imidazole Hairpin Polyamides with Pyrene Conjugation at Their -Turn
Vaijayanthi, T.; Bando, T.; Hashiya, K.; Pandian, G. N.; Sugiyama, H.
Bioorg. Med. Chem. 2013, 21, 852-855.

235. Helical Structure and Circular Dichroism Spectra of DNA: A Theoretical Study
Miyahara, T.; Nakatsuji, H.; Sugiyama, H.
J. Phys. Chem. A. 2013, 117, 42-55.

234. Control of the Two-dimensional Crystallization of DNA Origami with Various Loop Arrangements
Rajendran, A.; Endo, M.; Hidaka, K.; Sugiyama, H.
Chem. Comm. 2013, 49, 686-688.

233. DNA Origami Technology for Biomaterials Applications
Endo, M.; Yang, Y.; Sugiyama, H.
Biomater. Sci. 2013, 1, 347-360.

232. Strategies to Modulate Heritable Epigenetic Defects in Cellular Machinery: Lessons from Nature
Pandian, G. N.; Sugiyama, H.
Pharmaceuticals 2013, 6, 1-24.

231. Photoreactivities of 5-Bromouracil-containing RNAs.
Morinaga, H.; Kizaki, S.; Takenaka, T.; Kanesato, S.; Sannohe, Y.; Tashiro, R.; Sugiyama, H.
Bioorg. Med. Chem. 2013, 21, 466-469.

230. G-Quadruplex Nanostructures Probed at the Single Molecular Level by Force-Based Methods
Dhakal, S.; Mao, H.; Rajendran, A.; Endo, M.; Sugiyama, H.
Guanine Quartets: Structure and Application(Royal Society of Chemistry) 2013, 73-85.


2012

229. Photo-Controllable DNA Origami Nanostructures Assembling into Predesigned Multiorientational Patterns
Yang, Y.; Endo, M.; Hidaka, K.; Sugiyama, H.
J. Am. Chem. Soc. 2012, 134, 20645-20653.

228. Immunotherapies: The Blockade of Inhibitory Signals
Wu, Y.; Liang, J.; Zhang, W.; Tanaka, Y.; Sugiyama, H.
Intl. J. Biol. Sci. 2012, 8, 1420-1430.

227. DNA as a Chiral Scaffold for Asymmetric Synthesis.
Park, S.; Sugiyama, H.
Molecules 2012, 17, 12792-12803.

226. Deciphering DNA-Based Asymmetric Catalysis through Intramolecular Friedel-Craft Alkylation.
Park, S.; Watabe, R.; Ikehata, K.; Hidaka, Y.; Rajendran, A.; Sugiyama, H.
Chem. Comm. 2012, 48, 10398-10400.

225. Binding of Hairpin Pyrrole and Imidazole Polyamides to DNA: Relationship between Torsion Angle and Association Rate Constants.
Han, Y-W.; Matsumoto, T.; Yokota, H.; Kashiwazaki, G.; Morinaga, H.; Hashiya, k.; Bando, T.; Harada, Y.; Sugiyama, H.
Nucleic Acids Res. 2012, 40, 11510-11517.

224. Progress and Prospects of Pyrrole-Imidazole Polyamide-Fluorophore Conjugate as Sequence-Selective DNA Probes.
Vaijayanthi, T.; Bando, T.; Pandian, G. N.; Sugiyama, H.
ChemBioChem. 2012, 13, 2170-2185.

223. Single-Molecule Visualization of the Hybridization and Dissociation of Photoresponsive Oligonucleotides and Their Reversible Switching Behavior in a DNA Nanostructure.
Endo, M.; Yang, Y.; Hidaka, K.; Sugiyama, H.
Angew. Chem. Int. Ed. 2012, 51, 10518-10522.

222. Synthesis of Pyrrole-Imidazole Polyamide seco-1-Chloromethyl-5-hydroxy-1,2-dihydro-3H-benz[e]indole Conjugates with a Vinyl Linker Recognizing 7 bp DNA sequence.
Takagaki, T.; Bando, T.; Sugiyama, H.
J. Am. Chem. Soc. 2012, 134, 13074-13081.

