Z-form DNA-RNA hybrid blocks DNA replication
S. Y. Wang, Y. Xu*
Nucleic Acids Res. 2025 53, gkaf135 (DOI)(IF = 16.7)

Mirror-Image RNA: a Right-Handed Z-Form RNA and its Ligand Complex
Y. Song, S. Y. Wang, Y. Xu*
Molecules 2024 29, 4900 (DOI)(IF = 4.927)

RNA structure promotes liquid-to-solid phase transition of short RNAs in neuronal dysfunction
S. Y. Wang, Y. Xu*
Commun. Biol. 2024, 7, 137 (DOI) (IF = 6.548)

DNA and RNA G-quadruplexes in human telomere: Structures, properties, and applications
Y. Xu*, M. Komiyama
Molecules 2024, 29, 174 (DOI) (IF = 4.927)

Unusual topological RNA G-quadruplex formed by an RNA duplex: Implications for the dimerization of SARS-CoV-2 RNA
S. Y. Wang, Y. Song, Z. Y. He, H. Saneyoshi, R. Iwakiri, P. Y. Xu, C. Q. Zhao, X. G. Qu, Y. Xu*
Chem. Commun. 2023, 59, 12703-12706 (DOI) (IF = 6.065)

A Unique G-Quadruplex Aptamer: A Novel Approach for Cancer Cell Recognition, Cell Membrane Visualization, and RSV Infection Detection
C. D. Xiao, M. Q. Zhong, Y. Gao, Z. L. Yang, M. H. Jia, X. H. Hu, Y. Xu, X. C. Shen
Int. J. Mol. Sci. 2023, 24, 14344 (DOI) (IF = 5.6)

Unveiling the role of G-quadruplex structure in promoter region: Regulation of ABCA1 expression in macrophages possibly via NONO protein recruitment
C. D. Xiao, M. H. Jia, M. Q. Zhong, Y. Xu, Z. T. Yu, Z. Y. He, X. Lu, Y. Zhou, L. U. Fu, X. C. Shen
Int J Biol Macromol. 2023, 245, 125442 (DOI) (IF = 8.025)

In Cell ¹⁹F NMR for G-quadruplex
Y. Xu*
Handbook of Chemical Biology of Nucleic Acids 2023, Springer Nature, In press (DOI)

Oligonucleotide containing 8-trifluoromethyl-2'-deoxy-guanosine as a Z-DNA probe
H. L. Bao, Y. Xu*
Method Mol. Biol. 2023, 2651, 115-130 (DOI)

A fish herpesvirus highlights functional diversities among ZAlpha domains related to phase separation induction and A-to-Z conversion
M.A.Diallo, S. Pirotte, Y. Hu, L.Morvan, K. Rakus, N.M.suarez, L.Po-Tsang, H. Saneyoshi, Y. Xu, A. J. Davison, P. Tompa, J. L. Sussman, A. Vanderplasschen
Nucleic Acids Res. 2023, 22, 806-830 (DOI) (IF = 19.160)

Click chemistry for fluorescence imaging by combination of a BODIPY-based 'Turn-On' probe and a norbornene glucosamine
Z.Y. He, T. Ishizuka, Y. Hishikawa, Y. Xu*
Chem. Commun. 2022, 58, 12479-12482 (DOI) (IF = 6.222)

ADAR1 masks the cancer immunotherapeutic promise of ZBP1-driven necroptosis
T. Zhang, C. Yin, A. Fedorov, L.J Qiao, H. L. Bao, N. Beknzarov, S.Y. Wang, A. Gautam, R.M. Williams, J.C.Crawford, S.Peri.V.Studitsky, A.A.Beg, P.Thomas,C.Walkley, Y. Xu, M.Poptsove, A.Herbert, S. Balachandran
Nature 2022, 606, 594-602 (DOI) (IF = 49.962)

An Advanced Detection System for In Situ Hybridization Using a Fluorescence Resonance Energy Transfer-based Molecular Beacon Probe
N. Choijookhuu, Y. Shibata, T. Ishizuka, Y. Xu, T. Koji, Y. Hishikawa
ACTA HISTOCHEMICA ET CYTOCHEMICA 2022, 55, 5 (DOI)

