Yang Laboratory

Jonathan Dickerhoff , Jinho Jang, and Danzhou Yang (2024) Best method to determine DNA G-quadruplex folding: The 1H–13C HSQC NMR experiment. Methods, Volume 221, January Pages 35-41. https://doi.org/10.1016/j.ymeth.2023.11.013.

Nicole M. Brundridge, Jonathan Dickerhoff, Danzhou Yang, Scott A. McLuckey (2023) Gas-phase Fragmentation as a Probe of G-quadruplex Formation. Anal. Chem., 95, 40, 15057–15067. https://doi.org/10.1021/acs.analchem.3c03143.

Han, Y., Dickerhoff, J., Yang, D. (2023) Structures of G-Quadruplexes and Their Drug Interactions. In: Sugimoto, N. (eds) Handbook of Chemical Biology of Nucleic Acids. Springer, Singapore. https://doi.org/10.1007/978-981-16-1313-5_10-1

Chen L, Dickerhoff J, Sakai S, Yang, D (2022) DNA G-quadruplex in human telomeres and oncogene promoters: structures, functions, and small molecule targeting. Accounts of Chemical Research 55 (18), 2628-2646 https://doi.org/10.1021/acs.accounts.2c00337

Fang S, Liu S, Yang D, Yang L, Hu C, and Wan J (2022) Decoding Regulatory Associations of G-quadruplex with Epigenetic and Transcriptomic Functional Components. Frontiers in Genetics. Sec. Human and Medical Genomics., 2022, https://doi.org/10.3389/fgene.2022.957023

Sakai S, Otsuka T, Matsuda S, Sakairi Y, Uchida R, Sugahara K, Kano A, Yang, D (2022) Sub-nanomolar sensitive stable isotopic determination in CO2 by tunable infrared laser absorption spectroscopy. Anal. Chem. 2022, 94, 17, 6446–6450. https://doi.org/10.1021/acs.analchem.1c05458.

Yang D, Dickerhoff J, Dynan WS. (2022) Editorial: NAR Cancer, Epigenetics and cancer. NAR Cancer, Volume 4, Issue 1, March 2022. https://doi.org/10.1093/narcan/zcac003

Kai-Bo Wang, Yushuang Liu, Yipu Li, Jonathan Dickerhoff, Jinzhu Li, Ming-Hua Yang, Danzhou Yang,* and Ling-Yi Kong* (2022) Oxidative Damage Induces a Vacancy G‑Quadruplex That Binds Guanine Metabolites: Solution Structure of a cGMP Fill-in Vacancy G‑Quadruplex in the Oxidized BLM Gene Promoter. J. Am. Chem. Soc. 2022, 144, 14, 6361. https://doi.org/10.1021/jacs.2c00435

Wang K, Dickerhoff J, and Yang D. (2021) Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-in Vacancy G-Quadruplex Formed in the PDGFR-β Promoter. J. Am. Chem. Soc. 143 (40), 16549-16555. DOI: 10.1021/jacs.1c06200.           

Dickerhoff J, Brundridge N, McLuckey SA and Yang D. (2021) Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution. J. Med. Chem. https://doi.org/10.1021/acs.jmedchem.1c01508.

Buric AJ, Dickerhoff J, Yang D. (2021) Novel DNA Bis-Intercalator XR5944 as a Potent Anticancer Drug—Design and Mechanism of Action. Molecules 2021, 26 (14), 4132. https://doi.org/10.3390/molecules26144132.

Dickerhoff J, Warnecke KR, Wang K, Deng N, and Yang D. (2021) Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNA. International Journal of Molecular Sciences. 22(19):10801. doi: 10.3390/ijms221910801.  

Sun J, Wu G, Pastor F, Rahman N, Wang WH, Zhang Z, Merle P, Hui L, Salvetti A, Durantel D, Yang D, Andrisani O. (2021) RNA helicase DDX5 enables STAT1 mRNA translation and interferon signalling in hepatitis B virus replicating hepatocytes. Gut. 2021 May 21:gutjnl-2020-323126. doi: 10.1136/gutjnl-2020-323126. Epub ahead of print. PMID: 34021034.