221. A Synthetic Small Molecule for Rapid Induction of Multiple Pluripotency Genes in Mouse Embryonic Fibroblast.
Pandian, G. N.; Nakano, Y.; Sato, S.; Morinaga, H.; Bando, T.; Nagase, H.; Sugiyama, H.
Sci. Rep. 2012, 2, 544.

220. Design and Development of Nanosized DNA Assemblies in Polypod-Like Structures as Efficient Vehicles for Immunostimulatory CpG Motifs to Immune Cells.
Mohri, K.; Nishikawa, M.; Takahashi, N.; Shiomi, T.; Matsuoka, N.; Ogawa, K.; Endo, M.; Hidaka, K.; Sugiyama, H.; Takahashi, Y.; Takakura, Y.
ACS Nano, 2012, 6, 5931-5940.

219. Direct Visualization of the Movement of a Single T7 RNA Polymerase and the Transcription on a DNA Nanostructure.
Endo, M.; Tatsumi, K.; Terushima, K.; Katsuda, Y.; Hidaka, K.; Harada, Y.; Sugiyama, H.
Angew. Chem. Int. Ed. 2012, 51, 8778-8782.

218. Recognition by Nonaromatic and Stereochemical Subunit-Containing Polyamides of the Four Watson-Crick Base Pairs in the DNA Minor Groove.
Zhang, H. F.; Wu, Y. L.; Jiang, S. K.; Wang, P.; Sugiyama, H.; Chen, X. L.; Zhang, W.; Ji, Y. J.; Guo, C. X.
ChemBioChem. 2012, 13, 1366-1374.

217. Programmable Genetic Switiches to Control Transcrpitional Machinery of Pluripotency.
Pandian, G. N.; Sugiyama, H.
Biotechnol. J. 2012, 7, 798-809.

216. Structural and Fuctional Analysis of Proteins by High-Speed Atomic Force Microscopy.
Rajendran, A.; Endo, M.; Sugiyama, H.
Adv. Protein Chem. Struct. Biol. 2012, 87, 5-55.

215. Development of Programmable Small DNA-Binding Molecules with Epigenetic Activity for Induction of Core Pluripotency Genes.
Pandian, G. N.; Ohtsuki, A.; Bando, T.; Sato, S.; Hashiya, K.; Sugiyama, H.
Bioorg. Med. Chem. 2012, 20, 2656-2660.

214. Sequence-Selective Single Molecule Alkylation with a Pyrrole-Imidazole Polyamide Visualized in a DNA Nanoscaffold.
Yoshidome, T.; Endo, M.; Kashiwazaki, G.; Hidaka, K.; Bando, T.; Sugiyama, H.
J. Am. Chem. Soc. 2012, 134, 4654-4660.

213. A DNA-Based Molecular Motor that can Navigate a Network of Tracks.
Wickham, S. F. J; Bath, J.; Katsuda, Y.; Endo, M.; Hidaka, K.; Sugiyama, H.; Tuberfield , A. J.
Nature Nanotechnol. 2012, 7, 169-173.

212. DNA Origami: Synthesis and Self-Assembly.
Rajendran, A.; Endo, M.; Sugiyama, H.
Curr. Protoc. Nucleic Acid Chem. 2012, 48, 12.9.1-12.9.18.

211. Single Strand DNA Catenane Synthesis Using the Formation of G-Quadruplex Structure.
Sannohe, Y.; Sugiyama, H.
Bioorg. Med. Chem. 2012, 20, 2030-2034.

210. Synthesis and Biological Properties of Highly Sequence-Specific-Alkylating N- Methylpyrrole- N- Methylimidazole Polyamide Conjugates.
Kashiwazaki, G.; Bando, T.; Yoshidome, T.; Masui, S.; Takagaki, T.; Hashiya, K.; Pandian, G.N.; Yasuoka, J.; Akiyoshi, K.; Sugiyama, H.
J. Med. Chem. 2012, 55, 2057-2066.