A small ligand that selectively binds to the G-quadruplex at the human vascular endothelial growth factor internal ribosomal entry site and represses the translation X. X. Hu, S. Q. Wang, S. Q. Gan, L.Liu. M. Q. Zhong, M. H. Jia, F. Jiang, Y. Xu, C. D. Xiao, X. C. Shen
Front Chem. 2021, 9, 781198 (DOI) (IF = 5.221)

Oligonucleotide containing 8-trifluoromethyl-2'-deoxy-guanosine as a Z-DNA probe H. L. Bao, Y. Xu*
Method Mol. Biol. 2021, in press

Systematic Approach to DNA Aptamer Design Using Amino Acid-Nucleic Acid Hybrids (ANHs) Targeting Thrombin J. H.Yum, T. Ishizuka, H. L. Bao, K. Fukumoto, D.Hori, Y. Xu, H. Sugiyama, S. Park
ACS Biomater Sci Eng. 2021, 7,4, 1338 (DOI) (IF = 4.152)

Synthesis of oligonucleotide DNA containing 8-trifluoromethyl-2-deoxyguanosine for observing Z-DNA structure H. L. Bao, Y. Xu*
Curr. Protoc. Nucleic Acid Chem. 2021, 1, e28 (DOI)

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Improving thermodynamic stability and anticoagulant activity of thrombin binding aptamer by incorporation of 8-trifluoromethyl-2'-deoxyguanosine H. L. Bao, T. Ishizuka, A, Yamashita, E. Furukoji, Y. Asada, Y. Xu*
J. Med. Chem. 2021, 1, 711-718 (DOI) (IF = 6.205)

             Selected as a " Cover"

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Linear Consecutive Hexaoxazoles as G4 Ligands Inducing Chair-type Anti-parallel Topology of Telomeric G-Quadruplex S.Sasaki, Y. Ma, T. Ishizuka, H. L. Bao, T, Hirokawa, Y. Xu M. Tera, K. Nagasawa
RSC Adv. 2020, 10, 43319-43323 (DOI) (IF = 3.070)

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Conformation of G-quadruplex controlled by click reaction C. D. Xiao, Z-Y. He, C-X. Guo, X-C. Shen, Y. Xu*
Molecules 2020, 25, 4339 (DOI) (IF = 3.268)

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Oligonucleotides DNA Containing 8-Trifluoromethyl-2'-Deoxyguanosine for Observing Z-DNA Structure H. L. Bao, T. Masuzawa, T. Oyoshi, Y. Xu*
Nucleic Acids Res. 2020, 48,7041-7051 (DOI) (IF = 19.160)

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Telomeric DNA-RNA-hybrid G-quadruplex exists in environmental conditions of HeLa cells H. L. Bao, Y. Xu
Chem. Commun. 2020, 56, 6547-6550 (DOI) (IF = 6.319)

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Characterization of Structure and Catalytic Activity of a Complex between Heme and an All Parallel-stranded Tetrameric G-quadruplex Formed from DNA/RNA Chimera Sequence d(TTA)r(GGG)dT K. Hayasaka, T. Shibata, A. Sugahara, A. Momotake, T. Matsui, S. Neya, T. Ishizuka, Y. Xu Y. Yamamoto
Bull Chem Soc Jpn 2020, 93, 621-629 (DOI) (IF = 4.43)

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Influenza Virus Z-RNAs Induce ZBP1-Mediated Necroptosis T. Zhang, C. Yin, D.F. Boyd, G. Quarato, J.P. Ingram, M. Shubina, K. B. Ragan, T. Ishizuka, J.C. Crawford, B.Tummers, D.A. Rodriguez, J. Xue, S.Peri, Y. Xu, J.W. Upton, D. R. Green, S. Balachandran
Cell 2020, 181, 1115-1129 (DOI) (IF = 36.2)

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A nucleoside derivative 5-vinyluridine (VrU) for imaging RNA in cells and animals H.S. Liu, T. Ishizuka, M. Kawaguchi, R. Nishii, H. Kataoka, Y. Xu*
Bioconjugate Chem. 2019, 30, 2958-2966 (DOI) (IF = 4.35)

