70. Sun, J., Rustom, M., Nguyen, T.D., Singh, J., Qin, P.Z., Sideris, C.*, “A Portable Dual-Mode Pulse and Continuous-Wave Electron Paramagnetic Resonance Spectrometer using a Subharmonic Direct Conversion Receiver,” accepted for IEEE Intl. Solid-State Circuits Conf., Feb 2024.
69. Zhang, M., Feng, J., Li, Y., Qin, P.Z., and Chai, Y.*, (2023), “Generation of tamoxifen-inducible Tfap2b-CreERT2 mice using CRISPR-Cas9.” Genesis, e23582.
68. Newsom, S.N., Wang, D., Rostami, S., Schuster, I., Parameshwaran, H.P., Joseph, Y.G., Qin, P.Z., Liu, J.,* Rajan, R.*, (2023), “Differential divalent metal binding by SpyCas9’s RuvC active site contributes to non-specific DNA cleavage.” CRISPR J., 6, 527-542.
67. Li, Y., Cooper, B. H., Liu, L., Wu, D., Zhang, X., Rohs, R., Qin, P.Z.*; (2023) “CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid.” Biochemistry, 62, 2541–2548.
66. Singh, J., Liu, K.G., Jiang, W., Qin, P.Z.*; (2023), “A DNA Unwinding Equilibrium Serves as a Checkpoint for CRISPR-Cas12a Target Discrimination.” Nucleic Acids Res., 51, 8730–8743.
65. Siegel, A., Singh, J., Qin, P.Z.*, Shan, Shu-ou* (2023), “Chapter 10: EPR Studies of Chaperone Interaction and Dynamics.” in Biophysics of Molecular Chaperones: Function, Mechanisms and Client Protein Interactions (ed. S. Hiller, M. Liu, and L. He, Royal Society of Chemistry), 29, 242-277.
64. Hu, Y.; Wang, T.; Singh, J.; Sun, R.; Xu, L.; Niu, X.; Huang, K.; Bai, G.; Liu, G.; Zuo, X.; Chen, C.; Qin, P.Z.; Fang, X.*; (2022) “Phosphorothioate-Based Posttranscriptional Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies.” ACS. Chem. Biol., 17, 2448–2460.
63. Li, Y., Liu, Y., Singh, J., Tangprasertchai, N.S., Trivedi, R., Fang, Y., and Qin, P.Z.* (2022) “Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM.” CRISPR J., 5, 341-352.
62. Babu, K.; Kathiresan, V.; Kumari, P.; Newsom, S.; Parameshwaran, H. P.; Chen, X.; Liu, J.; Qin, P.Z.*; Rajan, R.* (2021) “Coordinated Actions of Cas9 HNH and RuvC Nuclease Domains Are Regulated by the Bridge Helix and the Target DNA Sequence.” Biochemistry, 60, 3783–3800
61. Parameshwaran, H. P., Babu, K., Tran, C., Guan, K., Allen, A., Kathiresan, K, Qin, P.Z., Rajan, R.*, (2021), “Bridge helix of Cas12a imparts selectivity for cis-DNA cleavage and regulates trans-DNA cleavage.”, FEBS Lett., 595, 892-912
60. Wang, Y., Kathiresan, V., Chen, Y., Hu, Y., Jiang, W., Bai, G., Liu, G., Qin, P.Z.*, Fang, X.*, (2020), “Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions.” Chem. Sci., 11, 9655-9664
59. Ameri, H.,* Murat, C., Arbabi, A., Jiang, W., Janga, S.R., Qin, P.Z., Hamm-Alvarez, S.F., (2020), “Reduced Expression of VEGF-A in Human Retinal Pigment Epithelial Cells and Human Muller Cells Following CRISPR-Cas9 Ribonucleoprotein-Mediated Gene Disruption.” Trans. Vis. Sci. Tech. 9, 23
58. Jiang, W., Singh, J., Allen, A., Li, Y., Kathiresan, V., Qureshi, Q., Tangprasertchai, N., Zhang, X., Parameshwaran, H.P., Rajan, R., Qin, P. Z.* (2019), “CRISPR-Cas12a Nucleases Bind Flexible DNA Duplexes without RNA-DNA Complementarity.” ACS Omega, 4, 17140-17147