Jonathan Dickerhoff, Jixun Dai, Danzhou Yang. (2021) Structural recognition of the MYC promoter G-quadruplex by a quinoline derivative: insights into molecular targeting of parallel G-quadruplexes, Nucleic Acids Research, 2021;, gkab330, doi: 10.1093/nar/gkab330.

Wu G, Tillo D, Ray S, Chang T-C, Schneekloth JS, Vinson C, Yang D. Custom G4 (2020) “Microarrays Reveal Selective G-Quadruplex Recognition of Small Molecule BMVC: A Large-Scale Assessment of Ligand Binding Selectivity” Molecules, 25(15):3465. doi: 10.3390/molecules25153465. PMID: 32751510. PMCID: PMC7436161.

Cruz J, Wickstrom L, Yang D, Gallicchio E, Deng N (2020) Combining Alchemical Transformation with Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites. Chem. Theory Comput, DOI: 10.1021/acs.jctc.9b01119.

Ray S, Tillo D, Boer, R, Assad N, Barshai M, Oreinstein Y, Yang D, Schneekloth J, Vinson C. (2020) Custom DNA microarrays reveal diverse binding preferences of proteins and small molecules to thousands of G-quadruplexes. ACS Chemical Biology, DOI: 10.2174/156652411798062421. PMID: 21999150.

Wang K, Dickerhoff J, Wu G, Yang D. (2020) PDGFR-β Promoter Forms a Vacancy G-Quadruplex that Can be Filled-in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs. J. Am. Chem. Soc., 142(11): 5204-5211, DOI: 10.1021/jacs.9b12770
Wang et al. (2020) PDF

Liu W, Lin C, Wu G, Wang K. Chang T, Yang D. (2019) Solution structures of 1:1 and 2:1 complexes of a fluorescent carbazole BMVC and MYC promoter G-quadruplex: Insights into conformation adjustment towards G4-recognition. NAR, 47(22):11931–11942. DOI: 10.1093/nar/gkz1015.

Wu G, Xing Z, Tran EJ, Yang D. (2019) DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation. PNAS, 116 (41), 20453-20461. DOI: 10.1073/pnas.1909047116. Wu et al.(2019) PDF

Wang K, Elsayed MSA, Wu G, Deng D, Cushman M, Yang D. (2019) Indenoisoquinoline Topoisomerase Inhibitors Strongly Bind and Stabilize the MYC Promoter G-Quadruplex and Downregulate MYC. J. Am. Chem. Soc. 141(28), 11059-11070. DOI: 10.1021/jacs.9b02679. PMID: 31283877. Press release: Purdue University Research Foundation News: https://www.purdue.edu/newsroom/releases/2019/Q3/new-anticancer-agents-have-potential-to-better-control-tumor-growth-in-nearly-every-cancer-type.html, Science Daily, https://www.sciencedaily.com/releases/2019/07/190708172436.htm; Phys.org, EurekAlert!, Science News Release, News Medical, ecancer, etc.

Yang D. (2019) G-Quadruplex DNA and RNA, Methods Mol Biol. 2035:1-24. DOI: 10.1007/978-1-4939-9666-7_1. PMID:31444741.
Yang (2019) PDF

Wang K, Flaherty DP, Chen L, Yang D. (2019) High-throughput Screening of G-Quadruplex Ligands by FRET Assay. Methods Mol Biol. 2035:323-331. DOI: 10.1007/978-1-4939-9666-7_19. PMID: 31444759.

Onel B, Wu G, Sun D, Lin C, Yang D. (2019) Electrophoretic Mobility Shift Assay and Dimethyl Sulfate Footprinting for Characterization of G-Quadruplexes and G-Quadruplex-Protein Complexes. Methods Mol Biol. 2035:201-222. DOI: 10.1007/978-1-4939-9666-7_11. PMID: 31444751.

Lin C, Dickerhoff J, Yang D. (2019) NMR Studies of G-Quadruplex Structures and G-Quadruplex-interactive Compounds. Methods Mol Biol. 2035:157-176. DOI: 10.1007/978-1-4939-9666-7_9. PMID:31444749.

