2026

95. Li, Q., Kim, H.J. Liu, Y., Oh, J., Hou, P.N., Hoshika, S., Pintilie, G., Aiyer, S., Chong, J., Lyumkis, D., Benner, S.A.*, Wang, D.* (2026) Structural Basis of Transcription of the Hachimoji Eight-Letter Alphabet by E. coli RNA Polymerase. Nat. Commun. 17:9060. DOI: https://doi.org/10.1038/s41467-026-76668-0. PMID: 42686745, PMCID: PMC13538358.
Highlighted in UC San Diego Today:  Breakthrough Helps Expand Genetic Alphabet
Highlighted in ScienceDaily: Life uses 4 DNA letters. Scientists just made 8 work
Highlighted in EurekAlert!:  Research alert: Breakthrough helps expand genetic alphabet
Highlighted in Phys.org:  Eight-letter DNA alphabet is accurately transcribed by a natural enzyme
Highlighted in The Economic Times:  Life on Earth has always used four DNA letters, but scientists have created a bigger genetic alphabet and found something unexpected
Highlighted in ua.news:  In the US, RNA polymerase read a synthetic eight-letter DNA alphabet
Highlighted in earth.com: Life has run on four genetic letters for billions of years, and a bacterial enzyme just read eight
Highlighted in Azo Life Sciences: RNA Polymerase Successfully Transcribes an Expanded Genetic Alphabet
Highlighted in GKToday:  Scientists  Demonstrate Eight-Letter Genetic Alphabet Reading
Highlighted in 網易:  美国强行合成8字母DNA！改写地球生命最底层密码，细胞竟然读懂了
Highlighted in 搜狐: 细菌RNA聚合酶能识读“八字母”遗传信息｜#科学资讯# #分子生物学# #扩展遗传密码#
Highlighted in 解螺旋: UCSD发现RNA聚合酶可读取八字母扩展遗传密码
Highlighted in Youtube: 加州大学圣地亚哥分校科学家将DNA扩展至八个字母
Highlighted in FactSphere (Facebook): Fact of the Day
Highlighted in San Diego Biotech Networks: Breakthrough Helps Expand Genetic Alphabet
Highlighted in EcoGeneZap (Facebook): DNA JUST GOT A NEW ALPHABET — AND A NATURAL ENZYME CAN READ IT!
Highlighted in Brighter Side of News: Biology’s four-letter DNA alphabet just expanded to eight
Highlighted in The Times of India: All known life uses 4 DNA letters; UC San Diego showed an existing bacterial enzyme can accurately read and transcribe 8, doubling the genetic alphabet with synthetic letters
Highlighted in Yahoo!News: Biology’s four-letter DNA alphabet just expanded to eight

94. Li, Q., Hou, P. N., Kimoto, M., Oh, J., Liu, Y., Tan, H. P., Chong J., Hirao, C.*, Wang, D.* (2026) Hydrophobic Unnatural Base Pair Promotes Trigger Loop Closure and Catalysis in Cellular RNA Polymerase Independent of Hydrogen Bonding. Proc. Natl. Acad. Sci. USA. 123 (33) e2607774123. DOI: 10.1073/pnas.2607774123. PMID: 42585009, PMCID: PMC13486597.

93. Yi, G., Li, Q., Holmberg, H., Li, S., Clare, D.K., Wang, D.* Zhang, P.* (2026) Structural dynamics of RNA polymerase II throughout the nucleotide addition cycle. Nat. Commun. 17: 8440. DOI: 10.1038/s41467-026-75257-5. PMID: 42420282, PMCID: PMC13478619.

92. Li, Q., Yi, G., Wu, Y., Xu, S., Chong, J., Huang, X., Zhang, P. *, Wang, D.* (2026) Sub-2 Å Cryo-EM Structures of Transcribing RNA Polymerase II Reveal Critical Roles of Water Molecules in Catalysis. Mol. Cell. 86(10):1896-1910.e7. PMID: 42066756, PMCID: PMC7619134.
Highlighted in UC San Diego Today: Water Molecules Found to Actively Drive Gene Transcription Process
Highlighted in TheScientist: Water Molecules Play a Vital Role in Gene Transcription
Highlighted in Newswise: Water Molecules Found to Actively Drive Gene Transcription Process
Highlighted in Phys.org: Water molecules found to actively drive gene transcription process
Highlighted in Astrobiology: Water Molecules Found To Actively Drive Gene Transcription Process University of California – San Diego
Highlighted in Science Mission (Facebook): Water molecules drive gene transcription process 

91. Hou, P.N., Lee, C., Chong, J., Oh, J. *, Wang, D.* (2026) Structural basis of transcription-coupled RNA damage by incorporation of oxidized ribonucleotide. Proc. Natl. Acad. Sci. USA. 123 (16) e2602266123. DOI: https://doi.org/10.1073/pnas.2602266123. PMID: 41980106, PMCID: PMC13099631.

