{"id":161,"date":"2023-07-27T14:17:34","date_gmt":"2023-07-27T21:17:34","guid":{"rendered":"https:\/\/dornsife.usc.edu\/pzqin-lab\/?page_id=161"},"modified":"2026-02-04T18:51:10","modified_gmt":"2026-02-05T02:51:10","slug":"publication","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/pzqin-lab\/publication\/","title":{"rendered":"Publication"},"content":{"rendered":"\n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <p><strong>74.<\/strong> Schuster, I,, Shlipak, K.K., <strong>Qin, P.Z.<\/strong>,* (2026), \u201cImpacts of DNA Supercoiling on the Sequence-Dependent Nuclease Activity of CRISPR-Cas9 with Truncated Guides.\u201d <a href=\"https:\/\/doi.org\/10.1021\/acs.biochem.5c00693\"><em>Biochemistry<\/em>, in press.<\/a><\/p>\n<p><strong>73.<\/strong> Wu, D., Snead, S., Ganguly, C., Babu, K., Li, Y., Kathiresan, V., Shen, R., Zhang, X., Rajan, R., <strong>Qin, P.Z.<\/strong>,* (2025), &#8220;Structural integrity and side-chain interaction at the loop region of the bridge helix modulate Cas9 substrate discrimination.&#8221; <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkaf557\"><em>Nucleic Acid Res., 53, gkaf557<\/em><\/a>.<\/p>\n<p><strong>72.<\/strong> \u00a0Allen, A., Cooper, B.H., Singh, J., Rohs, R., <strong>Qin, P.Z.<\/strong>,* (2025), \u201cPAM-Adjacent DNA Flexibility Tunes CRISPR-Cas12a Off-Target Binding.\u201d <a href=\"http:\/\/dx.doi.org\/10.1038\/s41598-025-87565-9\"><i>Sci Rep,<\/i> <span style=\"text-decoration: underline;\">15<\/span>, 4930<\/a>.<\/p>\n<p><strong>71.<\/strong> \u00a0\u00a0Sun, J.-H., Wu, D. <strong>Qin, P.Z.<\/strong>, Sideris, C., (2024), &#8220;Design and Implementation of Integrated Dual-Mode Pulse and Continuous-Wave Electron Paramagnetic Resonance Spectrometers.\u201d, <a href=\"http:\/\/dx.doi.org\/10.1109\/TBCAS.2024.3465210\"><em>IEEE Trans Biomed Circuits Syst<\/em>, 18, 1209-1219<\/a>.<\/p>\n<p><strong>70.<\/strong> \u00a0\u00a0 Sun, J., Rustom, M., Nguyen, T.D., Singh, J., <strong>Qin, P.Z<\/strong>., Sideris, C.*, (2024), \u201cA29.5 A Portable 14GHz Dual-Mode Pulse and Continuous-Wave Electron Paramagnetic Resonance Spectrometer Using a Subharmonic Direct Conversion Receiver,&#8221; <em><a href=\"http:\/\/dx.doi.org\/10.1109\/ISSCC49657.2024.10454384\">IEEE International Solid-State Circuits Conference<\/a> (ISSCC) (conference paper)<\/em>.<\/p>\n<p><strong>69.<\/strong> \u00a0\u00a0 Zhang, M., Feng, J., Li, Y., <strong>Qin, P.Z<\/strong>., and Chai, Y.*, (2024), \u201cGeneration of tamoxifen-inducible Tfap2b-CreERT2 mice using CRISPR-Cas9.\u201d <a href=\"https:\/\/doi.org\/10.1002\/dvg.23582\"><em>Genesis,<\/em> 6, e23582<\/a>.<\/p>\n<p><strong>68.<\/strong> \u00a0\u00a0 Newsom, S.N., Wang, D., Rostami, S., Schuster, I., Parameshwaran, H.P., Joseph, Y.G., <strong>Qin, P.Z<\/strong>., Liu, J.,* Rajan, R.*, (2023), \u201cDifferential divalent metal binding by SpyCas9\u2019s RuvC active site contributes to non-specific DNA cleavage.