Wu G, Chen L, Liu W, Yang D. (2019) Molecular Recognition of the Hybrid-Type G-Quadruplexes in Human Telomeres. Molecules 2019, 24(8):1578. DOI: 10.3390/molecules24081578. PMID: 31013622. PMCID: PMC6514847.

Deng N, Xia J, Wickstrom L, Lin C, Wang K, He P, Yin Y, Yang D. (2019) Ligand Selectivity in the Recognition of Protoberberine Alkaloids by Hybrid-2 Human Telomeric G-Quadruplex: Binding Free Energy Calculation, Fluorescence Binding, and NMR Experiments. Molecules 24(8):1574. DOI: 10.3390/molecules24081574. PMID: 31010072. PMCID:PMC6515380.

Sakai S, Yang D, Yasuda T, Akiyama K, Kuga T, Kano A, Shiraishi F, Amekawa S, Ohtsuka S, Nakaguchi K, Yamaguchi S. (2019) Pulsed terahertz radiation for sensitive quantification of carbonate minerals. ACS Omega 4(2):2702-2707, DOI: 10.1021/acsomega8b03311, PMID: 31459506. PMCID:PMC6648234.

Dickerhoff J, Onel B, Chen L, Chen Y, Yang D. (2019) Solution Structure of a MYC Promoter G-Quadruplex with 1:6:1 Loop Length. ACS Omega, 4 (2), 2533–2539, DOI: 10.1021/acsomega8b03580, PMID: 30842981. PMCID: PMC6396123.

Liu W, Zhong YF, Liu LY, Zeng W, Wang F, Yang D,* Mao ZW.* (2018) Solution structures of multiple G-quadruplex complexes induced by a platinum(II)-based tripod reveal dynamic binding. Nature Communications 9, 3496, DOI: 10.1038/s41467-018-05810-4, PMID: 30158518. PMCID:PMC6115404.

Fu X, Guo C, Yang D, Zhang Y. (2018) Investigation of default mode networks in rhesus macaque brain with 7.0 T resting state fMRI. Chinese J. Medical Imaging Technol34(6):801-806, DOI: 10.13929/j.1003-3289.201709141.

Lin C, Wu G, Wang K, Onel B, Sakai S,  Yang D. (2018) Molecular Recognition of the Hybrid‐2 Human Telomeric G‐quadruplex by Epiberberine: Insights into Conversion of Telomeric G-quadruplex Structures. Angew. Chem. Int. Ed. (57),10888 –10893, DOI: 10.1002/anie.201804667, PMID: 29888501, PMCID:PMC6192034. F1000Prime Recommendation. DOI: 10.3410/f.733432559.793547061.

Onel B, Carver M, Agrawal P, Hurley L, Yang D. (2018) The 3′-End of the PDGFR-β Core Promoter Nuclease Hypersensitive Element Forms a Mixture of Two Unique End-Insertion G-Quadruplexes. Biochim Biophys Acta Gen Subj.1862(4):846-854, DOI: 10.1016/j.bbagen.2017.12.011, PMID: 29288770. PMCID: PMC6183060.

Onel B, Carver M, Agrawal P, Hurley L, Yang D. (2018) The 3′-End of the PDGFR-β Core Promoter Nuclease Hypersensitive Element Forms a Mixture of Two Unique End-Insertion G-Quadruplexes. Biochim Biophys Acta Gen Subj.1862(4):846-854, DOI: 10.1016/j.bbagen.2017.12.011, PMID: 29288770. PMCID: PMC6183060.

Nanjie D, Lauren W, Cieplak P, Lin C, Yang D. (2017) Resolving the Ligand Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment. J. Phys. Chem. B, 121(46):10484-10497, DOI: 10.1021/acs.jpcb.7b09406, PMID: 29086571. PMCID: PMC5825213.