Selected as a " Cover"

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¹⁹F NMR spectroscopy for the analysis of DNA G-quadruplex structures using ¹⁹F-labeled nucleobase T. Ishizuka, H. L. Bao, Y. Xu*
Method Mol. Biol. 2019, 2035, 407-433 (DOI)

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Hybrid-type and two-tetrad antiparallel telomere DNA G-quadruplex structures in living human cells H. L. Bao, H. S. Liu, Y. Xu*
Nucleic Acids Res. 2019, 47, 4940-4947. (DOI) (IF = 11.561)

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Stability and properties of Z-DNA containing artificial nucleobase 2'-O-methyl-8-methyl guanosine T. Balasubramaniyam, T. Ishizuka, Y. Xu*
Bioorg. Med. Chem. 2019 , 27, 364-569. (DOI)

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2'-O-Methyl-8-methylguanosine as a Z-Form RNA Stabilizer for Structural and Functional Study of Z-RNA
T. Balasubramaniyam, T. Ishizuka, C. D. Xiao, H. L. Bao, Y. Xu*
Molecules 2018 , 23 , 2572. (DOI) (IF = 3.268)

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Recent progress in human telomere RNA structure and function
Y. Xu*
Bioorg. Med. Chem. Lett. 2018 , 28 , 2577-2584. (DOI)

Selected as a " Cover Picture " "

An intramolecular antiparallel G-quadruplex formed by human telomere RNA
C. D. Xiao, T. Shibata, Y.Yamamoto, Y. Xu*
Chem. Commun. 2018 , 54 , 3944-3946. (DOI) (IF = 6.319)

Selected as a "

Investigation of higher-order RNA G-quadruplex structures in vitro and in living cells by ¹⁹F NMR spectroscopy
H. L. Bao, Y. Xu*
Nature Protocols 2018 , 13 , 652-665. (DOI) (IF = 10.032)

HnRNPA1 Specifically Recognizes the Base of Nucleotide at the Loop of RNA G-Quadruplex
X. Liu, Y. Xu*
Molecules 2018 , 23 , 237. (DOI) (IF = 2.861)

Studying DNA G-quadruplex aptamer by ¹⁹F NMR
T. Ishizuka, A.Yamashita,Y. Asada, Y. Xu*
ACS Omega 2017 , 2 , 8843-8848. (DOI)

A Multi-functional Guanine Derivative for Studying DNA G-quadruplex Structure
T. Ishizuka, P. Y. Zhao, H. L. Bao, Y. Xu*
Analyst 2017 , 142 , 4083-4088. (DOI) (IF = 3.885)

Selected as a "

Allosteric Control of Nanomechanical DNA Origami Pinching Devices for Enhanced Target Binding
A. Kuzuya, Y. Sakai, T. Yamazaki, Y. Xu, Y. Yamanaka, Y. Ohya, M. Komiyama
Chem. Commun. 2017 , 53 , 8276-8279. (DOI) (IF = 6.319)

Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine
C. D. Xiao, T. Ishizuka, Y. Xu*
Sci. Rep. 2017 , 7 , 6695. (DOI) (IF = 5.228)

Structure-dependent Binding of hnRNPA1 to Telomere RNA
X. Liu, T. Ishizuka, H. L. Bao, K. Wada, Y. Takeda, K. Iida, K. Nagasawa, D. Yang, Y. Xu*
J. Am. Chem. Soc. 2017 , 139 , 7533-7539. (DOI) (IF = 13.038)

A Simple and Sensitive ¹⁹F NMR Approach for Studying the Interaction of RNA G-Quadruplex with Ligand Molecule and Protein
H. L. Bao, T. Ishizuka, A. Iwanami, T. Oyoshi, Y. Xu*
ChemistrySelect 2017 , 2 , 4170-4175. (DOI)

Selected as a "

Unusual Topological RNA Architecture with an Eight-Stranded Helical Fragment Containing A-, G-, and U-Tetrads
C. D. Xiao, T. Ishizuka, X. Q. Zhu, Y. Li, H. Sugiyama, Y. Xu*
J. Am. Chem. Soc. 2017 , 139 , 2565-2568. (DOI) (IF = 13.038)