\u201d <a href=\"https:\/\/dx.doi.org\/10.1089\/crispr.2023.0022\"><em>CRISPR J.<\/em>, 6, 527-542<\/a><em>.<\/em><\/p>\n<p><b>67<\/b>. \u00a0 Li, Y., Cooper, B. H., Liu, L., Wu, D., Zhang, X., Rohs, R., <b>Qin, P.Z.<\/b>*; (2023) &#8220;CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA\/DNA Hybrid.&#8221; <a href=\"https:\/\/doi.org\/10.1021\/acs.biochem.3c00250\"><i>Biochemistry<\/i>, 62, 2541\u20132548.<\/a><\/p>\n<p><b>66<\/b>. \u00a0\u00a0Singh, J., Liu, K.G., Jiang, W., <b>Qin, P.Z.<\/b>*; (2023), &#8220;A DNA Unwinding Equilibrium Serves as a Checkpoint for CRISPR-Cas12a Target Discrimination.&#8221; <a href=\"https:\/\/dx.doi.org\/10.1093\/nar\/gkad636\"><i>Nucleic Acids Res.<\/i>, 51, 8730\u20138743<em>.<\/em><\/a><\/p>\n<p><b>65<\/b>. \u00a0\u00a0 Siegel, A., Singh, J., <b>Qin, P.Z.<\/b>*, Shan, Shu-ou* (2023), \u201cChapter 10: EPR Studies of Chaperone Interaction and Dynamics.\u201d in <em>Biophysics of Molecular Chaperones: Function, Mechanisms and Client Protein Interactions<\/em> (ed. S. Hiller, M. Liu, and L. He, Royal Society of Chemistry), <a href=\"https:\/\/dx.doi.org\/10.1039\/BK9781839165986-00242\">29, 242-277.<\/a><\/p>\n<p><b>64<\/b>. \u00a0\u00a0 Hu, Y.; Wang, T.; Singh, J.; Sun, R.; Xu, L.; Niu, X.; Huang, K.; Bai, G.; Liu, G.; Zuo, X.; Chen, C.; <strong>Qin, P.Z.<\/strong>; Fang, X.*; (2022) &#8220;Phosphorothioate-Based Posttranscriptional Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies.&#8221; <a href=\"https:\/\/doi.org\/10.1021\/acschembio.2c00199\"><i>ACS. Chem. Biol.<\/i>, 17, 2448\u20132460.<\/a><\/p>\n<p><b>63<\/b>. Li, Y., Liu, Y., Singh, J., Tangprasertchai, N.S., Trivedi, R., Fang, Y., and <b>Qin, P.Z.<\/b>* (2022) &#8220;Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA\/DNA Pairing in Sequences Distal to the PAM.&#8221; <a href=\"https:\/\/doi.org\/10.1089\/crispr.2021.0100\"><i>CRISPR J.<\/i>, 5, 341-352.<\/a><\/p>\n<p><b>62<\/b>. Babu, K.; Kathiresan, V.; Kumari, P.; Newsom, S.; Parameshwaran, H. P.; Chen, X.; Liu, J.; <b>Qin, P.Z.<\/b>*; Rajan, R.* (2021) &#8220;Coordinated Actions of Cas9 HNH and RuvC Nuclease Domains Are Regulated by the Bridge Helix and the Target DNA Sequence.&#8221; <a href=\"https:\/\/doi.org\/10.1021\/acs.biochem.1c00354\"><i>Biochemistry<\/i>, 60, 3783\u20133800<\/a><\/p>\n<p><b>61<\/b>. Parameshwaran, H. P., Babu, K., Tran, C., Guan, K., Allen, A., Kathiresan, K, <b>Qin, P.Z.<\/b>, Rajan, R.*, (2021), &#8220;Bridge helix of Cas12a imparts selectivity for cis-DNA cleavage and regulates trans-DNA cleavage.&#8221;, <a href=\"https:\/\/dx.doi.org\/10.1002\/1873-3468.14051\"><i>FEBS Lett.<\/i>, 595, 892-912<\/a><\/p>\n<p><b>60<\/b>. Wang, Y., Kathiresan, V., Chen, Y., Hu, Y., Jiang, W., Bai, G., Liu, G., <b>Qin, P.Z.*<\/b>, Fang, X.*, (2020), &#8220;Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions.&#8221; <a href=\"https:\/\/dx.doi.org\/10.1039\/D0SC01717E\"><i>Chem. Sci.