Sakai S, Matsuda S, Hikida T, Shimono A, McManus B, Zahniser M, Nelson D, Dettman D, Yang D, Ohkouchi N. (2017) High-precision simultaneous 18O/16O, 13C/12C and 17O/16O analyses for microgram quantities of CaCO3 by tunable infrared laser absorption spectroscopy. Anal Chem 7;89(21):11846-11852, DOI: 10.1021/acs.analchem.7b03582, PMID: 28937751. PMCID: PMC6152922.

Kaiser CE, Van Ert NA, Agrawal P, Chawla R, Yang D, Hurley L. (2017) Insight into the Complexity of the i-Motif and G-Quadruplex DNA Structures Formed in the KRAS Promoter and Subsequent Drug-Induced Gene Repression. J. Am. Chem. Soc., 28;139(25):8522-8536, DOI: 10.1021/jacs.6b10028, PMID: 28570076. PMCID: PMC5978000.

Xiao L, Ishizuka I, Hong-Liang b, Wada, K, Takada, Y, Iida, K, Nagasawa K, Yang D, Xu, Y. (2017) Structure-dependent binding of hnRNP A1 to telomere RNA. J. Am. Chem. Soc., 139(22):7533-7539, DOI: 10.1021/jacs.7b01599, PMID: 28510424. PMCID: PMC5977995.

Brown RV, Wang T, Chappeta VR, Wu G, Onel B, Chawla R, Quijada H, Camp SM, Chiang ET, Lassiter OR, Lee C, Phanse S, Megan A, Zhou TP, Garcia JGN, Gokhale V, Yang D, Hurley L. (2017) The Consequences of Overlapping G‑Quadruplexes and i‑Motifs in the Platelet-Derived Growth Factor Receptor β Core Promoter Nuclease Hypersensitive Element Can Explain the Unexpected Effects of Mutations and Provide Opportunities for Selective Targeting of Both Structures by Small Molecules To Downregulate Gene Expression. J. Am. Chem. Soc., 7;139(22):7456-7475, DOI: 10.1021/jacs.6b10028, PMID: 28471683. PMCID: PMC5977998.

Wang KB, Li DH, Bao Y, Cao F, Wang WJ, Lin C, Bin W, Bai J, Pei YH, Jing YK, Yang D, Li ZL, Hua HM. (2017) Structurally Diverse Alkaloids from the Seeds of Peganum harmala. J. Nat. Prod.80(2):551-559, DOI: 10.1021/acs.jnatprod.6b01146, PMID: 28128938. PMCID:PMC5518681.

Lin C. and Yang Y. (2017) Human Telomeric G-Quadruplex Structures and G-Quadruplex-Interactive Compounds. Telomeres and Telomerase: Methods Mol Biol, 735:77-96, DOI: 10.1007/978-1-4939-6892-3_17.

Mo H, Harwood JS, Yang D, Post CB. (2017) A simple method for NMR t1 noise suppression. Journal of Magnetic Resonance, Volume 276, pp 43-50, DOI: 10.1016/j.jmr.2016.12.014.

Onel B, Carver M, Wu G, Timonina D, Kalarn S, Larriva M, Yang D. (2016) A new G-quadruplex with hairpin loop immediately upstream of the human BCL-2 P1 promoter modulates transcription. J. Am. Chem. Soc., 138 (8), pp 2563–2570, DOI: 10.1021/jacs.5b08596, PMID: 26841249.

Zhang L, Liu H, Shao Y, Lin C, Jia H, Chen G, Yang D, Wang Y. (2015) Selective Lighting Up of Epiberberine Alkaloid Fluorescence by Fluorophore-Switching  Aptamer and Stoichiometric Targeting of Human Telomeric DNA G‑Quadruplex Multimer. Analytical Chemistry87, 730−737, DOI: 10.1021/ac503730j, PMID: 25429435.

Lin C. and Yang D. (2014) DNA Recognition by a DNA Bis-intercalating Anticancer Drug XR5944. Current Topics in Medicinal Chemistry, 15, 1385-1397.

Onel B, Lin C, Yang D. (2014) DNA G-Quadruplex and Its Potential as Anticancer Drug Target. SCIENCE CHINA Chemistry, 57 (12): 1605-1614, DOI: 10.1007/s11426-014-5235-3.