209. SWI/SNF-Mediated Chromatin Remodeling Induces Z-DNA Formation on a Nucleosome.
Mulholland, N.; Xu, Y.; Sugiyama, H.; Zhao, K.
Cell and Bioscience, 2012, 2:3.

208. Zinc Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures.
Nakata, E.; Fong, L.W.; Uwatoko, C.; Kiyonaka, S.; Mori, Y.; Katsuda, Y.; Endo, M.; Sugiyama, H.; Morii, T.
Angew. Chem. Int. Ed. 2012, 51, 2421-2424.

207. Transcription Regulation System Mediated by Mechanical Operation of a DNA Nanostructure. Endo, M.; Miyazaki, R.; Emura, T.; Hidaka, K.; H.; Sugiyama, H.
J. Am. Chem. Soc. 2012, 134, 2852-2855.

206. Intramolecular Folding in Three Tandem Guanine Repeats of Human Telomeric DNA.
Koirala, D.; Mashimo, T.; Sannohe, Y.; Yu, Z.; Mao, H.; Sugiyama, H.
Chem. Comm. 2012, 48, 2006-2008.

205. Single-Molecule Analysis Using DNA Origami.
Rajendran, A.; Endo, M.; Sugiyama, H.
Angew. Chem. Int. Ed. 2012, 51, 874-890.

204. Discrimination between T/A and A/T Base Pairs with Pyrrole-Imidazole Polyamides Substituted with Chiral -Hyroxyl--Aminobutyric Acid/-Alanine Pair.
Zhang, W.; Jiang, S.K.; Wu, Y.L.; Guo, C.X.; Zhang, H.F.; Sugiyama, H.; Chen, X.L.
ChemBioChem, 2012, 13, 47-50.


2011

203. Single-Molecule Platform for Investigation of Interactions Between G-Quadruplex and Small-Molecule Ligands.
Koirala, D.; Dhakal, S.; Ashbridge, B.; Sannohe, Y.; Rodriguez, R.; Sugiyama, H.; Balasubramanian, S.; Mao, H.
Nature Chemistry. 2011, 3, 782-787.

202. Synthetic Small Molecules for Epigenetic Activation of Pluripotency Genes In Mouse Embryonic Fibroblasts.
Pandian, G. N.; Shinohara, K.; Ohtsuki, A.; Nakano, Y.; Minoshima, M.; Bando, T.; Nagase, H.; Yamada, Y.; Watanabe, A.; Terada, N.; Sato, S.; Morinaga, H.; Sugiyama, H.
ChemBioChem. 2011, 12, 2822-2828.

201. A DNA Ligand Designed to Antagonize EBNA1 Represses EPSTEIN-BARR Virus-Induced Immortalization.
Noguchi, K.; Yasuda, A.; Minoshima, M.; Kashiwazaki, G.; Kanda, T.; Katayama, K.; Mitsuhashi, J.; Bando, T.; Sugiyama, H.; Sugimoto, Y.
Cancer Sci. 2011, 102, 2221-2230.

200. Cysteine Cyclic Pyrrole-Imidazole Polyamide for Sequence-Specific Recognition In the DNA Minor Groove.
Morinaga, H.; Bando, T.; Takagaki, T.; Yamamoto, M.; Hashiya, K.; Sugiyama, H.
J. Am. Chem. Soc. 2011, 133, 18924-18930.

199. Evalution of PI polyamide Conjugates With Eight-Base Pair Recognition and Improvement of The Aqueous Solubility by PEGylation.
Takagaki, T.; Bando, T.; Kitano, M.; Hashiya, K.; Kashiwazaki, G.; Sugiyama, H.
Bioorg. Med. Chem. 2011, 19, 5896-5902.