<\/i>, 11, 9655-9664<\/a><\/p>\n<p><b>59<\/b>. Ameri, H.,* Murat, C., Arbabi, A., Jiang, W., Janga, S.R., <b>Qin, P.Z.<\/b>, Hamm-Alvarez, S.F., (2020), &#8220;Reduced Expression of VEGF-A in Human Retinal Pigment Epithelial Cells and Human Muller Cells Following CRISPR-Cas9 Ribonucleoprotein-Mediated Gene Disruption.&#8221; <a href=\"https:\/\/dx.doi.org\/10.1167\/tvst.9.8.23\"><i>Trans. Vis. Sci. Tech.<\/i> 9, 23<\/a><\/p>\n<p><b>58<\/b>. Jiang, W., Singh, J., Allen, A., Li, Y., Kathiresan, V., Qureshi, Q., Tangprasertchai, N., Zhang, X., Parameshwaran, H.P., Rajan, R., <b>Qin, P. Z.<\/b>* (2019), \u201cCRISPR-Cas12a Nucleases Bind Flexible DNA Duplexes without RNA-DNA Complementarity.\u201d <a href=\"http:\/\/dx.doi.org\/10.1021\/acsomega.9b01469\"><i>ACS Omega<\/i>, 4, 17140-17147<\/a><\/p>\n<p><b>57<\/b>. Ding, Y., Kathiresan, V., Zhang, X., Haworth, I.S.; <b>Qin, P. Z.<\/b>* (2019), &#8220;Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1021\/acs.jpca.9b01027\"><i>J. Phys. Chem., A<\/i>, 123, 3592-3598<\/a><\/p>\n<p><b>56<\/b>. Babu, K., Amrani, N., Jiang, W., Yogesha, S.D., Nguyen, R., <b>Qin, P. Z.<\/b>, Rajan R.* (2019), &#8220;Bridge Helix of Cas9 Modulates Target DNA Cleavage and Mismatch Tolerance.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1021\/acs.biochem.8b01241\"><i>Biochemistry<\/i>, 58, 1905-1917<\/a><\/p>\n<p><b>55<\/b>. 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, <b>Qin, P. Z.<\/b>*, and J. Du* (2018), &#8220;Single DNA Electron Spin Resonance Spectroscopy in Aqueous Solutions.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1038\/s41592-018-0084-1\"><i>Nat. Meth.<\/i>, 15, 697\u2013699<\/a><\/p>\n<p><b>54<\/b>. Zhong, Y.-F., H. Zhang, W.-T. Liu, X.-H. Zheng, Y.-W. Zhou, Q. Cao, Y. Shen, Y. Zhao, <b>P.Z. Qin<\/b>, L.-N. Ji, and Z.-W. Mao (2017), &#8220;A Platinum(II)-based Photosensitive Tripod as an Effective Photodynamic Anticancer Agent through DNA Damage&#8221;. <a href=\"http:\/\/dx.doi.org\/10.1002\/chem.201703598\"><i>Chem. Eur. J.<\/i>, 23, 16442\u201316446<\/a><\/p>\n<p><b>53<\/b>. Tangprasertchai, N.S., Di Felice, R., Zhang, X., Slaymaker, I.M., Reyes, C.V., Jiang, W., Rohs, R., and <b>Qin, P. Z.<\/b>* (2017), \u201cCRISPR-Cas9 mediated DNA unwinding detected using site-directed spin labeling.&#8221;<a href=\"http:\/\/dx.doi.org\/10.1021\/acschembio.6b01137\"><i> ACS Chem. Biol.<\/i>, 12, 1489\u20131493<\/a><\/p>\n<p><b>52<\/b>. Yang, J., Cao, Q.,* Hu, W.L., Ye, R.R., He, L., Ji, L.N., <b>Qin, P. Z.<\/b>, and Mao, Z.W.* (2017), \u201cTheranostic TEMPO-functionalized Ru(ii) complexes as photosensitizers and oxidative stress indicators.\u201d <a href=\"http:\/\/dx.doi.org\/10.1039\/c6dt04028d\"><i> Dalton Trans. <\/i>, 46, 445-454<\/a><\/p>\n<p><b>51<\/b>. Cao, Q., Li, Y., Freisinger, E., <b>Qin, P. Z.<\/b>*, Sigel,R.K.O.*, and Mao, M.Z.* (2017), \u201cG-quadruplex DNA targeted metal complexes acting as potential anticancer drugs.\u201d <a href=\"http:\/\/dx.doi.org\/10.1039\/C6QI00300A\"><i> Inorg. Chem. Front.