Lin C, Mathad RI, Zhang Z, Sidell N, Yang D. (2014) Solution Structure of a 2:1 Complex of Anticancer Drug XR5944 with TFF1 Estrogen Response Element: Insights into DNA Recognition by a Bis-intercalator. Nucleic Acid Research, 42 (9), 6012-6024, DOI: 10.1093/nar/gku219, PMID: 24711371.

Kendrick S, Kang HJ, Alam M, Madathil M, Agrawal P, Gokhale V, Yang D, Hecht SM, Hurley L. (2014) The Dynamic Character of the BCL2 Promoter i-Motif Provides a Mechanism for Modulation of Gene Expression by Compounds That Bind Selectively to the Alternative DNA Hairpin Structure. J. Am. Chem. Soc., 136, 4161-4171, DOI: 10.1021/ja410934b.

Agrawal P, Lin C, Mathad RI, Carver M, Yang D. (2014) The Major G-Quadruplex Formed in the Human BCL-2 Proximal Promoter Adopts a Parallel Structure with a 13-nt Loop in K+ Solution. J. Am. Chem. Soc., 136 (5), 1750–1753,  DOI: 10.1021/ja4118945, PMID: 24450880.

Agrawal P, Hatzakis E, Guo K, Carver M, Yang D. (2013) Solution structure of the major G-quadruplex formed in the human VEGF promoter: Insights into loop interactions of the parallel G-quadruplexes. Nucleic Acid Research, 41(22), 10584-10592, DOI: 10.1093/nar/gkt784, PMID: 24005038.

Kaiser C, Gokhale V, Yang D, Hurley L. (2013) Gaining Insights into the Small Molecule Targeting of the G-Quadruplex in the c-MYC Promoter Using NMR and an Allele-Specific Transcriptional Assay. Topics in Current Chemistry:Quadruplex Nucleic Acids, Volume 330, pp 1-21, DOI: 10.1007/128_2012_333.

Chen Y. and Yang D. (2012) Sequence, Stability, Structure of G-Quadruplexes and Their Drug Interactions. Current Protocols in Nucleic Acid Chemistry, 50:17.5.1–17.5.17, DOI: 10.1002/0471142700.nc1705s50.

Chen Y, Agrawal P, Brown RV, Hatzakis E, Hurley L, Yang D. (2012) The Major G-Quadruplex Formed in the Human Platelet-Derived Growth Factor Receptor b (PDGFR-b) Promoter Adopts a Novel Broken-Strand Primarily Parallel Structure. J. Am. Chem. Soc. 134 (32), 13220–13223, DOI: 10.1021/ja305764d, PMID: 22866911.

Dai J, Carver M, Hurley H, Yang D. (2011) Solution structure of a 2:1 quindoline–c-MYC G-quadruplex.  Drug-induced reorientation of the flanking sequence and implications for drug design. J Am Chem Soc, 133 (44), 17673–17680, DOI: 10.1021/ja205646q, PMID: 21967482.

Mathad RI, Hatzakis E, Dai J, Yang D. (20122) c-Myc promoter G-quadruplex formed at the 5’-end of NHE III1 element: insights into biological relevance and parallel-stranded G-quadruplex stability. Nucleic Acid Research, 39(20): 9023-9033, DOI: 10.1093/nar/gkr612, PMID: 21795379.

Sidell N, Mathad RI, Shu F, Zhang Z, Kallen CB, Yang D. (2011) Intercalation of XR5944 with the estrogen response element is modulated by the tri-nucleotide spacer sequence between half-sites. Journal of Steroid Biochemistry and Molecular Biology, 124: 121-127, DOI: 10.1016/j.jsbmb.2011.02.003, PMID: 21333738.

Mathad RI and Yang D. (2011) G-Quadruplex Structures and G-Quadruplex-interactive Compounds. Telomeres and Telomerase: Methods Mol Biol, 735:77-96, DOI: 10.1007/978-1-61779-092-8_8.