90. Van Sluis, M., Hansen, C.G., Li, Q., Lans, H.*, Wang, D.*, Marteijn, J*. (2026) Mechanisms of transcription-coupled repair and DNA damage surveillance in health and disease. Nature Rev. Mol. Cell Biol. 27: 234-251. DOI: 10.1038/s41580-025-00915-3. PMID: 41254380, PMCID: PMC13389823.

2025

89. Shao, C., Hao, Y., Jiang, L., Wang, D., Wang, R., Li, Y., Wang, H., Ge, Y., Bai, R., Du, X., Chen, X., Wu, T., Gou, L., Wan, R., Xu, Y., Ji, X., Fu, X.-D. (2025) Dynamic U2AF Cycling Defines Two Phases of Co-Transcriptional Pre-mRNA Splicing. Science. 389, eadj9141. DOI: https://www.science.org/doi/10.1126/science.adj9141.

88. Kay, T.M., Inman, J.T., Lubkowska, L., Le, T.T., Qian, J., Hall, P.M. Wang, D. Kashlev, M., and Wang, M.D. (2025) RNA Polymerase II is a Polar Roadblock to a Progressing DNA Fork. Nature Comm. 16:8631. DOI: https://doi.org/10.1038/s41467-025-63662-1.

87. Santos-Aledo, A., Plaza-Pegueroles, A., Sanz-Murillo, M., Ruiz, FM., Hou, P.,  Xu, J., Gil-Carton, D., Wang, D.*, Fernández-Tornero, C.* (2025) Cryo-EM uncovers a sequential mechanism for RNA polymerase I stalling at abasic DNA lesions. Nature Commun. 16:5254. DOI: https://doi.org/10.1038/s41467-025-60536-4.

86. Oh, J., Konovalov, K.A., Hou, P., Chong, J., Huang, X., Wang, D.*(2025) Transcription-coupled template reconfiguration of 8-Oxoguanine for error-prone transcription revealed by time-resolved X-ray crystallography and molecular dynamics. J. Am. Chem. Soc. 147 (19), 16396–16403.

85. Zhang, H., Li, Y., Shah, S.B., Li, S., Li, Q., Oaks, J. Lv, T., Shi, L.Z., Wang, H., Wang, D., Wu, X. (2025) ATM priming and end resection-coupled phosphorylation of MRE11 is important for fork protection and replication restart.  Proc. Natl. Acad. Sci. USA.  122(16):e2422720122. PMID: 40249789.

84. Paul, T., Yan, C., Yu, J., Tsutakawa, SE., Tainer, JA, Wang, D., Ivanov, I. (2025) Molecular model of TFIIH recruitment to the transcription-coupled repair machinery. Nature Commun. 16(1):2341. PMCID: PMC11890784.

83. Sahan, A. Z., Chen, M., Su, Q., Li, Q., Wang, D., Zhang, J.* (2025) Lysosomal PIP3 revealed by genetically encoded lipid biosensors. Proc. Natl. Acad. Sci. USA. 122(13):e2426929122. PMID: 40127277.

2024

82. Ma, J., Yi, G., Ye, M., MacGregor-Chatwin, C., Sheng, Y., Lu, Y., Li, M., Li, Q., Wang, D., Gilbert, R.J.C., Zhang, P.* (2024) Open Architecture of Archaea MCM and dsDNA Complexes Resolved Using Monodispersed Streptavidin Affinity CryoEM. Nature Commun. 15:10304. PMCID: PMC11603195.

81. Gao, S., Hou, P., Wang, D.*, Greenberg, M.* (2024) T7 RNA Polymerase Catalyzed Transcription of the Epimerizable DNA Lesion, Fapy•dG and 8-Oxo-2'-deoxyguanosine. J. Biol. Chem. DOI: https://doi.org/10.1016/j.jbc.2024.107719.

80. Selvam, K., Xu, J., Wilson, H.E., Oh, J., Li, Q., Wang, D.*, Wyrick, J.J.* (2024) Elf1 promotes transcription-coupled repair in yeast by using its C-terminal domain to bind TFIIH. Nat. Commun. 15:6223. DOI: https://doi.org/10.1038/s41467-024-50539-y

79. Zhang, X., Xu, J., Hao, Y., Wang, D.*, Fu, X.-D.* (2024) Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation. Nat. Commun. Jul 17;15(1):6031. DOI: https://doi.org/10.1038/s41467-024-50298-w

78. Chen, J., Li, Q., Xia, S., Arsala, D., Sosa, D., Wang, D.*, Long, M.* (2024) The Rapid Evolution of De Novo Proteins in Structure and Complex. Genome Biol. Evol. evae107. DOI: https://doi.org/10.1093/gbe/evae107

