Publications


41. Toews, S., Wacker, A., Faison, E.M., Duchardt-Ferner, E., Richter, C., Mathieu, D., Battaro, S., Zhang, Q., and Schwalbe, H.*, “The 5’-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH,” Nucleic Acids Res., In press

40. Cho, M.#, Kumar, R. J.#, Lin, C., Boyer, J. A., Shahir, J. A., Fagan-Solis, K., Simpson, D. A., Fan, C., Foster, C. E., Goddard, A. M., Lerner, L. M., Ellington, S. W., Wang, Q., Wang, Y., Ho, A. Y., Liu, P., Perou, C. M., Zhang, Q., McGinty, R. K., Purvis, J. E., and Gupta, G. P.*, “MRE11 Liberates cGAS from Nucleosome Sequestration during Tumorigenesis,” Nature, 625, 585–592 (2024) (# Contributed Equally) pubmed

39. Treadway, C. J, Boyer, J. A., Yang, S., Yang, H., Liu, M., Li, Z., Cheng, M., Marzluff, W. F., Ye, D., Xiong, Y., Baldwin, A. S.*, Zhang, Q.*, and Brown, N. G.* “Using NMR to Monitor TET-Dependent Methylcytosine Dioxygenase Activity and Regulation,” ACS Chem. Biol., 19, 15–21 (2024) pubmed

38. Faison, E. M, Nallathambi, A., and Zhang, Q.*, “Characterizing Protonation-Coupled Conformational Ensembles in RNA via pH-Differential Mutational Profiling with DMS Probing,” J. Am. Chem. Soc., 145:18773-18777 (2023) pubmed

37. Liu, X.#, Wang, J.#, Boyer, J. A., Gong, W., Zhao, S., Xie, L., Wu, Q., Zhang, C., Jain, K., Guo, Y., Rodriguez, J., Li, M., Uryu, H., Liao, C., Hu, L., Zhou, J., Shi, X., Tsai, Y. H., Yan, Q., Luo, W., Chen, X., Strahl, B. D., von Kriegsheim, A., Zhang, Qi., Wang, G. G.*, Baldwin, A. S.*, and Zhang, Qing.*, “Histone H3 Proline 16 Hydroxylation Regulates Mammalian Gene Expression”, Nature Genetics, 54:1721–1735 (2022) (# Contributed Equally) pubmed

36. Krishnarjuna, B.#, Ravula, T.#, Faison, E. M.#, Tonelli, M., Zhang, Q.*, and Ramamoorthy, A.*, “Polymer-Nanodiscs as a Novel Alignment Medium for High-Resolution NMR-Based Structural Studies of Nucleic Acids”, Biomolecules, 12:1628 (2022) (# Contributed Equally) pubmed

35. Welsh, K. A., Bolhuis, D. L., Nederstigt, A. E., Boyer, J., Temple, B. R., Bonacci, T., Gu, L., Ordureau, A., Harper, J. W., Steimel, J. P., Zhang, Q., Emanuele, M. J., Harrison, J. S.*, and Brown, N. G.*, “Functional Conservation and Divergence of the Helix-turn-helix Motif of E2 Ubiquitin-conjugating Enzymes”, EMBO J., 41:e108823 (2022) pubmed

34. Baisden, J. T., Boyer, J. A., Zhao, B., Hammond, S. M., and Zhang, Q.*, “Visualizing a Protonated RNA State that Modulates MicroRNA-21 Maturation,” Nature Chem. Biol., 17:80-88 (2021) pubmed

33. Boyer, J. A.#, Spangler, C. J.#, Strauss, J. D.#, Cesmat, A. P., Liu, P., McGinty, R. K.*, and Zhang, Q.*, Structural Basis of Nucleosome-dependent cGAS Inhibition, Science, 370:450-454 (2020) (# Contributed Equally) pubmed

32. Zhang, Y.#, Ma, Z.#, Wang, Y.#, Boyer, J., Ni, G., Cheng, L., Su, S., Zhang, Z., Zhu, Z., Qian, J., Su, L., Zhang, Q., Damania, B.*, and Liu, P.*, “Streptavidin Promotes DNA Binding and Activation of cGAS to Enhance Innate Immunity,” iScience, 23:101463 (2020) (# Contributed Equally) pubmed