57. Ding, Y., Kathiresan, V., Zhang, X., Haworth, I.S.; Qin, P. Z.* (2019), “Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.” J. Phys. Chem., A, 123, 3592-3598
56. Babu, K., Amrani, N., Jiang, W., Yogesha, S.D., Nguyen, R., Qin, P. Z., Rajan R.* (2019), “Bridge Helix of Cas9 Modulates Target DNA Cleavage and Mismatch Tolerance.” Biochemistry, 58, 1905-1917
55. Shi, F., F. Kong, P. Zhao, X. Zhang, M. Chen, S. Chen, Q. Zhang, M. Wang, X. Ye, Z. Wang, Z. Qin, X. Rong, J. Su, P. Wang, Qin, P. Z.*, and J. Du* (2018), “Single DNA Electron Spin Resonance Spectroscopy in Aqueous Solutions.” Nat. Meth., 15, 697–699
54. Zhong, Y.-F., H. Zhang, W.-T. Liu, X.-H. Zheng, Y.-W. Zhou, Q. Cao, Y. Shen, Y. Zhao, P.Z. Qin, L.-N. Ji, and Z.-W. Mao (2017), “A Platinum(II)-based Photosensitive Tripod as an Effective Photodynamic Anticancer Agent through DNA Damage”. Chem. Eur. J., 23, 16442–16446
53. Tangprasertchai, N.S., Di Felice, R., Zhang, X., Slaymaker, I.M., Reyes, C.V., Jiang, W., Rohs, R., and Qin, P. Z.* (2017), “CRISPR-Cas9 mediated DNA unwinding detected using site-directed spin labeling.” ACS Chem. Biol., 12, 1489–1493
52. Yang, J., Cao, Q.,* Hu, W.L., Ye, R.R., He, L., Ji, L.N., Qin, P. Z., and Mao, Z.W.* (2017), “Theranostic TEMPO-functionalized Ru(ii) complexes as photosensitizers and oxidative stress indicators.” Dalton Trans. , 46, 445-454
51. Cao, Q., Li, Y., Freisinger, E., Qin, P. Z.*, Sigel,R.K.O.*, and Mao, M.Z.* (2017), “G-quadruplex DNA targeted metal complexes acting as potential anticancer drugs.” Inorg. Chem. Front., 4, 10-32
50. Reyes, C.V., Tangprasertchai, N.S., Yogesha, S.D., Nguyen, R.H., Zhang, X., Rajan, R. and Qin, P. Z.* (2017), “Nucleic-acid dependent conformational changes in CRISPR-Cas9 revealed by site-directed spin labeling.” Cell Biochem Biophys, 75, 203-210
49. Akiel RD, Zhang X, Abeywardana C, Stepanov V, Qin, P. Z.*, Takahashi,S* (2016), “Investigating Functional DNA Grafted on Nanodiamond Surface Using Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy.” J. Phys. Chem. B., 120, 4003–4008
48. Xu CX, Zhang X, Zhou YW, Wang H, Cao Q, Shen Y, Ji LN, Mao ZW,* and Qin, P. Z.* (2016), “A Nitroxide Tagged Platinum(II) Complex Enables the Identification of DNA G-quadruplex Binding Mode.” Chem. Eur. J., 22, 3405–3413
47. Zhang X, Xu CX, Di Felice R, Sponer J, Islam B, Stadlbauer P, Ding Y, Mao L, Mao ZW, and Qin, P. Z.* (2016), “Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label.” Biochemistry, 55, 360–372
46. Tangprasertchai, N. S., Zhang, X., Ding, Y., Tham, K., Rohs, R., Haworth, I. S., and Qin, P. Z.* (2015), “An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.” Method Enzymol. , 564, 427-453
45. Beasley, K. N., Sutch, B.T., Hatmal, M., Langen, R., Qin, P.Z., Haworth, I.S.*, (2015), “Computer modeling of spin labels: NASNOX, PRONOX and ALLNOX”, Method Enzymol., 563, 569-593
