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| 151. | Fu, Y.; Jia, G.; Pang, X.; Wang, R. N.; Wang, X.; Li, C. J.; Smemo, S.; Dai, Q.; Bailey, K. A.; Nobrega, M. A.; Han, K.-L.; Cui, Q.; He, C. FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA. Nat. Commun. 2013, 4, 1798. [pdf]
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| 150. | Zheng, G.; Dahl, J. A.; Niu, Y.; Fu, Y.; Klungland, A.; Yang, Y. G.; He, C. Sprouts of RNA epigenetics: The discovery of mammalian RNA demethylases. RNA Biol. 2013. [ahead of print]
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| 149. | Song, C. X.; Szulwach, K. E.; Dai, Q.; Fu, Y.; Mao, S. Q.; Lin, L.; Street, C.; Li, Y.; Poidevin, M.; Wu, H.; Gao, J.; Liu, P.; Li, L.; Xu, G. L.; Jin, P.*; He, C.* Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming. Cell. 2013, 153, 678-691. [pdf] [cover]
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| 148. | Deng, X.; Weerapana, E.; Ulanovskaya, O.; Sun, F.; Liang, H.; Ji, Q.; Ye, Y.; Fu, Y.; Zhou, L.; Li, J.; Zhang, H.; Wang, C.; Alvarez, S.; Hicks, L. M.; Lan, L.; Wu, M.; Cravatt, B. F.; He, C. Proteome-wide Quantification and Characterization of Oxidation-Sensitive Cysteines in Pathogenic Bacteria. Cell Host Microbe. 2013, 13, 358-370. [pdf]
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| 147. | Chang, C.J. and He, C. Using chemistry to study and control metals in biology. Curr. Opin. Chem. Biol. 2013. 17, 127-128. [pdf]
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| 146. | Ji, Q.; Zhang, L.; Jones, M. B.; Sun, F.; Deng, X.; Liang, H.; Cho, H.; Brugarolas, P.; Gao, Y. N.; Peterson, S. N.; Lan, L.; Bae, T.; He, C. Molecular mechanism of quinone signaling mediated through S-quinonization of a YodB family repressor QsrR. Proc. Natl. Acad. Sci. 2013, 110, 5010-5015.[pdf]
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| 145. | Zhang, L.; Szulwach, K. E.; Hon, G. C.; Song, C. X.; Park, B.; Yu, M.; Lu, X.; Dai, Q.; Wang, X.; Street, C. R.; Tan, H.; Min, J. H.; Ren, B.; Jin, P.; He, C. Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nat. Commun. 2013, 4, 1517. [pdf]
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| 144. | Liu, J.; Karpus, J.; Wegner, S. V.; Chen, P. R.; He, C. Genetically Encoded Copper(I) Reporters with Improved Response for Use in Imaging. J. Am. Chem. Soc. 2013.135, 3144-3149 [pdf]
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| 143. | Liang, H.; Deng, X.; Bosscher, M.; Ji, Q.; Jensen, M. P.; He, C. Engineering Bacterial Two-Component System PmrA/PmrB to Sense Lanthanide Ions. J. Am. Chem. Soc. 2013, 135, 2037-2039.[pdf][news]
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| 142. | Clark, T. A.; Lu, X.; Luong, K.; Dai, Q.; Boitano, M.; Turner, S. W.; He, C.; Korlach, J. Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation. BMC. Biol. 2013, 11, 4.[pdf]
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| 141. | Yi, C.; He, C. DNA repair by reversal of DNA damage. Cold Spring Harb Perspect Biol. 2013, 5, a012575.[pdf]
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| 140. | Zheng, G.; Dahl, J. A.; Niu, Y.; Fedorcsak, P.; Huang, C.-M.; Li, Charles J.; Vågbø, Cathrine B.; Shi, Y.; Wang, W.-L.; Song, S.-H.; Lu, Z.; Bosmans, Ralph P. G.; Dai, Q.; Hao, Y.-J.; Yang, X.; Zhao, W.-M.; Tong, W.-M.; Wang, X.-J.; Bogdan, F.; Furu, K.; Fu, Y.; Jia, G.; Zhao, X.; Liu, J.; Krokan, Hans E.; Klungland, A.*; Yang, Y.-G.*; He, C.* ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility. Mol. Cell. 2013, 18-29.[pdf][news]
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| 139. | Yu, P.; Xiao, S.; Xin, X.; Song, C. X.; Huang, W.; McDee, D.; Tanaka, T.; Wang, T.; He, C.; Zhong, S. Spatiotemporal clustering of epigenome reveals rules of dynamic gene regulation. Genome. Res. 2012, 23, 352-364. [pdf] |
| 2012 | |
| 138. | Jia, G.; Fu, Y.; He, C. Reversible RNA adenosine methylation in biological regulation. Trends in Genetics. 2012, 29, 108-115.[pdf]
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| 137. | Yu, M.; Hon, G. C.; Szulwach, K. E.; Song, C. X.; Jin, P.; Ren, B.; He, C. Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat. Protoc. 2012, 7, 2159-2170.[pdf]
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| 136. | Hitosugi, T.; Zhou, L.; Elf, S.; Fan, J.; Kang, H.-B.; Seo, Jae H.; Shan, C.; Dai, Q.; Zhang, L.; Xie, J.; Gu, T.-L.; Jin, P.; Ale kovi, M.; LeRoy, G.; Kang, Y.; Sudderth, Jessica A.; DeBerardinis, Ralph J.; Luan, C.-H.; Chen, Georgia Z.; Muller, S.; Shin, Dong M.; Owonikoko, Taofeek K.; Lonial, S.; Arellano, Martha L.; Khoury, Hanna J.; Khuri, Fadlo R.; Lee, Benjamin H.; Ye, K.; Boggon, Titus J.; Kang, S.; He, C.*; Chen, J.* Phosphoglycerate Mutase 1 Coordinates Glycolysis and Biosynthesis to Promote Tumor Growth. Cancer Cell. 2012, 22, 585-600.[pdf]