<\/i>, 4, 10-32<\/a><\/p>\n<p><b>50<\/b>. Reyes, C.V., Tangprasertchai, N.S., Yogesha, S.D., Nguyen, R.H., Zhang, X., Rajan, R. and <b>Qin, P. Z.<\/b>* (2017), \u201cNucleic-acid dependent conformational changes in CRISPR-Cas9 revealed by site-directed spin labeling.\u201d <a href=\"http:\/\/dx.doi.org\/10.1007\/s12013-016-0738-5\"><i>Cell Biochem Biophys<\/i>, 75, 203-210<\/a><\/p>\n<p><b>49<\/b>. Akiel RD, Zhang X, Abeywardana C, Stepanov V, <b>Qin, P. Z.<\/b>*, Takahashi,S* (2016), &#8220;Investigating Functional DNA Grafted on Nanodiamond Surface Using Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1021\/acs.jpcb.6b00790\"><i>J. Phys. Chem. B.<\/i>, 120, 4003\u20134008<\/a><\/p>\n<p><b>48<\/b>. Xu CX, Zhang X, Zhou YW, Wang H, Cao Q, Shen Y, Ji LN, Mao ZW,* and <b>Qin, P. Z.<\/b>* (2016), &#8220;A Nitroxide Tagged Platinum(II) Complex Enables the Identification of DNA G-quadruplex Binding Mode.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1002\/chem.201504960\"><i>Chem. Eur. J.<\/i>, 22, 3405\u20133413<\/a><\/p>\n<p><b>47<\/b>. Zhang X, Xu CX, Di Felice R, Sponer J, Islam B, Stadlbauer P, Ding Y, Mao L, Mao ZW, and <b>Qin, P. 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Popova, Anna M., K\u00e1lai, Tam\u00e1s, Hideg, K\u00e1lm\u00e1n, <b>Qin, Peter Z.<\/b>, (2009) &#8220;Site-Specific DNA Structural and Dynamic Features Revealed by Nucleotide-Independent Nitroxide Probes&#8221; <a href=\"file:\/\/\/C:\/Qin_Lab\/pzq%20group%20page\/pzqhome_summer2023\/pzqhome\/&lt;http:\/\/dx.doi.org\/10.1021\/bi900860w &gt;\"><i>Biochemistry<\/i>, 48, 8540-8550<\/a><\/p>\n<p><b>25<\/b>. Grant, Gian Paola G., Boyd, Nathan, Herschlag, Daniel, <b>Qin, Peter Z.<\/b>, (2009) &#8220;Motions of the Substrate Recognition Duplex in a Group I Intron Assessed by Site-Directed Spin Labeling&#8221; <a href=\"file:\/\/\/C:\/Qin_Lab\/pzq%20group%20page\/pzqhome_summer2023\/pzqhome\/&lt;http:\/\/dx.doi.org\/10.1021\/ja808217s &gt;\"><i>J. Am. Chem. Soc.<\/i>, 131, 3136-3137<\/a><\/p>\n<p><b>24<\/b>. Sowa, Glenna Z., <b>Qin, Peter Z.<\/b>, (2008) &#8220;Site-directed spin labeling studies on nucleic acid structure and dynamics.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1016\/S0079-6603%2808%2900005-6\"><i>Prog. Nucleic Acids Res. Mol. Biol.<\/i>, 82, 147-197<\/a><\/p>\n<p><b>23<\/b>. Grant, Gian Paola G., Popova, Anna, <b>Qin, Peter Z.<\/b>, (2008) &#8220;Diastereomer characterizations of nitroxide-labeled nucleic acids&#8221; <a href=\"http:\/\/dx.doi.org\/10.1016\/j.bbrc.2008.04.088\"><i>Biochem. Biophys. Res. Commun.<\/i>, 371, 451-455<\/a><\/p>\n<p><b>22<\/b>. Fang, Yun, Shu, Dan, Xiao, Feng, Guo, Peixuan, <b>Qin, Peter Z.<\/b>, (2008) &#8220;Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging&#8221; <a href=\"http:\/\/dx.doi.org\/10.1016\/j.bbrc.2008.05.094\"><i>Biochem. Biophys. Res. Comm.