Hatzakis E, Okamoto K, Yang D. (2010) Thermodynamic stability and folding kinetics of the major G-quadruplex and its loop isomers formed in the Nuclease Hypersensitive Element in the human c-Myc promoter: Effect of loops and flanking segments on the stability of parallel-stranded intramolecular G-quadruplexes. Biochemistry, 49(43): 9152-60, Nov 2, DOI: 10.1021/bi100946g, PMID: 20849082.

Dai J, Hatzakis E, Hurley L, Yang D. (2010) I-motif structures formed in the human c-MYC promoter are highly dynamic–Insights into sequence redundancy and I-motif stability. PLoS ONE, 5(7): e11647, Jul 19, DOI: 10.1371/journal.pone.0011647.

Shu F, Sidell N, Yang D, Kallen CB. (2010) The Tri-Nucleotide Spacer Sequence Between Estrogen Response Element Half-Sites is Conserved and Modulates ERα-Mediated Transcriptional Responses. Journal of Steroid Biochemistry and Molecular Biology, Vol. 120, Issues 4-5, 172-179, DOI: 10.1016/j.jsbmb.2010.04.009.

Yang D. and Okamoto K. (2010) Structural Insights Into G-Quadruplexes: Towards New Anti-Cancer Drugs. Future Medicinal Chemistry, Vol. 2, No. 4, 619-646, DOI: 10.4155/fmc.09.172.

Zhang Z, Dai J, Veliath E, Jones RA, Yang D. (2010) Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution: insights into the interconversion of human telomeric G-quadruplex structures. Nucleic Acid Research, 38(3): 1009-21, DOI: 10.1093/nar/gkp1029, PMID: 19946019.

Punchihewa C, Carver M, Yang D. (2009) DNA sequence selectivity of human topoisomerase I-mediated DNA cleavage induced by camptothecin. Protein Sci. 18(6): 1326-31, DOI: 10.1002/pro.138.

Dai J, Ambrus A, Hurley L, Yang D. (2009) A direct and nondestructive approach to determine the folding structure of the I-motif DNA secondary structure by NMR. Communication, J Am Chem Soc 131(17): 6102-6104, DOI: 10.1021/ja900967r, PMID: 19400591.

Punchihewa C, and Yang D. (2009) Therapeutic Targets and Drugs-G-quadruplex inhibitors. Cancer Drug Discovery and Development: Telomeres and Telomerase in Cancer, Keiko Hiyama (Ed.), Humana Press, Springer (NJ, USA). 251-280, DOI: 10.1007/978-1-60327-879-9_11 (Book Chapter).

Dai J, Carver M, Yang D. (2008) Polymorphism of human telomeric G-quadruplex structures. Biochimie 90, 1172-1183, DOI: 10.1016/j.biochi.2008.02.026 (Invited Peer-reviewed).

Bates P*, Mergny JL*, Yang D*. (2007) (* denotes equal contribution and MS correspondence) “Quartets in G-major. The First International Meeting on Quadruplex DNA” EMBO report, 8, 1003-1010, DOI: 10.1038/sj.embor.7401073 (Peer-reviewed).

Dai J, Carver M, Punchihewa C, Jones RA, Yang D. (2007) Structure of the hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: Insights into structure polymorphism of the human telomeric sequence. Nucleic Acid Research, 35, 4927-4940, DOI: 10.1093/nar/gkm522, PMID: 17626043. (cover article) [ISI Web of Knowledge Essential Science IndicatorsSM (ESI) Highly Cited Paper (Top 1% )]

Ambrus A and Yang D. (2007) Diffusion ordered NMR spectroscopy for analysis of DNA secondary structural elements. Analytical Biochemistry, 367(1), 56-67, DOI: 10.1016/j.ab.2007.04.025.

Punchihewa C, Dai J, Carver M, Yang D. (2007) Human Topoisomerase I C-Terminal Domain Fragment Containing the Active Tyrosine Site is a Molten Globule: Implication for the Formation of Competent Productive Complex. J. Structural Biology 159(1), 111-121, DOI: 10.1016/j.jsb.2007.03.001.