44. Qin, P.Z., Warncke, K. (eds.), (2015), Methods Enzymol; Vol. 564, “Investigations of Biological Systems by Using Spin Labels, Spin Probes, and Intrinsic Metal Ions, Part B”
43. Qin, P.Z., Warncke, K. (eds.), (2015), Methods Enzymol; Vol. 563, “Investigations of Biological Systems by Using Spin Labels, Spin Probes, and Intrinsic Metal Ions, Part A”
42. Franck, J., Ding, Y., Stone, K., Qin, P.Z.*, Han, S.*, (2015), “Anomalously rapid hydration water diffusion dynamics found near DNA surfaces”. J. Am. Chem. Soc., 137, 12013–23
41. Nguyen, P. H., Popova, A. M., Hideg, K., and Qin, P.Z.* (2015) “A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids.” BMC Biophysics, 8: 6
40. Zheng, X.-H., Cao, Q., Ding, Y.-L., Zhong, Y.-F., Mu, G.,Qin, P.Z., Ji, L.-N. and Mao, Z.-W.* (2015) “Platinum(II) clovers targeting G-quadruplexes and their anticancer activities.” Dalton Trans, 44, 50–53
39. Ding, Y., Nguyen, P., Tangprasertchai, N.S., Reyes, C.V., Zhang, X. and Qin, P.Z.* (2015), “Nucleic acid structure and dynamics: perspectives from site-directed spin labeling” Electron Paramagnetic Resonance, 24, 122–147
38. Ding, Y., Zhang, X., Tham, K.W. and Qin, P.Z.* (2014) “Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe.” Nucl. Acids Res., 42, e140
37. Xu, C.-X., Shen, Y., Hu, Q., Zheng, Y.-X., Cao, Q., Qin, P.Z., Zhao, Y., Ji, L.-N. and Mao, Z.-W. (2014) “Stabilization of Human Telomeric G-Quadruplex and Inhibition of Telomerase Activity by Propeller-Shaped Trinuclear Pt(II) Complexes.” Chemistry – An Asian Journal, 9, 2519-2526
36. Zhang, X., Dantas Machado, A.C., Ding, Y., Chen, Y., Lu, Y., Duan, Y., Tham, K.W., Chen, L., Rohs, R.* and Qin, P.Z.* (2014) “Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling” Nucl. Acids Res., 42, 2789-2797
35. Nguyen, P., Shi, X., Sigurdsson, S.T., Herschlag, D. and Qin, P.Z.* (2013) “A Single-Stranded Junction Modulates Nanosecond Motional Ordering of the Substrate Recognition Duplex of a Group I Ribozyme” ChemBioChem, 14, 1720-1723
34. Chen, Y., Zhang, X., Dantas Machado, A.C., Ding, Y., Chen, Z., Qin, P.Z., Rohs, R. and Chen, L. (2013) “Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion” Nucl. Acids Res., 41, 8368-8376
33. Zhang, Xiaojun, Qin, Peter Z,* (2013) “Studying RNA Folding Using Site-Directed Spin Labeling.” In Russell, R. (ed.), Biophysics of RNA folding, 3, 69-87
32. Zhang, Xiaojun, Tung, Chang-Shung, Sowa, Glenna Z., Hatmal, Ma’mon M., Haworth, Ian S., Qin, Peter Z., (2012) “Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling” J. Am. Chem. Soc., 134, 2644–2652
31. Anna M. Popova, Ma’mon M. Hatmal, Maria Frushicheva, Eric A. Price, Peter Z. Qin,* Ian S. Haworth,* (2012) “Nitroxide Sensing of a DNA Microenvironment: Mechanistic Insights from EPR Spectroscopy and Molecular Dynamics Simulations” J. Phys. Chem. B, 116, 6387?6396
30. Phuong Nguyen, Peter Z. Qin, (2011) “RNA dynamics: perspectives from spin labels.” WIREs: RNA, 3, 62-72