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| 135. | Song, C. X.; Yi, C.; He, C. Mapping recently identified nucleotide variants in the genome and transcriptome. Nat. Biotechnol. 2012, 30, 1107-1116.[pdf]
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| 134. | Zhang, L.; Yu, M.; He, C. Mouse Tet1 Protein can Oxidize 5mC to 5hmC and 5caC on Single-stranded DNA. Acta. Chim. Sinica. 2012, 70, 2123-2126.[pdf]
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| 133. | Fu, Y.; He, C. Nucleic acid modifications with epigenetic significance. Current Opinion in Chemical Biology.2012, 516-524.[pdf]
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| 132. | Song, C. X.; He, C. Balance of DNA methylation and demethylation in cancer development. Genome. Biol. 2012, 13, 173.[pdf]
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| 131. | Jiang, X.; Huang, H.; Li, Z.; Li, Y.; Wang, X.; Gurbuxani, S.; Chen, P.; He, C.; You, D.; Zhang, S.; Wang, J.; Arnovitz, S.; Elkahloun, A.; Price, C.; Hong, G. M.; Ren, H.; Kunjamma, R. B.; Neilly, M. B.; Matthews, J. M.; Xu, M.; Larson, R. A.; Le Beau, M. M.; Slany, R. K.; Liu, P. P.; Lu, J.; Zhang, J.; He, C.; Chen, J. Blockade of miR-150 Maturation by MLL-Fusion/MYC/LIN-28 Is Required for MLL-Associated Leukemia. Cancer Cell. 2012, 22, 524-535.[pdf]
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| 130. | Li, Y.; Song, C. X.; He, C.; Jin, P. Selective Capture of 5-hydroxymethylcytosine from Genomic DNA. J. Vis. Exp. 2012, 68, e4441. [pdf]
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| 129. | Wang, T.; Pan, Q.; Lin, L.; Szulwach, K. E.; Song, C. X.; He, C.; Wu, H.; Warren, S. T.; Jin, P.; Duan, R.; Li, X. Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum. Hum. Mol. Genet. 2012, 5500-5510.[pdf]
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| 128. | Brugarolas, P.; Movahedzadeh, F.; Wang, Y.; Zhang, N.; Bartek, I. L.; Gao, Y. N.; Voskuil, M. I.; Franzblau, S. G.; He, C. The oxidation-sensing regulator (MosR) is a new redox dependent transcription factor in Mycobacterium tuberculosis. J. Biol. Chem. 2012, 37703-37712.[pdf]
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| 127. | Wang, J.; Karpus, J.; Zhao, B. S.; Luo, Z.; Chen, P. R.; He, C. A selective fluorescent probe for carbon monoxide imaging in living cells. Angew. Chem. Int. Ed. 2012, 51, 9652-9656.[pdf]
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| 126. | Sun, F.; Ding, Y.; Ji, Q.; Liang, Z.; Deng, X.; Wong, C. C.; Yi, C.; Zhang, L.; Xie, S.; Alvarez, S.; Hicks, L. M.; Luo, C.; Jiang, H.; Lan, L.; He, C. Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance. Proc. Natl. Acad. Sci. 2012, 109, 15461-15466.[pdf]
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| 125. | Jeong, D. W.; Cho, H.; Jones, M. B.; Shatzkes, K.; Sun, F.; Ji, Q.; Liu, Q.; Peterson, S. N.; He, C.; Bae, T. The auxiliary protein complex SaePQ activates the phosphatase activity of sensor kinase SaeS in the SaeRS two-component system of Staphylococcus aureus. Mol. Microbiol. 2012, 86, 331-348.[pdf]
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| 124. | Jiao, Z. W.; Zhang, S. Y.; He, C.; Tu, Y. Q.; Wang, S. H.; Zhang, F. M.; Zhang, Y. Q.; Li, H. Organocatalytic Asymmetric Direct Csp3-H Functionalization of Ethers: A Highly Efficient Approach to Chiral Spiroethers. Angew. Chem. Int. Ed. 2012, 51, 8811-8815.[pdf]
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| 123. | Kellinger, M. W.; Song, C. X.; Chong, J.; Lu, X. Y.; He, C.; Wang, D. 5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription. Nat. Struct. Mol. Biol. 2012, 19, 831-833. [pdf]
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| 122. | Yin, Y.; Wang, P.; Yang, X. X.; Li, X.; He, C.; Zhao, X. S. Panorama of DNA hairpin folding observed via diffusion-decelerated fluorescence correlation spectroscopy. Chem. Commun. 2012, 48, 7413-7415. [pdf]
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| 121. | Dai, Q.; Lu, X.; Zhang, L.; He, C. Synthesis of DNA oligos containing 2'-deoxy-2'-fluoro-D-arabinofuranosyl-5-carboxylcytosine as hTDG inhibitor. Tetrahedron. 2012, 68, 5145-5151. [pdf]
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| 120. | Yi, C.; Chen, B.; Qi, B.; Zhang, W.; Jia, G.; Zhang, L.; Li, C. J.; Dinner, A. R.; Yang, C. G.*; He, C.* Duplex interrogation by a direct DNA repair protein in search of base damage. Nat. Struct. Mol. Biol. 2012, 19, 671-676. [pdf] [cover]
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| 119. | Li, Y.; Lin, L.; Li, Z.; Ye, X.; Xiong, K.; Aryal, B.; Xu, Z.; Paroo, Z.; Liu, Q.; He, C.; Jin, P. Iron Homeostasis Regulates the Activity of the MicroRNA Pathway through Poly(C)-Binding Protein 2. Cell. Metab. 2012, 15, 895-904. [pdf]