77. Hardy, J. C., Pool, E. H., Bruysten, J.G.H., Zhou, X., Li, Q., Zhou, D.R., Palay, M., Tan, G., Chen, L., Choi, J.L.C., Lee, H.N., Strack, S., Wang, D., Taylor, S.S., Mehta, S., Zhang, J.* (2024) Molecular Determinants and Signaling Effects of PKA RIα Phase Separation. Mol. Cell 84 (online). DOI: https://doi.org/10.1016/j.molcel.2024.03.002

76. Gao, S., Hou, P., Oh, J., Wang, D.*, Greenberg, M.* (2024) Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy•dG. J. Am. Chem. Soc. 146, 9, 6274-6282.
Highlighted in X-mol: UCSD王栋课题组JACS：揭示DNA损伤Fapy•dG引起RNA聚合酶II转录突变的分子机制
Highlighted in Weixin: 【生化】UCSD王栋课题组JACS：揭示DNA损伤Fapy•dG引起RNA聚合酶II转录突变的分子机制

75. Aiyer, S., Baldwin, P. R., Tan, S. M., Shan, Z., Oh, J., Mehrani, A., Bowman, M. E., Louie, G., Passos, D. O., Đorđević-Marquardt, S., Mietzsch, M., Hull, J. A., Hoshika, S., Barad, B. A., Grotjahn, D. A., McKenna, R., Agbandje-McKenna, M., Benner, S. A., Noel, J. A. P., Wang, D., Tan, Y. Z., Lyumkis, D. (2024) Overcoming resolution attenuation during tilted cryo-EM data collection. Nat. Commun. 15, 389.
DOI: https://doi.org/10.1038/s41467-023-44555-7

74. Saram, R. D., Xu, J., Lahiri, I., Gong, W., Li, Q., Oh, J., Zhou, Z., Hou, P., Chong, J., Hao, N., Li, S.*, Wang, D.*, Leschziner, A. E*. (2024) Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair. Proc . Natl. Acad. Sci. USA. 121 (3), e2314245121.

2023

73. Oh, J., Shan, Z., Hoshika, S., Xu, J., Chong, J., Benner, S. A.*, Lyumkis, D.*, Wang, D.* (2023) A Unified Watson-Crick Geometry Drives Transcription of Six-Letter Expanded DNA Alphabets by E. coli RNA Polymerase. Nat. Commun. 14:8219.
One of the most read Nature Communications articles in life and biological sciences in 2023 (out of more than 8,500 articles published in Nat. Commun. in the last year): The Top 25 Life and Biological Sciences Articles of 2023
Reported by The Nikkei (one of the four national newspapers in Japan,  the world's largest financial newspaper): 人工DNAで新たんぱく質、6文字の塩基で 米研究チーム
Highlighted in UCSD Today 2023: Enzymes Can’t Tell Artificial DNA From the Real Thing (ucsd.edu)
Highlighted in Lab Manager: Enzymes Can’t Tell Artificial DNA from the Real Thing
Highlighted in Newswise: Enzymes Can’t Tell Artificial DNA From the Real Thing
Highlighted in EurekAlert!: Enzymes can’t tell artificial DNA from the real thing
Highlighted in Astrobiology Web: Enzymes Can’t Tell Artificial DNA From The Real Thing
Highlighted in Science Daily: Enzymes can't tell artificial DNA from the real thing
Highlighted in Interesting Engineering: Breakthrough: Artificial DNA opens door to designer proteins
Highlighted in City Life: Scientists Working Towards Expanding Genetic Code with Synthetic
Highlighted in City Life: Scientists Expand the Alphabet of DNA to Unlock New Possibilities
Highlighted in Tech Times: AEGIS Synthetic System: AI-Enhanced DNA Unlocks Precision Protein Design
Highlighted in Mirage News: Enzymes Unable to Differentiate Between Real and Artificial DNA
Highlighted in Technology Networks: RNA Polymerase Can’t Tell Artificial DNA From the Real Thing
Highlighted in Phys.org: Scientists create artificial DNA that can be transcribed by a natural enzyme
Highlighted in AZO Life Sciences: Scientists Crack the Code for Artificial DNA

72. Oh, J., Kimoto, M., Xu, H., Chong, J, Hirao, I*, Wang, D.* (2023) Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase. Nat. Commun. 14:195.

71. Unarta, I. C., Goonetilleke, E. C., Wang, D., Huang, X. H. (2023) Nucleotide Addition and Cleavage by RNA Polymerase II: Coordination of Two Catalytic Reactions using a Single Active Site. J. Biol. Chem. DOI: https://doi.org/10.1016/j.jbc.2022.102844

2022

70. Yan, W., Cao, M., Ruan, X., Jiang, L., Lee, S., Lemanek, A., Ghassemian, M., Pizzo, D.P., Wan, Y., Qiao, Y., Chin, A.R., Duggan, E., Wang, D., Nolan, J.P., Esko, J.D., Schenk, S.* & Wang, S.E.* (2022) Cancer-cell-secreted miR-122 suppresses O-GlcNAcylation to promote skeletal muscle proteolysis. Nat. Cell Biol. 24, 793-804.

