Publications
Independent work at UT Austin (2019-present)
9. Peng Y, Bryan C, Yang K. Mass Spectrometry Evidence for Forming Schiff Base 3′-DNA-Histone Cross-Links from Abasic Sites in Vitro and in Human Cells. (2024) Chem. Res. Toxicol. 37, 216-219. acs.chemrestox.3c00377
​
​
​
​
​
8. Peng Y, Wei X, Yang K. Synthesis and excision repair of site-specific 3′-end DNA-histone cross-links derived
from abasic sites. (2023) Bioconjugate Chemistry. 34, 983-987. acs.bioconjchem.3c00156
​
​
​
​
​
​
​
7. Wei X, Yang K. PARP1 incises abasic sites and covalently cross-links to 3′-DNA termini via cysteine addition
not reductive amination. (2023) Biochemistry. 62, 1527-1530. acs.biochem.3c00138
​
​
​
​
​
6. Bryan C, Le J, Wei X, Yang K. Saccharomyces cerevisiae apurinic/apyrimidinic endonuclease 1 repairs
abasic site-mediated DNA-peptide/protein cross-links. (2023) DNA Repair. 126, 103501.
​
​
​
​
​
​
5. Wei X, Person M, Yang K. Tyrosyl-DNA phosphodiesterase 1 excises the 3′-DNA-ALKBH1 cross-link and its
application for 3′-DNA-ALKBH1 cross-link characterization by LC-MS/MS. (2022) DNA Repair. 119, 103391.
4. Yang K, Wei X, Le J, Rodriguez N. Human TREX1 repairs 3′-end DNA lesions in vitro. (2022) Chem. Res.
Toxicol. 35, 935-939. acs.chemrestox.2c00087
​
​
​
​
3. Bryan C, Wei X, Wang Z, Yang K. In vitro eradication of abasic site-mediated DNA-peptide/protein cross-
links by Escherichia coli long-patch base excision repair. (2022) J. Biol. Chem. 298, 102055.
​
​
​
​
​
​
​
​
​
​
​
​
​
2. Wei X, Wang Z, Hinson C, Yang K. Human TDP1, APE1, and TREX1 repair 3′-DNA-peptide/protein cross-
links arising from abasic sites in vitro. (2022) Nucleic Acids Res. 50, 3638-3657. 10.1093/nar/gkac185
​
​
​
​
​
​
1. Wei X, Bryan C, Peng Y, Yang K. Mechanisms of DNA−protein cross-link formation and repair. (2021) BBA-
Proteins and Proteomics. 1869, 140669. 10.1016/j.bbapap.2021.140669
PhD and Postdoc work
19. Wen T, Yang K, Greenberg MM. Local alteration of ionic strength in a nucleosome core particle
and its effect on N7-methyl-2′-deoxyguanosine depurination. (2022) Biochemistry. 61, 2221-2228.
​
18. Shen S, Davidson G, Yang K, Zhuang Z. Photo-activated PCNA/Ub-PCNA probes for structural
characterization of S. cerevisiae Ub-PCNA/Pol η complex. (2021) Nucleic Acids Res. 49, 9374-9388.
​
17. Yang K, Sun H, Lowder L, Varadarajan S, Greenberg MM. Reactivity of N3-methyl-2′-
deoxyadenosine in nucleosome core particles. (2019) Chem. Res. Toxicol. 32, 2118-2124.
​
16. Yang K, Greenberg MM. DNA–protein cross-link formation in nucleosome core particles treated
with methyl methanesulfonate. (2019) Chem. Res. Toxicol. 32, 2144-2151.
​
15. Sun H, Zheng Li, Yang K, Greenberg MM. Positional dependence of DNA hole transfer efficiency in
nucleosome core particles. (2019) J. Am. Chem. Soc. 141, 10154-10158.
​
14. Yang K, Greenberg MM. Effect of Histone lysine methylation on DNA lesion reactivity in
nucleosome core particles. (2019) Chem. Res. Toxicol. 5, 910-916.
​
13. Byrne RS, Yang K, Rokita ES. Effect of nucleosome assembly on alkylation by a dynamic
electrophile. (2019) Chem. Res. Toxicol. 5, 917-925.
​
12. Rana A, Yang K, Greenberg MM. Reactivity of the major C5'-oxidative DNA damage product in
nucleosome core particles. (2019) ChemBioChem. 20, 672-676.
​
11. Yang K, Greenberg MM. Histone tail sequences balance their role in genetic regulation and the need
to protect DNA against destruction in nucleosome core particles containing abasic sites. (2019)
ChemBioChem. 20, 78-82.
​
10. Yang K, Park D, Tretyakova NY, Greenberg MM. Histone tails decrease N7-methyl-2'-
deoxyguanosine depurination and yield DNA-protein cross-links in nucleosome core particles and
cells. (2018) Proc. Natl. Acad. Sci. USA. 115, E11212-E11220.
​
9. Gui W, Ott CA, Yang K, Chung J, Zhuang Z. Cell-permeable activity-based ubiquitin probes enable
intracellular profiling of human deubiquitinases. (2018) J. Am. Chem. Soc. 140, 12424-12433.
​
8. Gong P, Davidson G, Gui W, Yang K, Bozza WP, Zhuang Z. Activity-based ubiquitin-protein probes
reveal target protein specificity of deubiquitinating enzymes. (2018) Chem. Sci. 9, 7859-7865.
​
7. Yang K, Greenberg MM. Enhanced strand scission at abasic sites within clustered lesions in NCPs.
(2018) ChemBioChem. 19, 2061-2065.
6. Wang R, Yang K, Banerjee S, Greenberg MM. Rotational effects within nucleosome core particles on
abasic site reactivity. (2018) Biochemistry. 57, 3945-3952.
​
5. Yang K#, Li G#, Gong P, Gui W, Yuan L, Zhuang Z. Chemical protein ubiquitylation with preservation
of the native cysteine residues. (2016) ChemBioChem. 17, 995-998.
​
4. Tsutakawa SE, Yan C, Xu X, Weinacht CP, Freudenthal BD, Yang K, Zhuang Z, Washington MT,
Tainer JA, Ivanov I. Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their
distinct roles in the DNA damage response. (2015) Structure. 23, 724-733.
​
3. Yang K, Gong P, Gokhale P, Zhuang Z. Chemical protein polyubiquitination reveals the role of a
noncanonical polyubiquitin chain in DNA damage tolerance. (2014) ACS Chem. Biol. 9, 1685-1691.
​
2. Yang K, Weinacht CP, Zhuang Z. Regulatory role of ubiquitin in eukaryotic DNA translesion
synthesis. (2013) Biochemistry. 52, 3217-3224.
​
1. Bozza WP, Yang K, Wang J, Zhuang Z. Developing peptide-based multivalent antagonists of
proliferating cell nuclear antigen and a fluorescence-based PCNA binding assay. (2012) Anal.
Biochem. 427, 69-78.
