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Peter Z. Qin - Publications

Affiliations: 
Chemistry: Doctor of Philosophy University of Southern California, Los Angeles, CA, United States 
Area:
General Biophysics
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63 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Newsom SN, Wang DS, Rostami S, Schuster I, Parameshwaran HP, Joseph YG, Qin PZ, Liu J, Rajan R. Differential Divalent Metal Binding by SpyCas9's RuvC Active Site Contributes to Nonspecific DNA Cleavage. The Crispr Journal. 6: 527-542. PMID 38108519 DOI: 10.1089/crispr.2023.0022  0.327
2023 Li Y, Cooper BH, Liu Y, Wu D, Zhang X, Rohs R, Qin PZ. CRISPR-Cas9 Activities with Truncated 16-Nucleotide RNA Guides Are Tuned by Target Duplex Stability Beyond the RNA/DNA Hybrid. Biochemistry. PMID 37552860 DOI: 10.1021/acs.biochem.3c00250  0.368
2023 Singh J, Liu KG, Allen A, Jiang W, Qin PZ. A DNA unwinding equilibrium serves as a checkpoint for CRISPR-Cas12a target discrimination. Nucleic Acids Research. PMID 37522352 DOI: 10.1093/nar/gkad636  0.395
2023 Singh J, Liu KG, Allen A, Jiang W, Qin PZ. A DNA Unwinding Equilibrium Serves as a Checkpoint for CRISPR-Cas12a Target Discrimination. Biorxiv : the Preprint Server For Biology. PMID 37292754 DOI: 10.1101/2023.05.16.541046  0.394
2022 Hu Y, Wang Y, Singh J, Sun R, Xu L, Niu X, Huang K, Bai G, Liu G, Zuo X, Chen C, Qin PZ, Fang X. Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies. Acs Chemical Biology. PMID 36069699 DOI: 10.1021/acschembio.2c00199  0.444
2022 Li Y, Liu Y, Singh J, Tangprasertchai NS, Trivedi R, Fang Y, Qin PZ. Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM. The Crispr Journal. PMID 35352981 DOI: 10.1089/crispr.2021.0100  0.41
2021 Babu K, Kathiresan V, Kumari P, Newsom S, Parameshwaran HP, Chen X, Liu J, Qin PZ, Rajan R. Coordinated Actions of Cas9 HNH and RuvC Nuclease Domains Are Regulated by the Bridge Helix and the Target DNA Sequence. Biochemistry. PMID 34757726 DOI: 10.1021/acs.biochem.1c00354  0.346
2020 Wang Y, Kathiresan V, Chen Y, Hu Y, Jiang W, Bai G, Liu G, Qin PZ, Fang X. Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions. Chemical Science. 11: 9655-9664. PMID 33224460 DOI: 10.1039/D0Sc01717E  0.536
2020 Liu Y, Li Y, Tangprasertchai N, Qin PZ. Mapping the Boundary of DNA Unwinding in CRISPR-Cas9 Target Recognition Biophysical Journal. 118: 224a. DOI: 10.1016/J.Bpj.2019.11.1326  0.315
2019 Jiang W, Singh J, Allen A, Li Y, Kathiresan V, Qureshi O, Tangprasertchai N, Zhang X, Parameshwaran HP, Rajan R, Qin PZ. CRISPR-Cas12a Nucleases Bind Flexible DNA Duplexes without RNA/DNA Complementarity. Acs Omega. 4: 17140-17147. PMID 31656887 DOI: 10.1016/J.Bpj.2019.11.1323  0.473
2019 Ding Y, Kathiresan V, Zhang X, Haworth IS, Qin PZ. Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes. The Journal of Physical Chemistry. A. PMID 30978022 DOI: 10.1021/Acs.Jpca.9B01027  0.526
2019 Babu K, Amrani N, Jiang W, Yogesha SD, Nguyen R, Qin PZ, Rajan R. Bridge Helix of Cas9 Modulates Target DNA Cleavage and Mismatch Tolerance. Biochemistry. PMID 30916546 DOI: 10.1021/Acs.Biochem.8B01241  0.394
2018 Shi F, Kong F, Zhao P, Zhang X, Chen M, Chen S, Zhang Q, Wang M, Ye X, Wang Z, Qin Z, Rong X, Su J, Wang P, Qin PZ, et al. Publisher Correction: Single-DNA electron spin resonance spectroscopy in aqueous solutions. Nature Methods. PMID 30108338 DOI: 10.1038/S41592-018-0119-7  0.37