69. Fei, J., Xu, J., Li, Z., Xu, K., Wang, D., Kassavetis, G.A. & Kadonaga, J.T. (2022) NDF is a transcription factor that stimulates elongation by RNA polymerase II. Genes Dev. 36, 294-299.

68. Oh, J., Jia, T., Xu, J., Chong, J., Dervan, P.B.* & Wang, D.* (2022) RNA polymerase II trapped on a molecular treadmill: structural basis of persistent transcriptional arrest by a minor groove DNA binder. Proc. Natl. Acad. Sci. USA. 119 (3), e2114065119.

2021

67. Yan, C., Dodd, T., Yu, J., Leung, B., Xu, J., Oh, J., Wang, D.* & Ivanov, I. * (2021) Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair. Nat. Commun. 12:7001.

66. Xu, J., Oh, J., Chong, J., Xu, L., & Wang, D.* (2021) Molecular Basis for Transcriptional Fidelity Control by RNA polymerase II. In R. Landick, J.D. Wang, & T. Strick (Eds) RNA Polymerases as Molecular Motors. 2nd Ed. Royal Society of Chemistry Press.

65. Xu, J., Chong, J. & Wang, D.* (2021) Strand-specific effect of Rad26 and TFIIS in rescuing transcriptional arrest by CAG trinucleotide repeat slip-outs. Nucleic Acids Res. doi: 10.1093/nar/gkab573.

64. Oh, J., Shin, J., Unarta, I.C., Wang, W., Feldman, A.W., Karadeema, R.J., Xu, L., Xu, J., Chong, J., Krishnamurthy, R., Huang, X., Romesberg, F.E. & Wang, D.* (2021) Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II. Nat. Chem. Biol. doi: 10.1038/s41589-021-00817-3.
Highlighted in UCSD Health News (2021)

Highlighted in AAAS EurekaAlert (2021): https://www.eurekalert.org/pub_releases/2021-06/uoc--hc061721.php

63. Konovalov, K.A., Wang, W., Wang, G., Gao, X., Wang, D. & Huang, X.* (2021) A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state models. J. Biol. Chem. doi: 10.1016/j.jbc.2021.100735.

62. Xu, J., Chong, J. & Wang, D.* (2021) Opposite roles of transcription elongation factors Spt4/5 and Elf1 on RNA polymerase II transcription through B-form versus non-B DNA structures. Nucleic Acids Res. doi: 10.1093/nar/gkab240.

61. Yuan, S., Yin, X., Meng, X., Chan, J.F.-W., Ye, Z.-W., Riva, L., Pache, L., Chan, C.C.-Y., Lai, P.M., Chan, C..C.-S., Poon, V.K.-M., Lee, A.C.-Y., Matsunaga, N., Pu, Y., Yuen, C.-K., Cao, J., Liang, R., Tang, K., Sheng, L., Du, Y., Xu, W., Lau, C.-Y., Sit, K.-Y., Au, W.-K., Wang, R., Zhang, Y.-Y., Tang, Y.-D., Clausen, T.M., Pihl, J., Oh, J., Sze, K.-H., Zhang, A.J., Chu, H., Kok, K.-H., Wang, D., Cai, X.-H., Esko, J.D., Hung, I.F.-N., Li, R.A., Chen, H., Sun, H., Jin, D.-Y., Sun, R.*, Chanda, S.K.* & Yuen, K.Y.* (2021) Clofazimine broadly inhibits coronaviruses including SARS-CoV-2. Nature. doi: 10.1038/s41586-021-03431-4.
Highlighted in Science Daily (2021): https://www.sciencedaily.com/releases/2021/03/210316083747.htm
Highlighted in Genetic Engineering & Biotechnology News (2021): https://www.genengnews.com/news/decades-old-leprosy-drug-inhibits-coronaviruses-may-treat-covid-19/

60. Milanovic, M., Shao, Z., Estes, V.M., Wang, X.S., Menolfi, D., Lin, X., Lee, B.J., Xu, J., Cupo, O.M., Wang, D. & Zha, S. (2021) FATC Domain Deletion Compromises ATM Protein Stability, Lymphocyte Development, and Promotes Lymphomagenesis. J. Immun. 206(6):1228-1239.

59. Oh, J., Xu, J.,, Chong, J. & Wang, D.* (2021) Molecular Basis of Transcriptional Pausing, Stalling, and Transcription-coupled Repair Initiation. Biochim. Biophys. Acta. Gene Regul. Mech. 1864(1):194659.

58. Milanovic, M., Sprinzen, L., Lee, J.H., Yamamoto, K., Li, Y., Lee, B.J., Xu, J., Estes, V.E., Wang, D., Mckinnon, P.J., Paull, T. & Zha, S. (2021) The Cancer-Associated ATM R3008H Mutation Reveals the Link between ATM activation and Its Exchange. Cancer Res. 81(2): 426-437.