Dai J, Punchihewa C, Ambrus A, Chen D, Jones RA, Yang D. (2007) Structure of the intramolecular human telomeric G-quadruplex in potassium solution: A novel adenine triple formation. Nucleic Acid Research 35, 2440 - 2450, DOI: 10.1093/nar/gkm009, PMID: 17395643. (featured on the cover of C&EN, issue of May 28th, 2007.)

Punchihewa C, De Alba A, Sidell N, Yang D. (2007) XR5944, a potent inhibitor of estrogen receptors. Molecular Cancer Therapeutics 6, 213-219, DOI: 10.1158/1535-7163.MCT-06-0392, PMID: 17218634. (featured in DailyUpdates/LeadDiscovery Headline Articles.)

Dai J, Chen D, Jones RA, Hurley L, Yang D. (2006) NMR Solution Structure of the Major G-Quadruplex Structure Formed in the Human BCL-2 Promoter Region. Nucleic Acid Research 34, 5133-5144, DOI: 10.1093/nar/gkl610.

Ambrus A, Chen D, Dai J, Bialis T, Jones RA, Yang D. (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acid Research 34(9), 2723-2735, DOI: 10.1093/nar/gkl348, PMID: 16714449. [ISI Web of Knowledge Essential Science IndicatorsSM (ESI) Highly Cited Paper (Top 1% )] [featured in C&EN, issue of July 31, 2006.)

Dai J, Dexheimer TS, Chen D, Carver M, Ambrus A, Jones RA, Yang D. (2006) An Intramolecular G-Quadruplex Structure with Mixed Parallel/Antiparallel G-strands Formed in the Human BCL-2 Promoter Region in Solution. J. of American Chemical Society 128, 1096–1098, DOI: 10.1021/ja055636a, PMID: 16433524. [ISI Web of Knowledge Essential Science IndicatorsSM (ESI) Highly Cited Paper (Top 1% )]

Hurley L, Von Hoff DD, Siddiqui-Jain A, Yang D. (2006) Drug Targeting of the C-MYC Promoter to Repress Gene Expression via a G-Quadruplex Silencer Element. Seminars in Oncology, 33(4), 498-512, DOI: 10.1053/j.seminoncol.2006.04.012.

Tangirala RS, Dixon R, Yang D. (2005) Attila Ambrus, Smitha Antony, Keli Agama, Yves Pommier, Dennis P. Curran “Total and semisynthesis and in vitro studies of both enantiomers of 20-fluorocamptothecin. Bioorganic & Medicinal Chemistry Letters, 15(21), 4736-4740, DOI: 10.1016/j.bmcl.2005.07.074.

Ambrus A, Chen D, Whatcott C, Somogyi A, Yang D. (2005) Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry protocol for monitoring the progress of enzymatic 13C/15N-labeled DNA syntheses. Analytical Biochemistry, 342(2), 246-253, DOI: 10.1016/j.ab.2005.04.008, PMID: 15697230. [ISI Web of Knowledge Essential Science IndicatorsSM (ESI) Highly Cited Paper]

Ambrus A, Chen D, Dai J, Jones RA, Yang D. (2005) Solution Structure of the Biologically Relevant G-Quadruplex Element in the Human c-MYC Promoter. Implications for G-Quadruplex Stabilization.  Biochemistry, 44, 2048-2058, DOI: 10.1021/bi048242p.

Dai J, Punchihewa C, Mistry P, Ooi AT, Yang D. (2004) Novel DNA Bis-intercalation by MLN944, a Potent Clinical Bisphenazine Anticancer Drug. J. Biological Chemistry, 279 (44), 46096-46103, DOI: 10.1074/jbc.M404053200, PMID: 15317822.

Gu JQ, Wang YH, Franzblau SG, Montenegro G, Yang D, Timmermann BN. (2004) Antitubercular Constituents of Valeriana laxiflora. Planta Medica, 70(6), 509-514, DOI: 10.1055/s-2004-827149.