Characterization of Human Telomere RNA G-Quadruplex Structures in vitro and in Living Cells using ¹⁹F NMR Spectroscopy
H. L. Bao, T. Ishizuka, T. Sakamoto, K. Fujimoto, T. Uechi, N. Kenmochi, Y. Xu*
Nucleic Acids Res. 2017 , 45 , 5501-5511. (DOI) (IF = 9.202)

Human Telomere RNA Structure and Function
Y. Xu*
Telomere and Telomerase 2016 , 3 , e1455. (DOI)

Click Chemistry Takes a Snapshot of DNA-RNA Hybrid G-Quadruplex in Living Cells
T. Ishizuka, Y. Xu*
J. Nat. Sci. 2016 , 2 , e237. (DOI)

Fluorescence Imaging of Chromosomal DNA using Click Chemistry
T. Ishizuka, H. S. Liu, K. Ito, Y. Xu*
Sci. Rep. 2016 , 6 , 33217. (DOI)

Formation and stabilization of the telomeric antiparallel G-quadruplex and inhibition of telomerase by novel benzothioxanthene derivatives with anti-tumor activity
W. Zhang, M. Chen, Y. Ling Wu, Y. Tanaka, Y. Juan Ji, S. Lin Zhang, C. He Wei, Y. Xu
Sci. Rep. 2015 , 5 , 13693. (DOI)

Clipping of Telomere from Human Chromosomes using Chemistry-based Artificial Restriction DNA Cutter
T. Ishizuka, Y. Xu*, M. Komiyama*
Curr. Protoc. Nucleic Acid Chem. 2015 , Unit6.13 , 1-13. (DOI)

Finding a Human Telomere DNA-RNA Hybrid G-Quadruplex Formed by Human Telomeric 6-mer RNA and 16-mer DNA using Click Chemistry: A Protective Structure for Telomere End
Y. Xu*, Y. Suzuki, T. Ishizuka, C. D. Xiao, X. Liu, T. Hayashi, M. Komiyama*
Bioorg. Med. Chem. 2014 , 22 , 4419-4421. (DOI) (IF = 3.151)

Targeting Human Telomeric Higher-Order DNA: Dimeric G-quadruplex Units Serve as Preferred Binding Site
C. Zhao, L. Wu, J. Ren, Y. Xu, X. Qu*
J. Am. Chem. Soc. 2013 , 135 , 18786-18789. (DOI) (IF = 10.677)

Conjugation of Peptide Nucleic Acid with Pyrrole-Imidazole Polyamide to Specifically Recognize and Cleave DNA
W. Kameshima, T. Ishizuka, M. Minoshima, M. Yamamoto, H. Sugiyama, Y. Xu*, M. Komiyama*
Angew. Chem., Int. Ed. 2013 , 52 , 13681-13684. (DOI) (IF = 13.734)

Direct Light-up of cAMP Derivatives in Living Cells by Click Reactions
K. Ito, H. Liu, M. Komiyama, T. Hayashi, Y. Xu*
Molecules 2013 , 18 , 12909-12915. (DOI) (IF = 2.428)

Evidence for G-Quadruplex DNA in Human Cells
Y. Xu*, M. Komiyama*
ChemBioChem 2013 , 14 , 927-928. (DOI) (IF = 3.944)
(Highlight)

A Chemistry-Based Method to Detect Individual Telomere Length at a Single Chromosome Terminus
T. Ishizuka, Y. Xu*, M. Komiyama*
J. Am. Chem. Soc. 2013 , 135 , 14-17. (DOI) (IF = 9.907)

Oligonucleotide Models of Telomeric DNA and RNA Form a Hybrid G-quadruplex Structure as a Potential Component of Telomeres
Y. Xu*, T. Ishizuka, J. Yang, K. Ito, H. Katada, M. Komiyama, T. Hayashi
J. Biol. Chem. 2012 , 287 , 41787-41796. (DOI) (IF = 4.773)

