Our research focuses on using mass spectrometry (MS) to understand important biological problems, and we are particularly interested in DNA damage induced by reactive oxygen species and covalent modifications of proteins.

1. Oxidative DNA Damage

In this research area, we employ a plethora of approaches, which include analytical chemistry, synthetic organic chemistry, biochemistry, and molecular biology, to understand the biological implications of oxidative DNA damage at the molecular level. Our emphasis has been placed on the identification, structure elucidation, and quantification of a class of oxidative DNA lesions where two neighboring nucleobases in the same strand are covalently linked. In this respect, we have been able to characterize the structures of a number of novel oxidative intrastrand crosslink lesions by mass spectrometric and NMR spectroscopic methods. In addition, we quantify the amounts of DNA lesions formed from a variety of oxidation conditions by LC-MS/MS with isotope-incorporated standards. Moreover, we characterize the biophysical and biochemical properties of oxidative DNA Lesions, and we are particularly interested in investigating the thermodynamic as well as the in vitro and in vivo mutagenic properties of various oxidative DNA lesions.

2. Covalent Modifications of Proteins

Current projects in this area encompass the post-translational modifications of chromosomal high-mobility group (HMG) proteins, histones, DNA repair enzymes, and methyl-CpG binding proteins. In this respect, we use mass spectrometry for the identification of the sites and types of modifications, and we also examine the biological functions of these modifications.

We have in our laboratory a ThermoFinnigan Deca XP ion trap and an IonSpec FT-ICR mass spectrometer. We also have access to an Applied Biosystems Voyager DE-STR MALDI-TOF and a Micromass Global Ultima Q-TOF mass spectrometers in the Analytical Chemistry Instrumentation Facility as well as a Q-STAR XL O-MALDI Q-TOF mass spectrometer in the W. M. Keck Proteomics Laboratory. Students in our lab have the opportunity to gain hands-on experience with various state-of-the-art mass spectrometers. Depending on the nature of individual research project, they are also exposed to synthetic organic chemistry, biochemistry, molecular biology, and molecular modeling.

A group picture taken in front of the new chemistry building (Physical Sciences I, occupied in Feb. 2005)

Selected Publications

Wang, Y. *. HPLC isolation and mass spectrometric characterization of two isomers of thymine glycols in oligodeoxynucleotides. Chem. Res. Toxicol., 2002, 15, 671-676.

Wang, Y.*, Liu, Z., and Dixon, C. Major adenine products from 2-methyl-1,4-naphthoquinone-sensitized photoirradiation at 365 nm. Biochem. Biophys. Res. Commun. 2002, 291, 1252-1257.

Wang, Y.*, Vivekananda, S, and Zhang, K. ESI-MS/MS for the differentiation of diastereomeric pyrimidine glycols in mononucleosides. Anal. Chem. 2002, 74, 4505-4512.

Wang, Y.*, Men, L., and Vivekananda, S. Fragmentation of deprotonated ions of oligodeoxynucleotides carrying a 5-formyluracil or 2-aminoimidazolone. J. Am. Soc. Mass Spectrom. 2002, 13, 1190-1194.

Wang, Y.* and Liu, Z. Mechanisms for the formation of major oxidation products of adenine upon 365-nm irradiation with 2-methyl-1,4-naphthoquinone as a sensitizer. J. Org. Chem., 2002, 67, 8507-8512.

Liu, Z., Gao, Y. and Wang, Y.* Identification and characterization of a novel crosslink lesion in d(CpC) upon 365 nm-irradiation in the presence of 2-methyl-1,4-naphthoquinone. Nucleic Acids Res. 2003, 31, 5413-24.

Zhang, Q. and Wang, Y.* Independent generation of 5-(2’-deoxycytidinyl)methyl radical and the formation of a novel crosslink lesion between 5-methylcytosine and guanine. J. Am. Chem. Soc. 2003, 125, 12795-802.

Wang, Y. and Wang, Y.* Structure elucidation of DNA interstrand crosslink lesions by a combination of nuclease P1 digestion with mass spectrometry. Anal. Chem. 2003, 75, 6306-13.

Wang, Y.*, Vivekananda, S., Men, L., and Zhang, Q. Fragmentation of protonated ions of peptides containing cysteine, cysteine sulfinic acid, and cysteine sulfonic acid. J. Am. Soc. Mass Spectrom. 2004, 15, 698-703.

Zou, Y.; Jiang, X.; Wang, Y.* Identification of novel in vivo phosphorylation sites in high mobility group N1 protein from the MCF-7 human breast cancer cells. Biochemistry, 2004, 43, 6322-9.

Gu, C. and Wang, Y.* LC-MS/MS identification and yeast polymerase h bypass of a novel g-irradiation-induced intrastrand crosslink lesion G[8-5]C. Biochemistry, 2004, 43, 6745-50.

Zeng, Y. and Wang, Y.* Facile formation of an intrastrand crosslink lesion between cytosine and guanine upon Pyrex-filtered UV light irradiation of d(BrCG) and duplex DNA containing 5-bromocytosine. J. Am. Chem. Soc. 2004, 126, 6552-3.

Wang, Y., Zhang, Q. and Wang, Y.* Tandem mass spectrometry for the determination of the sites of DNA interstrand crosslink. J. Am. Soc. Mass Spectrom. 2004, 15, 1565-71.

Zhang, Q. and Wang, Y.* Independent generation of the 5-hydroxy-5,6-dihydrothymidin-6-yl radical and its reactivity in dinucleoside monophosphates. J. Am. Chem. Soc. 2004, 126, 13287-97.

Liu, Z.; Gao, Y.; Zeng, Y.; Fang, F.; Chi, D.; Wang, Y.* Isolation and characterization of a novel crosslink lesion in d(CpC) induced by one-electron photooxidation. Photochem. Photobiol. 2004, 80, 209-15.

Jiang, X. and Wang, Y.* b-elimination combined with tandem mass spectrometry for the identification of the in vivo and in vitro sites of phosphorylation of dehydrin DHN1 protein. Biochemistry, 2004, 43, 15567-15576.

Men, L. and Wang, Y.* Further studies on the fragmentation of protonated ions of peptides containing aspartic acid, glutamic acid, cysteine sulfinic acid, and cysteine sulfonic acid. Rapid Commun. Mass Spectrom., 2005, 19, 23-30.

Zhang, Q. and Wang, Y.* Generation of 5-(2’-deoxycytidinyl)methyl radical and the formation of intrastrand cross-link lesions in oligodeoxyribonucleotides. Nucleic Acids Res., 2005, 33, 1593-1603.

Zou, Y. and Wang, Y.* Tandem mass spectrometry for the examination of the post-translational modifications of high-mobility group A1 proteins: Symmetric and asymmetric dimethylation of Arg25 in HMGA1a protein. Biochemistry, 2005, 44, 6293-6301.

Gu, C. and Wang, Y.* Thermodynamic and in-vitro replication studies of an intrastrand crosslink lesion G[8-5]C. Biochemistry, 2005, 44, 8883-8889.

Hong, H. and Wang, Y.* Formation of intrastrand crosslink products between cytosine and adenine from UV irradiation of d(BrCA) and duplex DNA containing a 5-bromocytosine. J. Am. Chem. Soc., 2005, 127, 13969-13977.

Zhang, Q.; Wang, Y.* The reactivity of the 5-hydroxy-5,6-dihydrothymidin-6-yl radical in oligodeoxyribonucleotides. Chem. Res. Toxicol., 2005, in press.