31. Zhao, B.#, Baisden, J. T.#, and Zhang, Q.*, “Probing Excited Conformational States of Nucleic Acids by Nitrogen CEST NMR Spectroscopy,” J. Magn. Reson., 310:106642 (2020) (# Contributed Equally) pubmed

30. Thompson, R. D., Baisden, J. T., and Zhang, Q.*, “NMR Characterization of RNA Small Molecule Interactions,” Methods, 167:66-77 (2019) pubmed

29. Eubanks, C. S., Zhao, B., Patwardhan, N. N., Thompson, R. D., Zhang, Q., and Hargrove, A. E.*, “Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules,” J. Am. Chem. Soc., 141:5692-5698 (2019) pubmed

28. Williams, B.#, Zhao, B.#, Tandon, A., Ding, F., Weeks, K. M., Zhang, Q.*, and Dokholyan, N. V.*, “Structure Modeling of RNA Using Sparse NMR Constraints,” Nucleic Acids Research, 45:12638-12647 (2017) (# Contributed Equally) pubmed

27. Zhao, B., Guffy, S. L., Williams, B., and Zhang, Q.*, “An Excited State Underlies Gene Regulation of a Transcriptional Riboswitch,” Nature Chem. Biol., 13:968-974 (2017) pubmed

26. Wang, Y., Yesselman, J. D., Zhang, Q., Kang, M,. and Feigon, J.*, Structural Conservation in the Template/Pseudoknot Domain of Vertebrate Telomerase RNA from Teleost Fish to Human,” Proc. Natl. Acad. Sci. USA, 113:E5125-5134 (2016) pubmed

25. Zhao, B., and Zhang, Q.*, “Measuring Residual Dipolar Couplings in Excited Conformational States of Nucleic Acids by CEST NMR Spectroscopy,” J. Am. Chem. Soc., 137:13480-13483 (2015) pubmed

24. Frank, A.T., Zhang, Q., Al-Hashimi, H.M.,and Andricioaei I.*, “Slowdown of Interhelical Motions Induces a Glass Transition in RNA,” Biophys. J., 108:2876-2885 (2015) pubmed

23. Zhao, B., and Zhang, Q.*, “Characterizing Excited Conformational States of RNA by NMR Spectroscopy,” Curr. Opin. Struct. Biol., 30:134-146 (2015) pubmed

22. Zhao, B., Hansen, A.L., and Zhang, Q.*, “Characterizing Slow Chemical Exchange in Nucleic Acids by Carbon CEST and Low Spin-lock Field R1ρ NMR Spectroscopy,” J. Am. Chem. Soc., 136:20-23 (2014) pubmed

21. Kim, N.K., Zhang, Q., and Feigon, J.*, “Structure and Sequence Elements of the CR4/5 Domain of Medaka Telomerase RNA Important for Telomerase Function,” Nucleic Acids Res., 42:3395-3408 (2014) pubmed

20. Shen, K., Wang, Y., Fu, Y.H., Zhang, Q., Feigon, J., and Shan, S.O.*, “Molecular Mechanism of GTPase Activation at the SRP RNA Distal End,” J. Biol. Chem., 288:36385-36397 (2013) pubmed

19. Hartman, E., Wang, Z., Zhang, Q., Roy, K., Chanfreau, G., Feigon, J.*, “Intrinsic Dynamics of an Extended Hydrophobic Core in the S. cerevisiae RNase III dsRBD Contributes to Recognition of Specific RNA Binding Sites,” J. Mol. Biol., 425:546-562 (2013) pubmed

18. Zhang, Q., Kim, N.K., and Feigon, J.*, “The Architecture of Human Telomerase RNA,”Proc. Natl. Acad. Sci. USA, 108:20325-20332 (2011) pubmed

17. Zhang, Q., Kang, M., Peterson, R.D., and Feigon, J.*, “Comparison of Solution and Crystal Structures of PreQ1 Riboswitch Reveals Calcium-induced Changes in Conformation and Dynamics.,” J. Am. Chem. Soc., 133:5190-5193 (2011) pubmed

16. Zhang, Q., Kim, N.K., Peterson, R.D., Wang, Z., and Feigon, J.*, “Structurally Conserved Five Nucleotide Bulge Determines the Overall Topology of the Core Domain of Human Telomerase RNA,” Proc. Natl. Acad. Sci. USA, 107:18761–18768 (2010). Featured in a Research Highlight in Nat. Struct. Mol. Biol., 17:1291 (2010) pubmed