G-rich Sequence-Specific Recognition and Scission of Human Genome by PNA/DNA Hybrid G-quadruplex Formation
T. Ishizuka, J. Yang, M. Komiyama*, Y. Xu*
Angew. Chem., Int. Ed. 2012 , 51 , 7198-7202. (DOI) (IF = 13.455)

Human Telomere RNA: A Potential Target for Ligand Recognition
Y. Xu*
Curr. Pharm. Des. 2012 , 18 , 2096-2101. (DOI) (IF = 4.774)

Structure, Function and Targeting of Human Telomere RNA
Y. Xu*, M. Komiyama*
Methods 2012 , 57 , 100-105. (DOI) (IF = 4.596)

SWI/SNF-Mediated Chromatin Remodeling Induces Z-DNA Formation on a Nucleosome
N. Mulholland, Y. Xu, H. Sugiyama, K. Zhao*
Cell Biosci. 2012 2:3 doi:10.1186/2045-3701-2-3. (DOI)

Inhibition of Translation by Small RNA-Stabilized mRNA Structures in Human Cells
K. Ito, S. Go, M. Komiyama, Y. Xu*
J. Am. Chem. Soc. 2011 , 133 , 19153-19159. (DOI) (IF = 9.907)

Nanomechanical DNA Origami 'Single-Molecule Beacons' Directly Imaged by Atomic Force Microscopy
A. Kuzuya*, Y. Yamazki. T, Sakai, Y. Xu, M. Komiyama*
Nat. Commun. 2011 , 2:449 doi:10.1038/ncomms 1452. (DOI)

Chemistry in Human Telomere Biology: Structure, Function and Targeting of Telomere DNA/RNA
Y. Xu*
Chem. Soc. Rev. 2011 , 40 , 2719-2740. (DOI) (IF = 28.760)

Telomeric Repeat-Containing RNA Structure in Living Cells
Y. Xu*, Y. Suzuki, K. Ito, M. Komiyama*
Proc. Natl. Acad. Sci. USA. 2010 , 107 , 14579-14584. (DOI) (IF = 9.681)

A U-Tetrad Stabilizes Human Telomeric RNA G-Quadruplex Structure
Y. Xu*, T. Ishizuka, T. Kimura, M. Komiyama*
J. Am. Chem. Soc. 2010 , 132 , 7231-7233. (DOI) (IF = 9.907)

A Chiral Wedge Molecule Inhibits Telomerase Activity
K. Shinohara, Y. Sannohe, S. Kaieda, K.Tanaka, H. Osuga, H.Tahara, Y. Xu, T. Kawase, T. Bando, H, Sugiyama
J. Am. Chem. Soc. 2010 , 132 , 3778-3782. (DOI) (IF = 9.907)

A 6-mer Photocontrolled Oligonucleotide as an Effective Telomerase Inhibitor
Y. Xu*, K. Ito, Y. Suzuki, M. Komiyama*
J. Am. Chem. Soc. 2010 , 132 , 631-637. (DOI) (IF = 9.907)

DNA structures: Mysterious end
Y. Xu*
NPG Asia Materials 2009 , 10.1038/asiamat.2009.34 (DOI) (IF = 9.157)

Consecutive Formation of G-Quadruplexes in Human Telomeric-Overhang DNA: A Protective Capping Structure for Telomere Ends
Y. Xu*, T. Ishizuka, K Kurabayashi, M. Komiyama*
Angew. Chem., Int. Ed. 2009 , 48 , 7833-7836. (DOI) (IF = 13.455)

Click Chemistry for the Identification of G-Quadruplex Structures: Discovery of a DNA-RNA G-Quadruplex
Y. Xu*, Y. Suzuki, M. Komiyama*
Angew. Chem., Int. Ed. 2009 , 48 , 3281-3284. (DOI) (IF = 13.455)

Human Telomeric DNA Sequence-Specific Cleaving by G-Quadruplex Formation
Y. Xu*, Y. Suzuki, T. Lönnberg, M. Komiyama*
J. Am. Chem. Soc. 2009 , 131 , 2871-2874. (DOI) (IF = 9.907)