2020

57. Wang, D.* (2020) Using Genetics to Reveal Protein Structure. Science. 370(6522): 1269-1270.

56. Xu, J., Wang, W., Xu, L., Chen, J.Y., Chong, J., Oh, J., Leschziner, A.E., Fu, X.D. & Wang, D.* (2020) Cockayne Syndrome B Protein Acts as an ATP-Dependent Processivity Factor that Helps RNA Polymerase II Overcome Nucleosome Barriers. Proc. Natl. Acad. Sci. USA. doi: 10.1073/pnas.2013379117.

55. Wang, D.* (2020) A Panorama of Transcription-Coupled Repair in Yeast Chromatin. Proc. Natl. Acad. Sci. USA. doi:10.1073/pnas.2014392117.

54. Oh., J., Fleming, A.M., Xu, J., Chong, J., Burrows, C.J. & Wang, D.* (2020) RNA Polymerase II Stalls on Oxidative DNA Damage via a "Torsion-Latch" Mechanism Involving Lone Pair-Pi and CH-Pi Interactions. Proc. Natl. Acad. Sci. USA. 117(17): 9338-9348. PMCID: PMC7196775.

53. Di, L., Fu, Y., Sun, Y., Li, J., Liu, L., Yao, J., Wang, G., Wu, Y., Lao, K., Lee, R.W., Zheng, G., Xu, J., Oh, J., Wang, D., Xie, X.S., Huang, Y. & Wang J. (2020) RNA Sequencing by Direct Tagmentation of RNA/DNA Hybrids. Proc. Natl. Acad. Sci. USA. 117(6):2886-2893. PMCID: PMC7022195.

2019

52. Lahiri, I., Xu, J., Han, B.G., Oh, J., Wang, D., DiMaio, F. & Leschziner, A.E.* (2019) 3.1 Å structure of Yeast RNA Polymerase II Elongation Complex Stalled at a Cyclobutane Pyrimidine Dimer Lesion Solved Using Streptavidin Affinity Grids. J. Struct. Biol. pii: S1047-8477(19)30133-9.

51.  Konovalov, K.A., Pardo-Avila, F., Tse, C.K.M., Oh, J., Wang, D.* & Huang,  X.* (2019) 8-oxo-Guanine DNA Damage Induces Transcription Errors By Escaping Two Distinct Fidelity Control Checkpoints of RNA Polymerase II.  J. Biol. Chem. doi: 10.1074/jbc.RA118.007333.

50.  Wang, W., Xu, J., Limbo, O., Fei, J., Kassavetis, G.A., Chong, J., Kadonaga, J.T., Russell, P., Li, B. & Wang, D.* (2019) Molecular Basis of Chromatin Remodeling By Rhp26, A Yeast CSB Ortholog. Proc. Natl., Acad. Sci. USA. 116(13):6120-6129.

49.  Tse, C.K.M., Xu, J., Xu, L., Sheong, F.K., Wang, S., Chow, H.Y., Gao, X., Li, X., Cheung, P.P.*, Wang, D.*, Zhang, Y.* & Huang, X.* (2019) Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-Independent Mechanism Assisted By Transcript Phosphate. Nat. Catal. 2:228-235.

48.  Oh, J., Xu, J., Chong, J. & Wang, D.* (2019) Structural and Biochemical Analysis of DNA Lesion-Induced RNA Polymerase II Arrest. Methods. doi: 10.1016/j.ymeth.2019.02.019. (Invited Review)

2018

47.  Wang, W., Xu, J., Chong, J. & Wang, D.* (2018) Structural Basis of DNA Lesion Recognition for Eukaryotic Transcription-Coupled Nucleotide Excision Repair. DNA Repair. 71(2018):43-55. (Invited Review)

46.  Sanz-Murillo, M., Xu, J., Belogurov, G.A., Calvo, O., Gil-Carton, D., Moreno-Morcillo, M., Wang, D. & Fernández-Tornero, C. (2018) Structural Basis of RNA Polymerase I Stalling At UV Light-Induced DNA Damage. Proc. Natl. Acad. Sci. USA. 115(36):8972-8977.
Covered in UCSD Health News: Study Reveals How Enzyme Detects Ultraviolet Light Damage
Covered in Village News: UCSD researchers record activity of DNA-repairing enzyme in new study
Covered in Phys.org: Study reveals how enzyme detects ultraviolet light damage

45.  Wang, W., Walmacq, C., Chong, J., Kashlev, M.* & Wang, D.* (2018) Structural Basis of Transcriptional Stalling and Bypass of Abasic DNA Lesion By RNA Polymerase II. Proc. Natl. Acad. Sci. USA. 115(11):E2538-E2545.

44.  Local, A., Huang, H., Albuquerque, C.P., Singh, N., Lee, A.Y., Wang, W., Wang, C., Hsia, J.E., Shiau, A.K., Ge, K., Corbett, K.D., Wang, D., Zhou, H. & Ren, B. (2018) Identification of H3K4me1-Associated Proteins At Mammalian Enhancers. Nat. Genet. 50(1):73-82.