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| 118. | Hendrickx, A. P.; Poor, C. B.; Jureller, J. E.; Budzik, J. M.; He, C.; Schneewind, O. Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus. Mol. Microbiol. 2012, 85, 153-163. [pdf]
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| 117. | Yu, M.; Hon, G.C.; Szulwach, K.E.; Song, C.X.; Zhang, L.; Kim, A.; Li, X.K.; Dai, Q.; Shen, Y.; Park, B.; Min, J.H.; Jin, P.*; Ren, B.*; He, C.* Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Cell. 2012, 149, 1368-1380. [pdf][news]
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| 116. | Sun, F.; Liang, H.; Kong, X.; Xie, S.; Cho, H.; Deng, X.; Ji, Q.; Zhang, H.; Alvarez, S.; Hicks, L. M.; Bae, T.; Luo, C.; Jiang, H.; He, C. Quorum-sensing agr mediates bacterial oxidation response via an intramolecular disulfide redox switch in the response regulator AgrA. Proc. Natl. Acad. Sci. 2012, 9095-9100. [pdf]
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| 115. | Ji, Q.; Zhang, L.; Sun, F.; Deng, X.; Liang, H.; Bae, T.; He, C. Staphylococcus aureus CymR is a new thiol-based oxidation-sensing regulator of stress resistance and oxidative response. J. Biol. Chem. 2012, 21102-21109. [pdf]
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| 114. | Liang, H.; Deng, X.; Ji, Q.; Sun, F.; Shen, T.; He, C. Pseudomonas aeruginosa global regulator VqsR directly inhibits QscR to control quorum-sensing and virulence gene expression. J. Bacteriol. 2012, 287, 21102-21109. [pdf]
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| 113. | Yao, Q.; Song, C. X.; He, C.; Kumaran, D.; Dunn, J. J. Heterologous expression and purification of Arabidopsis thaliana VIM1 protein: In vitro evidence for its inability to recognize hydroxymethylcytosine, a rare base in Arabidopsis DNA. Protein Expr Purif 2012, 83, 104-111. [pdf]
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| 112. | Ekworomadu, M. T.; Poor, C. B.; Owens, C. P.; Balderas, M. A.; Fabian, M.; Olson, J. S.; Murphy, F.; Balkabasi, E.; Honsa, E. S.; He, C.; Goulding, C. W.; Maresso, A. W. Differential function of lip residues in the mechanism and biology of an anthrax hemophore. PLoS. Pathog. 2012, 8, e1002559. [pdf]
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| 111. | Zhang, L.; Lu, X.Y.; Lu, J.Y.; Liang, H.H.; Dai, Q.; Xu, G.L.; Luo, C.; Jiang, H.L.; He, C. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat. Chem. Biol. 2012, 8, 328-330. [pdf]
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| 110. | Deng, X.; Sun, F.; Ji, Q.; Liang, H.; Missiakas, D.; Lan, L.; He, C. Expression of multidrug resistance efflux pump gene norA is iron-responsive in Staphylococcus aureus. J. Bacteriol. 2012, 194, 1753-1762 . [pdf]
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| 109. | Sun, F.; Ji, Q.; Jones, M. B.; Deng, X.; Liang, H.; Frank, B.; Telser, J.; Peterson, S. N.; Bae, T.; He, C. AirSR, a [2Fe-2S] Cluster-Containing Two-Component System, Mediates Global Oxygen Sensing and Redox Signaling in Staphylococcus aureus. J. Am. Chem. Soc. 2012, 134, 305-314. [pdf]
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| 108. | Song, C. X.; Clark, T. A.; Lu, X. Y.; Kislyuk, A.; Dai, Q.; Turner, S. W.; He, C.*; Korlach, J.* Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat. Methods. 2012. 9, 75-77. [pdf]
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| 2011 | |
| 107. | Dai, Q.; He, C. Preparation of DNA containing 5-hydroxymethyl-2'-deoxycytidine modification through phosphoramidites with TBDMS as 5-hydroxymethyl protecting group. Curr Protoc Nucleic Acid Chem 2011, Chapter 4, Unit 4 47 41-18. [pdf]
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| 106. | Inoue, A.; Shen, L.; Dai, Q.; He, C.; Zhang, Y. Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development. Cell Res. 2011, 21, 1670-1676. [pdf]
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| 105. | Szulwach, K. E.; Li, X.; Li, Y.; Song, C. X.; Wu, H.; Dai, Q.; Irier, H.; Upadhyay, A. K.; Gearing, M.; Levey, A. I.; Vasanthakumar, A.; Godley, L. A.; Chang, Q.; Cheng, X.; He, C.; Jin, P. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat. Neurosci. 2011. 14, 1607-1616. [pdf]
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| 104. | Jia, G.; Fu, Y.; Zhao, X.; Dai, Q.; Zheng, G.; Yang, Y.; Yi, C.; Lindahl, T.; Pan, T.; Yang, Y. G.*; He, C.* N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 2011, 7, 885-887.[pdf] [news]
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| 103. | Song, C.X., He, C. ; "The hunt for 5-hydroxymethylcytosine: the sixth base", Epigenomics., 2011, 3, 521-523. [pdf]
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| 102. | Capretto, D. A.; Brouwer, C.; Poor, C. B.; He, C. Gold(I)-Catalyzed Formation of 3-Pyrazolines through Cycloaddition of Diaziridine to Alkynes. Org. Lett. 2011, 13, 5842-5845.[pdf]