198. Programmed Placement of Gold Nanoparticles Onto a Slit-Type DNA Origami Scaffold.
Endo, M.; Yang, Y.; Emura, T.; Hidaka, K.; Sugiyama, H.
Chem. Commun. 2011, 47, 10743-10745.

197. Photo-Cross-Linking-Assisted Thermal Stability of DNA Origami Structures and Its Application for Higher-Temperature Self-Assembly.
Rajendran, A.; Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H.
J. Am. Chem. Soc. 2011, 133, 14488-14491.

196. Recent Progress in DNA Origami Technology.
Endo, M.; Sugiyama, H.
Curr. Protoc. Nucleic Acid Chem. 2011, 12.8.1-17.8.19.

195. Direct Observation of Stepwise Movement of a Synthetic Molecular Transporter.
Wickham, S. F. J; Endo, M.; Katsuda, Y.; Hidaka, K.; Bath, J.; Sugiyama, H.; Turberfield, A. J.
Nature Nanotechnol. 2011, 6, 166-169.

194. Two-Dimensional DNA Origami Assemblies Using a Four-Way Connector.
Endo, M.; Sugita, T.; Rajendran, A.; Katsuda, Y.; Emura, T.; Hidaka, K.; Sugiyama, H.
Chem. Commun. 2011, 47, 3213-3215.

193. Photo Controllable Sequence-Specific DNA Alkylation by Pyrrole-Imidazole Polyamide seco-CBI Conjugate.
Park, S.; Bando, T.; Shinohara, K.; Sugiyama, H.
Biocojugate Chem. 2011, 22, 120-124.

192. Direct AFM Observation of an Opening Event of a DNA Cuboid Constructed via a Prism Structure.
Endo, M.; Hidaka, K.; Sugiyama, H.
Org. Biomol. Chem.2011, 9, 2075-2077.

191. Programmed Two-Dimensional Self-Assembly of Multiple DNA Origami Jigsaw Pieces.
Rajendran, A.; Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H.
ACS Nano, 2011, 5, 665-671.

190. Transcriptional Inhibition of Progressive Renal Disease by the Gene Silencing Pyrrole-Imidazole polyamide Targeted to the TGF-1Promoter.
Matsuda, H.; Fukuda, N.; Ueno, T.; Katakawa, M.; Wang, X.; Watanabe, T.; Matsui, S.; Aoyama, T.; Saito, K.; Bando, T.; Matsumoto, Y.; Nagase, H.; Matsumoto, K.; Sugiyama, H.
Kidney Int. 2011, 79, 46-56.


2010

189. A Versatile DNA Nanochip for Direct Analysis of DNA Base-Excision Repair.
Endo, M.; Katsuda,Y.;Hidaka, K,; Sugiyama, H.
Angew. Chem. Int. Ed. 2010, 49, 9412-9416.

188. Visualization of Dynamic Conformation Switching of the G-Quadruplex in a DNA Nanostructure.
Sannohe, Y.; Endo, M.; Katsuda, Y.; Hidaka, K.; Sugiyama, H.
J. Am. Chem. Soc. 2010, 132, 16311-16313.

187. Error-Prone Translesion DNA Synthesis by Escherichia coli DNA Polymerase IV (DinB) Templates Containing 1,2-Dihydro-2-oxoadenine.
Hori, M.; Yonekura, S.I.; Nohmi, T.; Gruz, P.; Sugiyama, H.;Yonei, S.; Zhang Akiyama, Q. M.
J. Nucleic Acids. 2010, 807579-807588.

186. The Distance between Donor and Acceptor Affects the Proportion of C1' and C2' Oxidation Products of DNA in a BrU-containing Excess Electron Transfer System.
Tashiro, R.; Ohtsuki, A.; Sugiyama, H.
J. Am. Chem. Soc. 2010, 132, 14361-14363.

185. Folding Pathways of Human Telomeric Type-1 and Type-2 G-Quadruplex Structures.
Mashimo, T.; Yagi, H.; Sannohe, Y.; Rajendran, A.; Sugiyama, H.
J. Am. Chem. Soc. 2010, 132, 14910-14918.