15. Stelzer, A.C., Kratz, J.D., Zhang, Q., and Al-Hashimi, H.M.*, “RNA Dynamics by Design: Biasing Ensembles Towards the Ligand-bound State,” Angew. Chem. Int. Ed., 49:5731-5733 (2010) (Cover) pubmed

14. Dethoff, E. A., Hansen, A. L., Zhang, Q., and Al-Hashimi, H. M.*, “Variable Helix Elongation As A tool to Modulate RNA Alignment and Motional Couplings,” J. Magn. Reson., 202:117-121 (2010) pubmed

13. Musselman, C., Zhang, Q., Al-Hashimi, H. M.*, and Andricioaei, I.*, “Referencing Strategy for the Direct Comparison of Nuclear Magnetic Resonance and Molecular Dynamics Motional Parameters in RNA,” J. Phys. Chem. B, 114:929-939 (2010) pubmed

12. Zhang, Q., and Al-Hashimi, H. M.*, “Domain-elongation NMR Spectroscopy Yields New Insights into RNA Dynamics and Adaptive Recognition,” RNA, 15:1941-1948 (2009) (Invited review for the RNA Society/Scaringe Young Scientist Award) pubmed

11. Kim, N.K., Zhang, Q., Zhou, J., Theimer, C.A., Peterson, R.D., and Feigon, J.*, “Solution Structure and Dynamics of the Wild-type Pseudoknot of Human Telomerase RNA,” J. Mol. Biol., 384:1249-1261 (2008) pubmed

10. Fisher, C.K., Zhang, Q., Stelzer, A.C., and Al-Hashimi, H.M.*, “Ultra-High Resolution Characterization of Domain Motions and Correlations by Multi-Alignment and Multi-Reference RDC NMR”, J. Phys. Chem. B., 112:16815-16822 (2008) pubmed

9. Zhang, Q., and Al-Hashimi, H. M.*, “Extending the NMR Spatial Resolution Limit for RNA by Motional Couplings,” Nature Methods, 5:243-245 (2008) pubmed

8. Zhang, Q., Stelzer, A., Fisher, C.K., and Al-Hashimi, H. M.*, “Visualizing Spatially Correlated Dynamics that Directs RNA Conformational Transitions,” Nature, 450:1263-1267 (2007) pubmed

7. Getz, M.M., Sun, X., Casiano-Negroni, A., Zhang, Q., and Al-Hashimi, H.M.*, “NMR Studies of RNA Dynamics and Structural Plasticity using NMR Residual Dipolar Couplings,” Biopolymers, 86:384-402 (2007) pubmed

6. Sun, X., Zhang, Q., and Al-Hashimi, H. M.*, “Resolving Fast and Slow Motions in the Internal Loop Containing Stem-loop 1 of HIV-1 that Are Modulated by Mg2+ Binding: Role in the Kissing-duplex Structural Transition,” Nucleic Acids Res., 35:1698-1713 (2007) pubmed

5. Chen, Y., Zhang, Q., and Ding, J.*, “A Coarse-grained Model for the Formation of Alpha Helix with A Noninteger Period on Simple Cubic Lattices,” J. Chem. Phys., 124:184903-184908 (2006) pubmed

4. Zhang, Q., Sun, X., Watt, E.D., and Al-Hashimi, H. M.*, “Resolving the Motional Modes that Code for RNA Adaptation,” Science, 311:653-656 (2006) pubmed

3. Pitt, S.W., Zhang, Q., Patel, D. J., and Al-Hashimi, H. M.*, “Evidence that Electrostatic Interactions Dictate the Ligand-induced Arrest of RNA Global Flexibility,” Angew. Chem. Int. Ed., 44:3412-3415 (2005) pubmed

2. Chen, Y., Zhang, Q., and Ding, J.*, “A Coarse-grained Model and Associated Lattice Monte Carlo Simulation of the Coil-helix Transition of A Homopolypeptide,” J. Chem. Phys., 120:3467-3474 (2004) pubmed

1. Zhang, Q., Throolin, R., Pitt, S.W., Serganov, A., and Al-Hashimi, H.M.*, “Probing Motions Between Equivalent RNA Domains Using Magnetic Field Induced Residual Dipolar Couplings: Accounting for Correlations Between Motions and Alignment,” J. Am. Chem. Soc., 125:10530-10531 (2003) pubmed