2017

43.  Xu, J., Lahiri, I., Wang, W., Wier, A., Cianfrocco, M.A., Chong, J., Hare, A.A., Dervan, P.B., DiMaio, F., Leschziner, A.E.* & Wang, D.* (2017) Structural Basis for the Initiation of Eukaryotic Transcription-Coupled DNA Repair. Nature. 551:653-657.
Featured in UCSD Health Sciences Blog:Frozen in Action: How Cells Repair DNA, as it's Being Transcribed

42.  Wang, W., Xu, L., Hu, L., Chong, J., He, C. & Wang, D.* (2017) Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing. J. Am. Chem. Soc.139(41):14436-14442.

41.  Xu, L., Wang, W., Wu, J., Shin, J.H., Wang, P., Unarta, I.C., Chong, J., Wang, Y.* & Wang, D.* (2017) Mechanism of DNA Alkylation-Induced Transcriptional Stalling, Lesion Bypass, and Mutagenesis. Proc. Natl. Acad. Sci. U.S.A. 114(34):E7082-E7091.

40.  Cui, M., Feng, H., Guo, D., Wang, D. & Zheng, B.* (2017) A Droplet-Based Microfluidic Platform for Measuring Both Rapid and Slow Kinetics. Sensor. Actuat. B-Chem. 253:731-737.

39.  Shin, J.H., Xu, L. & Wang, D.* (2017) Mechanism of Transcription-Coupled DNA Modification Recognition. Cell Biosci. 7:9. (Invited Review)

2016

38.  Xu, L., Wang, W., Gotte, D., Yang, F., Hare, A.A., Welch, T.R., Li, B.C., Shin, J.H., Chong, J., Strathern, J.N.*, Dervan, P.B.* & Wang, D.* (2016) RNA Polymerase II Senses Obstruction in the DNA Minor Groove Via a Conserved Sensor Motif. Proc. Natl. Acad. Sci. U.S.A. 113(44):12426-12431.

37.  Yamamoto, K., Wang, J., Sprinzen, L., Xu, J., Haddock, C.J., Li, C., Lee, B.J., Loredan, D.G., Jiang, W., Vindigni, A., Wang, D., Rabadan, R. & Zha, S.* (2016) Kinase-Dead ATM Protein Is Highly Oncogenic and Can Be Preferentially Targeted By Topo-Isomerase I Inhibitor. eLife. doi:10.7554/eLife.14709.

36.  Hwang, C.S., Xu, L., Wang, W., Ulrich, S., Zhang, L., Chong, J., Shin, J.H., Huang, X., Kool, E.T., McKenna, C.E.* & Wang, D.* (2016) Functional Interplay Between NTP Leaving Group and Base Pair Recognition During RNA Polymerase II Nucleotide Incorporation Revealed By Methylene Substitution. Nucleic Acids Res. 44(8):3820-8.

35.  Shin, J.H., Xu, L. & Wang, D.* (2016) RNA Polymerase II Acts as a Selective Sensor for DNA Lesions and Endogenous DNA Modifications. Transcription. 7(3):57-62. (Invited Review)

34.  Zhang, L., Pardo-Avila, F., Unarta, I.C., Cheung, P.P., Wang, G., Wang, D. & Huang, X.* (2016) Elucidation of the Dynamics of Transcription Elongation for RNA Polymerase II Using Kinetic Network Models. Acc. Chem. Res. 49(4):687-94. (Invited Review)

33. Da, L.T., Pardo-Avila, F., Xu, L., Silva, D.A., Zhang, L., Gao, X., Wang, D.* & Huang, X.* (2016) Bridge Helix Bending Promotes RNA Polymerase II Backtracking Through a Critical and Conserved Threonine Residue. Nat. Commun. 7:11244.

2015

32.  Xu, L., Wang, W., Chong, J., Shin, J.H., Xu, J. & Wang, D.* (2015) RNA Polymerase II Transcriptional Fidelity Control and Its Functional Interplay with DNA Modifications. Crit. Rev. Biochem. Mol. Biol. 50(6):503-19. (Invited Review)

31.  Zhang, L., Silva, D.A., Pardo-Avila, F., Wang, D. & Huang, X.* (2015) Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes. PLoS Comput. Biol. 11(7):e1004354.

30.  Wang, L., Zhou, Y., Xu, L., Xiao, R., Lu, X., Chen, L., Chong, J., Li, H., He, C., Fu, X-D.* & Wang, D.* (2015) Molecular Basis for 5-Carboxycytosine Recognition By RNA Polymerase II Elongation complex. Nature. 523(7562):621-25.

29.  Xu, L., Wang, W., Zhang, L., Chong, J., Huang, X. & Wang, D.* (2015) Impacts of Template Backbone Heterogeneity on RNA Polymerase II Transcription. Nucleic Acids Res. 43(4):2232-41.