<\/i>, 372, 589-594<\/a><\/p>\n<p><b>21<\/b>. <b>Qin, Peter Z<\/b>, 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) &#8220;Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe&#8221; <a href=\"http:\/\/dx.doi.org\/10.1038\/nprot.2007.308\"><i>Nat. Protocols<\/i>, 2, 2354-2365<\/a><\/p>\n<p><b>20<\/b>. Price, Eric A., Sutch, Brian T., Cai, Qi , <b>Qin, Peter Z.<\/b>, Haworth, Ian S., (2007) &#8220;Computation of nitroxide-nitroxide distances for spin-labeled DNA duplexes.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1002\/bip.20769\"><i>Biopolymers<\/i>, 87, 40-50<\/a><\/p>\n<p><b>19<\/b>. Grant, Gian Paola G., <b>Qin, Peter Z.<\/b>, (2007) &#8220;A facile method for attaching nitroxide spin labels at the 5&#8242; terminus of nucleic acids.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1093\/nar\/gkm240\"><i>Nucl. Acids Res.<\/i>, 35, e77<\/a><\/p>\n<p><b>18<\/b>. Cai, Qi, Kusnetzow, Ana Karin, Hideg, Kalman, Price, Eric A., Haworth, Ian S., <b>Qin, Peter Z.<\/b>, (2007) &#8220;Nanometer Distance Measurements in RNA Using Site-Directed Spin Labeling.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1529\/biophysj.107.109439\"><i>Biophys. J.<\/i>, 93, 2110-2117<\/a><\/p>\n<p><b>17<\/b>. <b>Qin, P.Z.<\/b>, Jennifer, I., Oki, A., (2006) &#8220;A model system for investigating lineshape\/structure correlations in RNA site-directed spin labeling.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1016\/j.bbrc.2006.02.138\"><i>Biochem. Biophys. Res. Commun.<\/i>, 343, 117-124<\/a><\/p>\n<p><b>16<\/b>. Cai, Q., Kusnetzow, A.K., Hubbell, W.L., Haworth, I.S., Gacho, G.P.C., Van Eps, N., Hideg, K., Chambers, E.J., <b>Qin, P.Z.<\/b>, (2006) &#8220;Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1093\/nar\/gkl546\"><i>Nucl. Acids Res.<\/i>, 34, 4722-4734<\/a><\/p>\n<p><b>15<\/b>. <b>Qin, P.Z.<\/b>, Feigon, J., Hubbell, W. L., (2005) &#8220;Site-directed spin labeling studies reveal solution conformational changes in a GAAA tetraloop receptor upon Mg2+-dependent docking of a GAAA tetraloop.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1016\/j.jmb.2005.06.007\"><i>J Mol Biol<\/i>, 351, 1-8<\/a><\/p>\n<p><b>14<\/b>. Fang, Y., Cai, Q., <b>Qin, P.Z.<\/b>, (2005) &#8220;The procapsid binding domain of phi29 packaging RNA has a modular architecture and requires 2&#8242;-hydroxyl groups in packaging RNA interaction.&#8221; <a href=\"http:\/\/dx.doi.org\/10.1021\/bi0475020\"><i>Biochemistry<\/i>, 44, 9348-58<\/a><\/p>\n<p style=\"text-align: right;\">[updated August, 2023]<\/p>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":9,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-content-detail.php","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-161","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Publication - Peter Qin Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/dornsife.usc.edu\/pzqin-lab\/publication\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publication - 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