Yang Y, Dai J, Wang AHJ. (2003) Structures and Mechanisms of Anticancer Drugs-Target Interactions. Cancer Chemotherapy and Chemoprevention, Rui Han, Yan Shun, DaoPei Lu (Eds.), Beijing, Science Press (Book Chapter).

Zhang Y, Yuan F, Xin H, Wu X, Rajpal DK, Yang D, Wang Z. (2000) Human DNA Polymerase k Synthesizes DNA with Extraordinarily Low Fidelity. Nucleic Acids Research, vol. 28, No. 21, 4147-4156, DOI: 10.1093/nar/28.21.4147.

Gryczynski I, Gryczynski Z, Lakowicz JR, Yang D, Burke TG. (1999) Fluorescence Spectral Properties of the Anticancer Drug Topotecan By Steady-State and Frequency-Domain Fluorometry with One-Photon and Multi-Photon Excitation. Photochemistry and Photobiology 69(4), 421-428, DOI: 10.1111/j.1751-1097.1999.tb03307.x.

Yang D, Strode JT, Spielmann HP, Wang AHJ, Burke TG. (1998) DNA Interactions of Two Clinical Camptothecin Drugs Stabilize Their Active Lactone Forms. J. of American Chemical Society vol. 120, No. 12, 2979-2980, DOI: 10.1021/ja973433j.

Yang D and Wang AHJ. (1996) The Structural Studies of Interactions between Anticancer Platinum Drugs and DNA. Progress in Biophysics and Molecular Biology vol. 66 No.1, 81-111 (Invited Review), DOI: 10.1016/S0079-6107(96)00017-X.

Stella SGE, van Boom J, Yang D, Reedijk J, van der Marel GA, Wang AHJ. (1996) Structural Effect of Intra-strand Cisplatin-crosslink on Palindromic DNA Sequences. Journal of Biomolecular Structure & Dynamics vol 13 No. 6, 989-998 (cover article), DOI: 10.1080/07391102.1996.10508913

Yang D, van Boom SSGE, Reedijk J, van Boom J, Wang AHJ. (1995) Structure and Isomerization of an Intra-strand Cisplatin-crosslinked Octamer DNA Duplex by NMR Analysis. Biochemistry  34, 12912-12920, DOI: 10.1021/bi00039a054

Yang D, van Boom SSGE, Reedijk J, van Boom JH, Farrell N, Wang AHJ. (1995) A novel DNA structure induced by the new dinuclear anticancer compound m-(1,4-diaminobutane)-bis[trans-diamminechloroplatinum (II)] crosslinked to a GpC site in DNA. Nature Structural Biology  vol 2 No. 7, 577-586 (cover article), DOI: 10.1038/nsb0795-577.

Sriram M, Yang D, Gao Y, Wang AHJ. (1994) Crystal and Solution Structure of d(CGC[e6G]AATTCGCG)-Drug Complexes Reveal Conformational Polymorphism of O6-Ethyl-Guanine:Cytosine Base Pair. Annals of the New York Academy of Sciences - Symposium on DNA damage: Effects on DNA Structure and Protein Recognition. pp18-45, DOI: 10.1111/j.1749-6632.1994.tb52794.x.

Robinson H, Yang D, Wang AHJ. (1994) Structure and dynamics of the antitumor drugs nogalamycin and disnogalamycin complexed to d(CGTACG)2: comparison of crystal and solution structures. Gene 149, 179-188, DOI: 10.1016/0378-1119(94)90427-8.

Yang D and Andrew H.-J. Wang AHJ. (1994) Structure by NMR of Antitumor Drugs Aclacinomycin A and B Complexed to d(CGTACG). Biochemistry 33, 6595-6604, DOI: 10.1021/bi00187a029.

Yang D, Gao, Y, Robinson H, van der Marel GA, van Boom JH, Wang AHJ. (1993) Structural Effects of C2-Methylhypoxanthine: Cytosine Base Pair in B-DNA: A Combined NMR and X-ray Diffraction Study of d(CGC[m2I]AATTCGCG). Biochemistry 32, 8672-8681, DOI: 10.1021/bi00084a039 .