G-Quadruplex Formation by Human Telomeric Repeats-Containing RNA in Na⁺ Solution
Y. Xu*, K Kaminaga, M. Komiyama*
J. Am. Chem. Soc. 2008 , 130 , 11179-11184. (DOI) (IF = 9.907)

Stable Lariat Formation Based on a G-Quadruplex Scaffold
Y. Xu*, H. Sato, Y. Sannohe, K. Shinohara, H. Sugiyama
J. Am. Chem. Soc. 2008 , 130 , 16470-16471. (DOI) (IF = 9.907)

Photochemical Determination of Different DNA Structures
Y. Xu, R. Tashiro, H. Sugiyama
Nat. Protoc. 2007 , 2 , 78-87. (DOI)

The New Models of the Human Telomere d[AGGG(TTAGGG)₃] in K⁺ Solution
Y. Xu, Y. Noguchi, H. Sugiyama
Bioorg. Med. Chem. 2006 , 14 , 5584-5591. (DOI)




(News story describing this work was highlighted in Chem. & Eng. News 2006, July 31) (Link)
(Most Cited Paper awarded for 2005-2008 at Bioorganic & Medicinal Chemistry)

Formation of G-Quartet and I-Motif Structures in the Retinoblastoma Susceptibility Genes (Rb)
Y. Xu, H. Sugiyama
Nucleic Acids Res. 2006 , 34 , 949-954. (DOI)

Photochemical Approach to Probing Different DNA Structures
Y. Xu, H. Sugiyama
Angew. Chem., Int. Ed. 2006 , 45 , 1354-1362. (DOI)
(Minireview)

(P)-Helicene Displays Chiral Selection in Binding to Z-DNA
Y. Xu, Y. X. Zhang, H. Sugiyama, T. Umano, H. Osuga, K. Tanaka
J. Am. Chem. Soc. 2004 , 126 , 6566-6567. (DOI)

Highly Efficient Photochemical 2'-Deoxyribonolactone Formation at the Diagonal Loop of a 5-Iodouracil-Containing Antiparallel G-Quartet
Y. Xu, H. Sugiyama
J. Am. Chem. Soc. 2004 , 126 , 6274-6279. (DOI)

8-Methylguanosine: A Powerful Z-DNA Stabilizer
Y. Xu, R. Ikeda, H. Sugiyama
J. Am. Chem. Soc. 2003 , 125 , 13519-13524. (DOI)

I-Motif and Quadruplex-Based Device That Can Control a Protein Release or Bind and Release Small Molecule to Influence Biological Processes
Y. Xu, Y. Hirao, Y. Nishimura, H. Sugiyama
Bioorg. Med. Chem. 2007 , 15 , 1275-1279. (DOI)

Efficient and Erroneous Incorporation of Oxidized DNA Precursors by Human DNA Polymerase η
M. Shimizu, P. Gruz, H. Kamiya, C. Masutani, Y. Xu, Y. Usui, H. Sugiyama, H. Harashima, F. Hanaoka, T. Nohmi
Biochemistry 2007 , 46 , 5515-5522. (DOI)

Structure of a Human Telomeric DNA Sequence Stabilized by 8-Bromoguanosine Substitutions, as Determined by NMR in a K⁺ Solution
A. Matsugami, Y. Xu, Y. Noguchi, H. Sugiyama, M. Katahira
FEBS J. 2007 , 274 , 3545-3556. (DOI)

Efficient Generation of 2'-Deoxyuridin-5-yl at 5'-(G/C)AA^XU^XU-3' (X = Br, I) Sequences in Duplex DNA under UV Irradiation
T. Watanabe, T. Bando, Y. Xu, R. Tashiro, H. Sugiyama
J. Am. Chem. Soc. 2005 , 127 , 44-45. (DOI)

Binding of Distamycin A to UV-Damaged DNA
A. Inase, T. S. Kodama, J. Sharif, Y. Xu, H. Ayame, H. Sugiyama, S. Iwai
J. Am. Chem. Soc. 2004 , 126 , 11017-11023. (DOI)

Frontiers in Organic Chemistry
Y. Xu and H. Sugiyama
Bentham Science Publishers Ltd., Atta-ur-Rahman (Ed.) 2005 , 1 , 129-144. (Netherlands)