184. Synthesis of Bicyclic Enediynes That Possess a Photosensitive Triggering Device and Exhibit strong DNA Cleaving Activity.
Tanaka, H,; Tanaka, Y,; Minoshima, M.; Yamaguchi, S.; Takahashi, H.; Fuse, S.; Doi, T.; Kusumi, T.;Kawauchi, S.; Sugiyama, H.; Takahashi, T.
Chem. Commum. 2010, 46, 5942-5944.

183. Programmed-Assembly System Using DNA Jigsaw Pieces.
Endo, M.;Sugita, T.; Katsuda, Y.; Hidaka, K.; Sugiyama, H.
Chem. Eur. J. 2010, 16, 5362-5368.

182. Alkylation of a Human Telomere Sequence by Heterotrimeric Chlorambucil PI Polyamide Conjugates.
Kashiwazaki, G.; Bando, T.; Shinohara, K.; Minoshima, M.; Kumamoto, H.; Nishijima, S.; Sugiyama, H.
Bioorg. Med. Chem. 2010, 18, 2887-2893.

181. Inhibition of MMP-9 Transcription and Suppression of Tumor Metastasis by Pyrrole-Imidazole Polyamide.
Wang, X.; Nagase, H.; Watanabe, T.; Nobusue, H.; Suzuki, T.; Kimura, M.; Mishra, R.; Shinojima, Y.; Kawashima, H.;Takagi, K.; Igarashi, J.; Takayama, T.; Fukuda, N.; Sugiyama, H.
Cancer Sci. 2010, 101, 759-766.

180. DNA-Based Hybrid Catalysts for an Asymmertic Organic Synthesis.
Park, S.; Sugiyama, H.
Angew. Chem. Int. Ed. 2010, 49, 3870-3878.

179. Overview of Formation of G-quadruplex Structure.
Sannohe, Y.; Sugiyama, H.
Curr. Protoc. Nucleic Acid Chem. 2010, 17.2.1-17.2.17.

178. Chiral Wedge Molecule inhibits Telomerase Activity.
Shinohara, K.; Sannohe, Y.; Kaieda, S.; Tanaka, K.; Osuga, H.; Xu, Y.; Bando, T.; Sugiyama, H.
J. Am. Chem Soc. 2010, 132, 3778-3782.

177. Regulation of DNA Methylation using Different Tensions in the Double Strands Constructed in a Defined DNA Nanostructure.
Endo, M., Katsuda, Y.; Hidaka, K.; Sugiyama, H.
J. Am. Chem. Soc. 2010, 132, 1592-1597.

176. Anticancer Activities of Alkylating Pyrrole-Imidazole Polyamides with Specific Sequence Recognition.
Shinohara, K.; Bando, T.; Sugiyama, H.
Anticancer Drugs. 2010, 21, 228-242.

175. Comparative Analysis of DNA Alkylation by Conjugates between Pyrrole-Imidazole Hairpin Polyamides and Chlorambucil or seco-CBI.
Minoshima, M.; Bando, T.; Shinohara, K.; Kashiwazaki, K.; Nishijima, S.; Sugiyama, H.
Bioorg. Med. Chem. 2010, 18, 1236-1243.

174. Cell Permeability of Py-Im Polyamide-Fluorescein Conjugates: Influence of Molecular Size and Py/Im Content.
Nishijima, S.; Shinohara, K.; Bando,T.; Minoshima, M.; Kashiwazaki, G.; Sugiyama, H.
Bioorg. Med. Chem. 2010, 18, 978-983.

173. Potent Activity Against K562 Cells by Polyamide-seco-CBI Conjugates Targeting Histone H4 Genes.
Minoshima, M.; Chou, J. C.; Lefebvre, S.; Bando, T.; Shinohara, K.; Gottesfeld, J. M.; Sugiyama, H.
Bioorg. Med. Chem. 2010, 18, 168-174.