28.  Walmacq, C., Wang, L., Chong, J., Scibelli, K., Lubkowska, L., Gnatt, A., Brooks, P.J., Wang, D.* & Kashlev, M.* (2015) Mechanism of RNA Polymerase II Bypass of Oxidative Cyclopurine DNA Lesions. Proc. Natl. Acad. Sci. U.S.A. 112(5):E410-9.

2014

27.  Wang, L., Limbo, O., Fei, J., Chen, L., Kim, B., Luo, J., Chong, J., Conaway, R.C., Conaway, J.W., Ranish, J.A., Kadonaga, J.T., Rusell, P. & Wang, D.* (2014) Regulation of the Rhp26ERCC6/CSB Chromatin Remodeler By a Novel Conserved Leucine Latch Motif. Proc. Natl. Acad. Sci. U.S.A. 111(52):18566-71.

26.  Xu, L., Chen, Y.-C., Chong, J., Fin, A., McCoy, L.S., Xu, J., Zhang, C. & Wang, D.* (2014) Pyrene-Based Quantitative Detection of the 5-Formylcytosine Loci Symmetry in the CpG Duplex Content During TET-Dependent Demethylation. Angew. Chem. Int. Ed. Engl. 53(42):11223-7. 

25.  Xu, L., Zhang, L., Chong, J., Xu, J., Huang, X. & Wang, D.* (2014) Strand-Specific (Asymmetric) Contribution of Phosphodiester Linkages on RNA Polymerase II Transcriptional Efficiency and Fidelity. Proc. Natl. Acad. Sci. U.S.A. 111(32):E3269-76.

24.  Silva, D.A., Weiss, D., Pardo-Avila, F., Da, L.T., Levitt, M., Wang, D.*, & Huang, X.* (2014) Millisecond Dynamics of RNA Polymerase II Translocation at Atomic Resolution. Proc. Natl. Acad. Sci. U.S.A. 111(21):7665-70.

23.  Eun, C.*, Ortiz-Sánchez, J.M., Da, L., Wang, D.* & McCammon, J.A. (2014) Molecular Dynamics Simulation Study of Conformational Changes of Transcription Factor TFIIS During RNA Polymerase II Transcriptional Arrest and Reactivation. PLoS One. 9(5):e97975.

22.  Xu, L., Da, L., Plouffe, S.W., Chong, J., Kool, E.* & Wang, D.* (2014) Molecular Basis of Transcriptional Fidelity and DNA Lesion-Induced Transcriptional Mutagensis. DNA Repair (Amst). 19:71-83. (Invited Review)

21.  Xu, L., Butler, K.V., Chong, J., Wengel, J., Kool, E.T. & Wang, D.* (2014) Dissecting the Chemical Interactions and Substrate Structural Signatures Governing RNA Polymerase II Trigger Loop Closure By Synthetic Nucleic Acid Analogues. Nucleic Acids Res. 42(9):5863-70.

20.  Xu, L., Chen, Y-C., Nakajima, S., Chong, J., Wang, L., Lan, L., Zhang, C.* & Wang, D.* (2014) A Chemical Probe Targets DNA 5-Formylcytosine Sites and Inhibits TDG Excision, Polymerases Bypass, and Gene expression. Chem. Sci. 5(2):567-574.

2013

19.  Xu, L., Plouffe, S.W., Chong, J., Wengel, J. & Wang, D.* (2013) A Chemical Perspective on Transcriptional Fidelity: Dominant Contributions of Sugar Integrity Revealed By Unlocked Nucleic Acids. Angew. Chem. Int. Ed. Engl. 52(47):12341-5. (Inside Cover)

18.  Kellinger, M.W., Park, G.Y., Chong, J., Lippard, S.J.* & Wang, D.* (2013) Effect of a Monofunctional Phenanthriplatin-DNA Adduct on RNA Polymerase II Transcriptional Fidelity and Translesion Synthesis. J. Am. Chem. Soc. 135(35):13054-61.

17.  Zhang, S. & Wang, D.* (2013) Understanding the Molecular Basis of RNA Polymerase II Transcription. Isr. J. Chem. 53(6-7). (Invited Review)

16.  Da, L.T., Pardo-Avila, F., Wang, D. & Huang, X. (2013) A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase. PLoS Comput. Biol. 9(4):e1003020.