29. Zhang, Xiaojun, Lee, Sang Won, Zhao, Liang, Xia, Tianbing, Qin, Peter Z. , (2010) “Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling.” RNA, 16, 2474-2483
28. Popova, Anna M., Qin, Peter Z., (2010) “A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA.” Biophysical Journal, 99, 2180-2189
27. Zhang, Xiaojun, Cekan, Pavol, Sigurdsson, Snorri Th., Qin, Peter Z., (2009) “Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy.” Method Enzymol., 469, 303-328
26. Popova, Anna M., Kálai, Tamás, Hideg, Kálmán, Qin, Peter Z., (2009) “Site-Specific DNA Structural and Dynamic Features Revealed by Nucleotide-Independent Nitroxide Probes” Biochemistry, 48, 8540-8550
25. Grant, Gian Paola G., Boyd, Nathan, Herschlag, Daniel, Qin, Peter Z., (2009) “Motions of the Substrate Recognition Duplex in a Group I Intron Assessed by Site-Directed Spin Labeling” J. Am. Chem. Soc., 131, 3136-3137
24. Sowa, Glenna Z., Qin, Peter Z., (2008) “Site-directed spin labeling studies on nucleic acid structure and dynamics.” Prog. Nucleic Acids Res. Mol. Biol., 82, 147-197
23. Grant, Gian Paola G., Popova, Anna, Qin, Peter Z., (2008) “Diastereomer characterizations of nitroxide-labeled nucleic acids” Biochem. Biophys. Res. Commun., 371, 451-455
22. Fang, Yun, Shu, Dan, Xiao, Feng, Guo, Peixuan, Qin, Peter Z., (2008) “Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging” Biochem. Biophys. Res. Comm., 372, 589-594
21. Qin, Peter Z, Haworth, Ian S, Cai, Qi, Kusnetzow, Ana K, Grant, Gian Paola G, Price, Eric A, Sowa, Glenna Z, Popova, Anna, Herreros, Bruno, He, Honghang, (2007) “Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe” Nat. Protocols, 2, 2354-2365
20. Price, Eric A., Sutch, Brian T., Cai, Qi , Qin, Peter Z., Haworth, Ian S., (2007) “Computation of nitroxide-nitroxide distances for spin-labeled DNA duplexes.” Biopolymers, 87, 40-50
19. Grant, Gian Paola G., Qin, Peter Z., (2007) “A facile method for attaching nitroxide spin labels at the 5′ terminus of nucleic acids.” Nucl. Acids Res., 35, e77
18. Cai, Qi, Kusnetzow, Ana Karin, Hideg, Kalman, Price, Eric A., Haworth, Ian S., Qin, Peter Z., (2007) “Nanometer Distance Measurements in RNA Using Site-Directed Spin Labeling.” Biophys. J., 93, 2110-2117
17. Qin, P.Z., Jennifer, I., Oki, A., (2006) “A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling.” Biochem. Biophys. Res. Commun., 343, 117-124
16. Cai, Q., Kusnetzow, A.K., Hubbell, W.L., Haworth, I.S., Gacho, G.P.C., Van Eps, N., Hideg, K., Chambers, E.J., Qin, P.Z., (2006) “Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe.” Nucl. Acids Res., 34, 4722-4734
15. Qin, P.Z., Feigon, J., Hubbell, W. L., (2005) “Site-directed spin labeling studies reveal solution conformational changes in a GAAA tetraloop receptor upon Mg2+-dependent docking of a GAAA tetraloop.” J Mol Biol, 351, 1-8
14. Fang, Y., Cai, Q., Qin, P.Z., (2005) “The procapsid binding domain of phi29 packaging RNA has a modular architecture and requires 2′-hydroxyl groups in packaging RNA interaction.” Biochemistry, 44, 9348-58
[updated August, 2023]