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| 101. | Qian, Y.; Karpus, J.; Kabil, O.; Zhang, S. Y.; Zhu, H. L.; Banerjee, R.; Zhao, J.; He, C. Selective fluorescent probes for live-cell monitoring of sulphide. Nat. Commun. 2011, 2, 495.[pdf][news]
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| 100. | Sun, F.; Zhou, L.; Zhao, B. C.; Deng, X.; Cho, H.; Yi, C.; Jian, X.; Song, C. X.; Luan, C. H.; Bae, T.; Li, Z.; He, C. Targeting MgrA-mediated virulence regulation in Staphylococcus aureus. Chem. Biol. 2011, 18, 1032-1041.[pdf]
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| 99. | Aryal, B. P.; Brugarolas, P.; He, C. Binding of ReO(4) (-) with an engineered MoO (4) (2-)-binding protein: towards a new approach in radiopharmaceutical applications. J. Biol. Inorg. Chem. 2011, 17, 97-106 . [pdf]
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| 98. | Ozcubukcu, S.; Mandal, K.; Wegner, S.; Jensen, M. P.; He, C. Selective recognition of americium by peptide-based reagents. Inorg. Chem. 2011, 50, 7937-7939. [pdf]
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| 97. | He, Y. F.; Li, B. Z.; Li, Z.; Liu, P.; Wang, Y.; Tang, Q.; Ding, J.; Jia, Y.; Chen, Z.; Li, L.; Sun, Y.; Li, X.; Dai, Q.; Song, C. X.; Zhang, K.; He, C.; Xu, G. L. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 2011, 333, 1303-1307.[pdf]
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| 96. | Brugarolas, P.; Duguid, E. M.; Zhang, W.; Poor, C. B.; He, C. Structural and biochemical characterization of N5-carboxyaminoimidazole ribonucleotide synthetase and N5-carboxyaminoimidazole ribonucleotide mutase from Staphylococcus aureus. Acta Crystallogr. D Biol. Crystallogr. 2011, 67, 707-715.[pdf]
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| 95. | Ito, S.; Shen, L.; Dai, Q.; Wu, S. C.; Collins, L. B.; Swenberg, J. A.; He, C.; Zhang, Y. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011, 333, 1300-1303. [pdf]
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| 94. | Szulwach, K. E.; Li, X.; Li, Y.; Song, C. X.; Han, J. W.; Kim, S.; Namburi, S.; Hermetz, K.; Kim, J. J.; Rudd, M. K.; Yoon, Y. S.; Ren, B.; He, C.; Jin, P. Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet. 2011, 7, e1002154.[pdf]
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| 93. | Moran-Crusio, K.; Reavie, L.; Shih, A.; Abdel-Wahab, O.; Ndiaye-Lobry, D.; Lobry, C.; Figueroa, M. E.; Vasanthakumar, A.; Patel, J.; Zhao, X.; Perna, F.; Pandey, S.; Madzo, J.; Song, C.; Dai, Q.; He, C.; Ibrahim, S.; Beran, M.; Zavadil, J.; Nimer, S. D.; Melnick, A.; Godley, L. A.; Aifantis, I.; Levine, R. L. Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell 2011, 20, 11-24.[pdf]
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| 92. | Song, C. X.; Sun, Y.; Dai, Q.; Lu, X. Y.; Yu, M.; Yang, C. G.; He, C. Detection of 5-hydroxymethylcytosine in DNA by transferring a keto-glucose by using T4 phage beta-glucosyltransferase. ChemBioChem 2011, 12, 1682-1685.[pdf]
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| 91. | Dai, Q.; He, C. Syntheses of 5-formyl- and 5-carboxyl-dC containing DNA oligos as potential oxidation products of 5-hydroxymethylcytosine in DNA. Org. Lett. 2011, 13, 3446-3449.[pdf]
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| 90. | Dolan, K. T.; Duguid, E. M.; He, C. Crystal structures of SlyA protein, a master virulence regulator of Salmonella, in free and DNA-bound states. J. Biol. Chem. 2011, 286, 22178-22185.[pdf]
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| 89. | Song, C. X.; He, C. Bioorthogonal labeling of 5-hydroxymethylcytosine in genomic DNA and diazirine-based DNA photo-cross-linking probes. Acc. Chem. Res. 2011, 44, 709-717.[pdf]
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| 88. | Song, C. X.; Yu, M.; Dai, Q.; He, C. Detection of 5-hydroxymethylcytosine in a combined glycosylation restriction analysis (CGRA) using restriction enzyme Taq(alpha)I. Bioorg. Med. Chem. Lett. 2011, 21, 5075-5077.[pdf]
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| 87. | Dai, Q.; Song, C. X.; Pan, T.; He, C. Syntheses of two 5-hydroxymethyl-2'-deoxycytidine phosphoramidites with TBDMS as the 5-hydroxymethyl protecting group and their incorporation into DNA. J. Org. Chem. 2011, 76, 4182-4188.[pdf]
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| 86. | Wegner, S.V.; Sun, F.; Hernandez, N.; He, C.; "The tightly regulated copper window in yeast." Chem. Commun. 2011, 47, 2571-2573. [pdf] |
| 85. | Song, C.X.; Szulwach, K.E.; Fu, Y.; Dia, Q.; Yi, C.; Li, X.; Li, Y.; Chen, C.-H.; Zhang, W.; Jian, X.; Wang, J.; Zhang, L.; Looney, T.J.; Zhang, B.; Godley, L.A.; Hicks, L.M.; Lahn, B.T.; Jin, P.*; He, C.* "Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine" Nat. Biotechnol. 2011, 29, 68-72. [pdf] |