2012

15.  Kellinger, M.W., Song, C., Chong, J., Lu, X., He, C. & Wang, D.* (2012) 5-Formylcytosine and 5-Carboxylcytosine Reduce the Rate and Substrate Specificity of RNA Polymerase II Transcription. Nat. Struct. Mol. Biol. 19(8):831-3.
Commented in: Huang Y., Rao A. (2012) New functions for DNA modifications by TET-JBP. Nat. Struct. Mol. Biol. 19(11):1061-4.
Highlighted in UCSD Health Sciences Blog: Parsing a process of life

14.  Kellinger, M.W., Ultrich, S., Chong, J., Kool, E.T.* & Wang, D.* (2012) Dissecting Chemical Interactions Governing RNA Polymerase II Transcriptional Fidelity. J. Am. Chem. Soc. 134(19): 8231-40.
Reported in reviews: Svetlov, V. & Nudler, E. (2013) Basic mechanism of transcription by RNA polymerase II. Biochim. Biophys. Acta. 1829(1):20–28.Kaplan, C.D. (2013) Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. Biochim. Biophys. Acta. 1829(1):39-54. 

13.  Da, L-T., Wang, D.* & Huang, X.* (2012) Dynamics of Pyrophosphate Ion Release and Its Coupled Trigger Loop Motion from Closed to Open State in RNA Polymerase II. J. Am. Chem. Soc. 134(4): 2399-406.
Reported in reviews: Svetlov, V. & Nudler, E. (2013) Basic mechanism of transcription by RNA polymerase II. Biochim. Biophys. Acta.1829(1):20–28. Kaplan, C.D. (2013) Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. Biochim. Biophys. Acta. 1829(1):39-54.

2010

12.  Huang, X., Wang, D., Weiss, D.R., Bushnell, D.A., Kornberg, R.D. & Levitt, M. (2010) RNA Polymerase II Trigger Loop Residues Stabilize and Position the Incoming Nucleotide Triphosphate in Transcription. Proc. Natl. Acad. Sci. U.S.A. 107(36):15745-50.
Reported in: Faculty of 1000 Biology as recommended F1000 Factor 6.0

11.  Wang, D.*, Zhu, G., Huang, X. & Lippard, S.J.* (2010) X-ray Structure and Mechanism of RNA Polymerase II Stalled at an Antineoplastic Monofunctional Platinum-DNA Adduct. Proc. Natl. Acad. Sci. U.S.A. 107(21): 9584-9589.
Reported in: Faculty of 1000 Biology as recommended F1000 Factor 8.0

Postdoc at Stanford

10.  Liu, X., Bushnell, D.A., Wang, D., Calero, G. & Kornberg, R.D. (2010) Structure of an RNA Polymerase II-TFIIB Complex and the Transcription Initiation Mechanism. Science. 327(5962): 206-9.

9.  Wang, D., Bushnell, D.A., Westover, K.D., Huang, X., Levitt, M. & Kornberg, R.D. (2009) Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Å Resolution. Science. 324(5931): 1203-6.
Reported in: Faculty of 1000 Biology as Must Read F1000 Factor 10.0 ALSNews and SLAC today

8. Wang, D., Bushnell, D.A., Westover, K.D., Kaplan, C.D. & Kornberg, R.D. (2006) Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis. Cell. 127(5): 941-54. (Cover)
Reported in: SSRL Science Highlight & Light Source Science Highlight

7.  Takagi, Y., Masuda, C.A., Chang, W.H., Komori, H., Wang, D., Hunter, T., Joazeiro, C.A. & Kornberg, R.D. (2005) Ubiquitin Ligase Activity of TFIIH and the Transcriptional Response to DNA Damage. Mol. Cell. 18(2): 237-243.
Reported in: Faculty of 1000 Biology as Must Read F1000 Factor 8.0

Ph.D. at MIT

6.  Danford, A.J., Wang, D., Wang, Q., Tullius, T.D. & Lippard, S.J. (2005) Platinum Anticancer Drug Damage Enforces a Particular Rotational Setting of DNA in Nucleosomes. Proc. Natl. Acad. Sci. U.S.A. 102(35): 12311-6.

5. Wang, D. & Lippard, S.J. (2005) Cellular Processing of Platinum Anticancer Drugs. Nat. Rev. Drug Discov. 4(4): 307-20. (Invited Review)

4. Wang, D. & Lippard, S.J. (2004) Cisplatin-induced Post-Translational Modification of Histones H3 and H4. J. Biol. Chem. 279(20): 20622-5. 

3. Wang, D., Hara, R., Singh, G., Sancar, A. & Lippard, S.J. (2003) Nucleotide Excision Repair from Site-Specifically Platinum-Modified Nucleosomes. Biochemistry. 42(22): 6747-53. 

2.  Lee, K.B., Wang, D., Lippard, S.J. & Sharp, P.A. (2002) Transcription-Coupled and DNA Damage-Dependent Ubiquitination of RNA Polymerase II in vitro. Proc. Natl. Acad. Sci. U.S.A. 99(7): 4239-44. 

Undergraduate at PKU

1.  Guan, R. J., Wang, M., Wang, D. & Wang, D.C. (2001) A New Insect Neurotoxin AngP(1) with Analgesic Effect from the Scorpion Buthus martensii Karsch: Purification and Characterization. J. Pept. Res. 58(1): 27-35. (Now known as Chem. Biol. Drug Des.)