| 84. | Wegner, S. V.; Ertem, E.; Sunbul, M.; He, C.; "Metal-binding properties of Hpn from Helicobacter pylori and implications for the therapeutic activity of bismuth" Chem. Sci. 2011, Advance Article.[pdf] |
| 2010 | |
| 83. | Sun, F.; Cho, H.; Jeong, D.W.; Li, C.; He, C.; Bae, T.; "Aureusimines in Staphylococcus aureus are not involved in virulence." PLoS One 2010, 5, e15703 [pdf] |
| 82. | Yi, C.; Jia, G; Hou, G.; Dai, Q.; Zhang, W.; Zheng, G.; Jian, X.; Yang, C.-G.; Cui, Q.; He, C.; "Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase" Nature 2010, 468, 330-333.[pdf] |
| 81. | He, C.; "Grand Challenge Commentary: RNA epigenetics?" Nat. Chem. Bio. 2010, 6, 863-865.[pdf] |
| 80. | Chen, H.; Yi, C.; Zhang, J.; Zhang, W.; Ge, Z.; Yang, C.-G.; He, C.; "Structural insight into the oxidation sensing mechanism of the antibiotic resistance regulator MexR" EMBO Rep. 2010, 11, 685-690. [pdf] |
| 79. | Li, C.; Sun, F.; Cho, H.; Yelavarthi, V.; Sohn, C.; He, C.; Schneewind, O.; Bae, T.; "CcpA mediates proline auxotrophy and is required for the pathogenesis of Staphylococcus aureus infections" J. Bacteriol. 2010, 3883-3892. [pdf] |
| 78. | Chen, P.R.; Brugarolas, P.; He, C; "Redox Signaling in Human Pathogens" Antioxid. Redox Signal. 2010, 107-1118. [pdf] |
| 77. | Li, Y.; He. C.*; Jin, P.*; "Emergence of Chemical Biology Approaches to the RNAi/miRNA Pathway" Chem. Biol. 2010, 17, 584-589. [pdf] |
| 76. | Fu, Y.; Dai, Q.; Zhang, W.; Ren, J.; Pan, T.; He, C.; "The AlkB Domain of Mammalian ABH8 Catalyzes Hydroxylation of 5-Methoxycarbonylmethyluridine at the Wobble Position of tRNA" Angew. Chem. Intl. Ed. 2010, 49, 8885-8888. [pdf] |
75. |
Saikia, M.; Fu, Y.; Pavon-Eternod, M.; He, C.; Pan, T.; "Genome-wide Analysis of N1-methyl-adenosine Modification in Human tRNAs" RNA 2010, 1317-1327. [pdf] |
| 74. | Lan, L.; Cheng, A.; Dunman, P.M.; Missiakas, D; He, C.; "Golden Pigment Production and Virulence Gene Expression are Affected by Metabolisms in Staphylococcus aureus" J. Bacteriol. 2010, 192, 3068-3077. [pdf] |
| 73. | Lu, L.; Yi, C.; Jian, X.; Zheng, G.; He, C.; "Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system." Nucleic Acids Res. 2010, 4415-4425. [pdf] |
| 72. | Sun, F.; Li, C.; Jeong, D.; Sohn, C.; He, C.; Bae, T. "In the Staphylococcus aureus two component system sae, the response regulator SaeR binds to a direct repeat sequence and the DNA binding requires phosphorylation by the sensor kinase SaeS" J. Bacteriol. 2010, 192, 2111-2127. [pdf] |
71. |
Wegner, S.; Arslan, H.; Sunbul, M.; Yin, J; He, C. "Dynamic Copper(I) Imaging in Mammalian Cells with a Genetically Encoded Fluorescent Copper(I) Sensor" J. Am. Chem. Soc. 2010, , 132 , 2567-2569. [pdf] |
| 70. | Lan, L.; Murray, T.S.; Kazmierczak, B.I.; He, C. "Pseudomonas aeruginosa OspR is an oxidative stress sensing regulator that affects pigment production, antibiotic resistance and dissemination during infection" Mol. Microbiol. 2010, 75, 76-91. [pdf] |
| 69. | Yi, C. and He, C. "AlkB recognition of a bulky DNA base adduct stabilized by chemical cross-linking" Sci. China. Chem. 2010, 53, 86. |
| 2009 | |
| 68. | Budzik, J.M.; Poor, C.B.; Faull, K.F.; Whitelegge, J.P.; He, C.*; Schneewind, O.* "Intermolecular amide bonds stabilize pili on the surface of bacilli" Proc. Natl. Acad. Sci 2009, 106, 19992-19997. [pdf] |
| 67. | Jian, X.; Wasinger, E.C.; Lockard, J.V.; Chen, L.X.; He, C. " Highly Sensitive and Selective Gold(I) Recognition by a Metalloregulator in Ralstonia metallidurans" J. Am. Chem. Soc. 2009, 131, 10869-10871. [pdf] |
| 66. | Poor, C.B.; Chen, P.R.; Duguid, E.; Rice, P.A.; He, C. " Crystal structures of the reduced, sulfenic acid and mixed disulfide forms of sarz, a redox active global regulator in staphylococcus aureus" J. Biol. Chem. 2009, 284, 23517-23524. [pdf] |
| 65. | Lin, Y.; Zhao, T.; Jian, X.; Farooqui, Z.; Qu, X.; He,
C.; Dinner, A. R.; Scherer, N.F. "Using the Bias from Flow to Elucidate
Single DNA Repair Protein Sliding and Interactions with DNA" Biophys. J. 2009, 96, 1911-1917. [pdf] |
| 64. |
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63. |
Wegner, S.V.; Boyaci, H.; Chen, H.; Jensen, M.P.; He, C. "Engineering a Uranyl-Specific Binding Protein from NikR" Angew. Chem. Intl. Ed. 2009, 48, 2339-2341. [pdf] [press] |
| 62. | Yi, C.; Yang, C.-G.; He, C. "A Non-Heme
Iron-Mediated Chemical Demethylation in DNA and RNA" Acc. Chem. Res.
2009, 42, 519-529.
[pdf] |
| 61. |
Yang, C.-G.; Garcia, K.; He, C. "Damage
Detection and Base Flipping in Direct DNA Alkylation Repair"
ChemBioChem 2009, 10, 417-423.
[pdf] |
| 60. |
Richter, S; Anderson, V.J.; Garufi, G.; Lu,
L.; Budzik, J. M.; Joachimiak, A.;
He, C.; Schneewind, O.; Missiakas, D. "Capsule anchoring in Bacillus
anthracis occurs by a transpeptidation reaction that is inhibited by
capsidin" Mol. Microbiol. 2009, 71, 404-420.
[pdf] |
| 59. |
Chen, P.R.; Nishida, S.; Poor, C.B.; Cheng,
A.; Bae, T.; Kuechenmeister, L.; Dunman, P.M.; Missiakas, D.; He, C. "A
new oxidative sensing and regulation pathway mediated by the MgrA
homologue SarZ in Staphylococcus aureus" Mol. Microbiol.
2009, 71, 198-211.
[pdf] |
| 2008 | |
| 58. |
Shigdel, U.K. and He, C. "A New 1'-Methylenedisulfide
Deoxyribose that Forms an Efficient Cross-Link to DNA Cytosine-5 Methyltransferase (DNMT) J. Am. Chem. Soc. 2008,
130, 17634-17635.
[pdf] |
| 57. |
Qiu, Z.; Lu, L.; Jian, X.;
He, C. "A Diazirine-Based Nucleoside Analogue for Efficient DNA
Interstrand Photocross-Linking" J. Am. Chem. Soc. 2008,
130, 14398-14399.
[pdf] |
| 56. |
Jia, G.; Yang, C.-G.; Yang, S.; Jian, X.;
Yi, C.; Zhou, Z.; He, C. "Oxidative demethylation of 3-methylthymine and
3-methyluracil in single-stranded DNA and RNA by mouse and human FTO"
FEBS Letters 2008, 582, 3313-3319.
[pdf] |
| 55. |
Chen, H.; Hu, J.; Chen, P.R.; Lan, L.; Li,
Z.; Hicks, L.M.; Dinner, A.R; He, C. "The Pseudomonas aeruginosa
multidrug efflux regulator MexR uses an oxidation-sensing mechanism"
Proc. Natl. Acad. Sci. 2008, 105, 13586-13591.
[pdf] |
| 54. |
Li, X.; Ye, S.; He, C.; Yu, Z.-X.
"Mechanisms of Brønsted Acid Catalyzed Additions of
Phenols and Protected Amines to Olefins: A DFT Study" Eur. J. Org.
Chem. 2008, 25, 4296-4303.
[pdf] |
| 53. |
Shan, G.; Li, Y.; Zhang, J.; Li, W.;
Szulwach, K.E.; Duan, R.; Faghihi, M.A.; Khalil, A.M.; Lu, L.; Paroo,
Z.; Chan, A.W.S.; Shi, Z.; Liu, Q.; Wahlestedt, C.; He, C.; Jin, P. "A
small molecule enhances RNA interference and promotes microRNA
processing" Nature Biotechnology 2008,
26, 933-940.
[pdf]
[C&EN] |
| 52. |
Li, Z.; Brouwer, C.; He, C. "Gold-Catalyzed
Organic Transformations" Chem. Rev. 2008, 108,
3239-3265.
[pdf] Submitted for publication in the special issue:
Coinage Metals in Organic Synthesis |
| 51. |
Yang, C.-G.; Yi, C.; Duguid, E. M.;
Sullivan, C. T.; Jian, X.; Rice, P. A.; He, C. "Crystal structures of
DNA-RNA repair enzymes AlkB and ABH2 bound to dsDNA" Nature
2008, 452, 961-965.
[pdf] [U.
Chicago Press] [C&EN]
[AAAS]
[Argonne Lab Press] (For
additional news links, go to "Research
Highlights" |
| 50. |
Chen, P.R. and He, C. "Selective
recognition of metal ions by metalloregulatory proteins"
Curr. Opin. Chem. Biol. 2008,
12, 214-221.
[pdf] |
| 49. |
Chang, S.; Bray, S.M.;
Li, Z.; Zarnescu, D.C.; He, C.; Jin, P.; Warren, S.T. "Identification
of small molecules rescuing fragile X syndrome phenotypes in
Drosophila"
Nat. Chem. Biol. 2008,
4, 256-263.
[pdf] |
| 48. |
Shigdel, U. K.; Zhang,
J.; He, C. "Diazirine-Based DNA
Photo-Cross-Linking Probes for the Study of Protein-DNA Interactions"
Angew. Chem. Intl. Ed. 2008,
47, 90-93.
[pdf] |
| 47. |
Chen, C.-S.; Korobkova,
E.; Chen, H.; Zhu, J.; Jian, X.; Tao, S.-C.; He, C.*; Zhu, H.* "A
proteome chip approach reveals new DNA damage recognition activities in
Escherichia Coli" Nat. Methods,
2008, 5, 69-74.
[pdf]
[J. Proteome Res. press] |
| 2007 | |
| 46. |
Durek,
T.;
Zhang,
J.;
He,
C.;
Kent,
S.B.H.
"Synthesis of Photoactive Analogues of a Cysteine Knot Trypsin Inhibitor
Protein" Org. Lett. 2007,
9, 5497-5500.
[pdf] |
| 45. |
Sarkar, S.K.; Andoy, N.M.; Benitez, J.J.;
Chen, P.R.; Kong, J.S.; He, C.; Chen, P. "Engineered Holliday Junctions
as Single-Molecule Reporters for Protein-DNA Interactions with
Application to a MerR-Family Regulator"
J. Am. Chem. Soc. 2007, 129, 12461-12467. [pdf] |
| 44. |
Chen, P.R.; Wasinger, E. C.; Zhao, J.; van
der Lelie, D.; Chen, L.X. ; He, C. "Spectroscopic
Insights into Lead(II) Coordination by the Selective Lead(II)-Binding
Protein PbrR691"
J. Am. Chem. Soc. 2007, 129, 12350-12351.
[pdf] |
| 43. |
Li, Z.; Capretto, D.A.; Rahaman, R.O.; He,
C. "Gold(III)-Catalyzed Nitrene
Insertion into Aromatic and Benzylic C-H Groups" J. Am. Chem. Soc.
2007, 129,
12058-12059.
[pdf]
|
| 42. |
Brouwer, C.; Rahaman, R O..; He, C.
"Gold(I)-Mediated Hydrothiolation of Conjugated
Olefins" Synlett 2007, 11, 1785-1789.
[pdf]
(Invited Contribution) |
| 41. |
Li, Z.; Capretto, D.A.; Rahaman, R.O.; He,
C. "Silver-Catalyzed Intermolecular Amination of C-H Groups"
Angew. Chem. Intl. Ed. 2007, 46, 5184-5186.
[pdf]
[C&EN] |
| 40. | Wegner, S. V.; Okesli, A.; Chen, P.; He, C. "Design of an Emission Ratiometric Biosensor from MerR Family Proteins: A Sensitive and Selective Sensor for Hg2+" J. Am. Chem. Soc. 2007, 129, 3474-3475. [pdf] |
| 2006 | |
| 39. |
Chen, P.; Bae, T.; Williams, W. A.; Duguid,
E. M.; Rice, P. A.; Schneewind, O. and He, C. "An Oxidation Sensing
Mechanism is Used by A Global Regulator of Staphylococcus aureus"
Nature Chem. Biol. 2006, 2, 591-595.
[pdf]
[C&EN]
[IDBD Listing] |
|
38. |
Li, Z.; Zhang, J.; Brouwer, C.; Yang, C.-G.; Reich, N. W. and He, C. "Bronsted Acid Catalyzed Addition of Phenols, Carboxylic Acids and Tosylamides to Simple Olefin" Org. Lett. 2006, 8:4175-8. [pdf]
|
| 37. |
Li, Z.; Ding, X. and He, C. "Nitrene
Transfer Reactions Catalyzed by Gold Complexes" J. Org. Chem.
2006, 71:5876-80.
[pdf]
|
| 36. |
Li, Z. and He, C. "Recent Advances
in Silver-Catalyzed Nitrene, Carbene, and Silylene-Transfer Reactions",
Euro. J. Org. Chem.
2006, 4313-4322,
(an invited review).
[pdf]
|
| 35. |
Mishina, Y. and He, C. "Oxidative Dealkylation DNA Repair Mediated by the Mononuclear Non-Heme Iron AlkB Proteins" J. Inorg. Biochem. 2006, 100, 670-678, (an invited review). [pdf] |
| 34. |
Reich, N. W.; Yang, C.-G.; Shi, Z. and He, C. "Gold(I)-Catalyzed Synthesis of Dihydrobenzofurans from
Aryl Allyl Ethers" Synlett. 2006, 8, 1278-1280, (an invited contribution). [pdf] |
|
33. |
Brouwer, C. and He, C. “Efficient Gold-Catalyzed Hydroamination of 1,3-Dienes”, Angew Chem. Int. Ed. 2006, 45, 1744-1747. [pdf]
|
|
32. |
Zhang, J.; Yang, C.-G. and He, C. “Gold(I)-Catalyzed Intra- and Intermolecular Hydroamination of Unactivated Olefins ”, J. Am. Chem. Soc. 2006, 128, 1798-1799. [pdf]
|
|
31. |
Mishina, Y.; Duguid, M. E. and He, C. "Direct Reversal of DNA Alkylation Damage", Chem. Rev. 2006, 106, 215-232. [pdf] |
| 2005 | |
|
30. |
Yang, C.-G.; Reich, N. W. and He, C. “Intramolecular Additions of Alcohols and Carboxylic Acids to Inert Olefins Catalyzed by Silver(I) Triflate”, Org. Lett. 2005, 7, 4553-4556. [pdf]
|
|
29. |
Mishina, Y.; Yang, C.-G. and He, C. “Direct Repair of the Exocyclic DNA Adduct 1,N6-Ethenoadenine by E. coli AlkB and Human ABH3”, J. Am. Chem. Soc. 2005, 127, 14594-14595. [pdf]
|
|
28. |
Li, Z.; Shi, Z. and He, C. "Addition of Heterocycles to Electron Deficient Olefins and Alkynes Catalyzed by Gold(III)", J. Organom. Chem. 2005, 690, 5049-5054 (an invited contribution). [pdf]
|
|
27. |
Yang, C.-G. and He, C. "Gold(I)-Catalyzed Intermolecular Addition of Phenols and Carboxylic Acids to Olefins", J. Am. Chem. Soc. 2005, 127, 6966-6967. [pdf]
|
|
26. |
Duguid, M. E.; Rice, P. A. and He, C. “Implications for How the Human DNA Repair Protein AGT Locates Damage as Revealed from A Unique X-ray Structure of Its DNA Bound Form”, J. Mol. Biol. 2005, 350, 657-666. [pdf]
|
|
25. |
Chen, P.; Greenberg, B.; Taghavi, S.; Romano, C.; van der Lelie, D. and He, C. "An Exceptionally Selective Lead(II)-Regulatory Protein from Ralstonia Metallidurans: Development of A Fluorescent Lead(II) Probe , Angew Chem. Int. Ed 2005, 44, 2715-2719. [pdf] C&EN, News1 News2 News3 News4 News5 News6 |
|
2004 |
|
|
24. |
Mishina, Y.; Chen, L. X. and He, C. “Preparation and Characterization of the Native Iron(II)-Containing AlkB Protein Directly from Escherichia coli”, J. Am. Chem. Soc 2004, 126, 16930-16936. [pdf]
|
|
23.. |
Shi, Z. and He, C. “Direct Functionalization of Arenes by Primary Alcohol Sulfonate Esters Catalyzed by Gold(III)”, J. Am. Chem. Soc. 2004, 126, 13596-13597. [pdf]
|
|
22. |
Cui, Y. and He, C. “A Silver-Catalyzed Intramolecular Amidation of Saturated C–H bonds”, Angew Chem. Int. Ed. 2004, 43, 4210-4212. [pdf]
|
|
21. |
Shi, Z. and He, C. “Efficient Functionalization of Aromatic C–H Bonds Catalyzed by Gold(III) under Mild and Solvent Free Conditions”, J. Org. Chem. 2004, 69, 3669-3671. [pdf]
|
|
20. |
Shi, Z. and He, C. “An Au-Catalyzed Cyclialkylation of Electron Rich Arenes with Epoxides to Prepare 3-Chromanols”, J. Am. Chem. Soc. 2004, 126, 5964-5965. [pdf]
|
|
19. |
Mishina, Y., Lee, C.-H. J. and He, C. “Potential DNA Preferences of Human and Bacterial AlkB Proteins as Revealed from Chemical Crosslink Studies”, Nucleic Acids Res. 2004, 32, 1548-1554. [pdf]
|
|
18. |
He, C. and Mishina, Y. “Modeling non-heme iron proteins”, Curr. Opin. Chem. Biol. 2004, 8, 201-208. [pdf]
|
|
17. |
Chen, P. and He, C. “Constructing Highly Sensitive and Selective Fluorescent Biosensors for Metal Ions by Using the MerR Family Proteins”, J. Am. Chem. Soc. 2004, 126, 728-729. [pdf], C&EN Analytical Chemistry |
|
2003 |
|
|
16. |
Cui, Y. and He, C. “Efficient Aziridination of Olefins Catalyzed by A Unique Disilver(I) Compound”, J. Am. Chem. Soc. 2003, 125, 16202-16203. [pdf]
|
|
15. |
Duguid, E. M.; Mishina, Y. and He, C. “A Chemical Disulfide Crosslinking Method to Investigate the Damage-Searching Mechanism of O6-Alkylguanine-DNA Alkyltransferases”, Chem. & Biol. 2003, 10, 827-835. [pdf]
|
|
14. |
Mishina, Y. and He, C. “Probing the Structure and Function of E. coli DNA Alkylation Repair AlkB Protein through Chemical Crosslinking”, J. Am. Chem. Soc. 2003, 125, 8730-8731. [pdf] |
| Other Publications: | |
|
13. He, C.; Sun, L. J.; Zhou, P.; Norman, D. P. G.; Dötsch, V.; Gross, J. D.; Lane, W. S.; Wagner, G. and Verdine, G. L. “A Zinc-Mediated Electrostatic Switch Controls the Adaptive Response of E. coli to Methylating Agents”, Mol. Cell. 2005, 20, 117-129. [pdf] 12. He, C.; Wei, H. and Verdine, G. L. “Converting the Sacrificial DNA Repair Protein N-Ada into a Catalytic Methyl Phosphotriester Repair Enzyme”, J. Am. Chem. Soc. 2003, 125, 1450-1451. 11. He, C. and Verdine, G. L. “Trapping Distinct Structural States of a Protein/DNA Interaction through Disulfide Cross-linking”, Chem. & Biol. 2002, 9, 1297-1303. 10. He, C.; DuBois, J. L.; Hedman, B.; Hodgson, K. O. and Lippard, S. J. “A short Copper-Copper Distance in a (m-1,2-Peroxo)dicopper(II) Complex Having 1,8-Naphthyridine Unit as an Additional Bridge”, Angew. Chem. Int. Ed. Engl. 2001, 40, 1484-1487. 9. He, C. and Lippard, S. J. “Synthesis and Electrochemical Studies of Diiron Complexes of 1,8-Naphthyridine-Based Dinucleating Ligands to Model Features of the Active Sites of Non-Heme Diiron Enzymes”, Inorg. Chem. 2001, 40, 1414-1420 (cover story). 8. He, C.; Barrios, A. M.; Lee, D.; Kuzelka, J.; Davydov, R. M. and Lippard, S. J. “Diiron Complexes of 1,8-Naphthyridine-Based Dinucleating Ligands as Models for Hemerythrin”, J. Am. Chem. Soc. 2000, 122, 12683-12690. 7. He, C. and Lippard, S. J. “Synthesis and Characterization of Several Dicopper(I) Complexes and a Spin-Delocalized Dicopper(I,II) Mixed-Valence Complex Using a 1,8-Naphthyridine-Based Dinucleating Ligand”, Inorg. Chem. 2000, 39, 5225-5231. 6. He, C. and Lippard, S. J. “Design and Synthesis of Multidentate Dinucleating Ligands Based on 1,8-Naphthyridine”, Tetrahedron 2000, 56, 8245-8252. 5. He, C.; Gomez, V.; Spingler, B. and Lippard, S. J. “Monodentate-Bridged Phosphodiester and Sulfate Complexes: Structural Insight into the Biological Activation of Phosphodiesters, Sulfate, and Sulfate Esters”, Inorg. Chem. 2000, 39, 4188-4189. 4. Kaminskaia, N. V.; He, C. and Lippard, S. J. “Reactivity of m-Hydroxodizinc(II) Centers in Enzymatic Catalysis through Model Studies”, Inorg. Chem. 2000, 39, 3365-3373. 3. He, C. and Lippard, S. J. “Modeling Carboxylate-Bridged Dinuclear Active Sites in Metalloenzymes Using a Novel Naphthyridine-Based Dinucleating Ligand”, J. Am. Chem. Soc. 2000, 122, 184-185. 2. He, C. and Lippard, S. J. “Aminoguanidinium Hydrolysis Effected by a Hydroxo-Bridged Dicobalt(II) Complexes”, J. Am. Chem. Soc. 1998, 120, 105-113. 1. Qian, Y.; Xie, Y.; He, C.; Li, J. and Chen, Z. “Hydrothermal Preparation and Characterization of Ultrafine Magnetite Powders”, Material Research Bulletin 1994, 29, 953-957. |
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