2018 Shi F, Kong F, Zhao P, Zhang X, Chen M, Chen S, Zhang Q, Wang M, Ye X, Wang Z, Qin Z, Rong X, Su J, Wang P, Qin PZ, et al. Single-DNA electron spin resonance spectroscopy in aqueous solutions. Nature Methods. PMID 30082898 DOI: 10.1038/S41592-018-0084-1  0.42
2017 Zhong YF, Zhang H, Liu WT, Zheng XH, Zhou YW, Cao Q, Shen Y, Zhao Y, Qin PZ, Ji LN, Mao ZW. A Platinum(II)-based photosensitive tripod as an effective photodynamic anticancer agent via DNA damage. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 28940718 DOI: 10.1002/Chem.201703598  0.305
2017 Tangprasertchai NS, Di Felice R, Zhang X, Slaymaker IM, Vazquez Reyes C, Jiang W, Rohs R, Qin PZ. CRISPR-Cas9 mediated DNA unwinding detected using site-directed spin labeling. Acs Chemical Biology. PMID 28437608 DOI: 10.1016/J.Bpj.2017.11.1081  0.519
2016 Vazquez Reyes C, Tangprasertchai NS, Yogesha SD, Nguyen RH, Zhang X, Rajan R, Qin PZ. Nucleic Acid-Dependent Conformational Changes in CRISPR-Cas9 Revealed by Site-Directed Spin Labeling. Cell Biochemistry and Biophysics. PMID 27342128 DOI: 10.1007/S12013-016-0738-5  0.536
2016 Akiel RD, Zhang X, Abeywardana C, Stepanov V, Qin PZ, Takahashi S. Investigating Functional DNA Grafted on Nanodiamond Surface Using Site-Directed Spin Labeling and Electron Paramagnetic Resonance Spectroscopy. The Journal of Physical Chemistry. B. PMID 27058261 DOI: 10.1021/Acs.Jpcb.6B00790  0.49
2016 Xu CX, Zhang X, Zhou YW, Wang H, Cao Q, Shen Y, Ji LN, Mao ZW, Qin PZ. A Nitroxide-Tagged Platinum(II) Complex Enables the Identification of DNA G-Quadruplex Binding Mode. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 26845489 DOI: 10.1002/Chem.201504960  0.397
2016 Zhang X, Xu C, Mao Z, Qin P. G-Quadruplexes Recognition by Platinum Complexes Probed by Site-Directed Spin Labeling Biophysical Journal. 110: 564a. DOI: 10.1016/J.Bpj.2015.11.3016  0.411
2016 Tangprasertchai NS, Vazquez Reyes C, Zhang X, Qin PZ. DNA Unwinding by CRISPR-Cas9 Studied using Site-Directed Spin Labeling Biophysical Journal. 110: 238a. DOI: 10.1016/J.Bpj.2015.11.1312  0.527
2015 Zhang X, Xu C, Di Felice R, Sponer J, Islam B, Stadlbauer P, Ding Y, Mao L, Mao ZW, Qin PZ. Conformations of Human Telomeric G-quadruplex Studied Using a Nucleotide-Independent Nitroxide Label. Biochemistry. PMID 26678746 DOI: 10.1021/Acs.Biochem.5B01189  0.53
2015 Beasley KN, Sutch BT, Hatmal MM, Langen R, Qin PZ, Haworth IS. Computer Modeling of Spin Labels: NASNOX, PRONOX, and ALLNOX. Methods in Enzymology. 563: 569-93. PMID 26478499 DOI: 10.1016/Bs.Mie.2015.07.021  0.524
2015 Tangprasertchai NS, Zhang X, Ding Y, Tham K, Rohs R, Haworth IS, Qin PZ. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids. Methods in Enzymology. 564: 427-53. PMID 26477260 DOI: 10.1016/J.Bpj.2018.11.2538  0.456
2015 Franck JM, Ding Y, Stone K, Qin PZ, Han S. Anomalously rapid hydration water diffusion dynamics near DNA surfaces. Journal of the American Chemical Society. PMID 26256693 DOI: 10.1021/Jacs.5B05813  0.392
2015 Nguyen PH, Popova AM, Hideg K, Qin PZ. A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids. Bmc Biophysics. 8: 6. PMID 25897395 DOI: 10.1186/S13628-015-0019-5  0.705
2015 Ding Y, Nguyen P, Tangprasertchai NS, Reyes CV, Zhang X, Qin PZ. Nucleic acid structure and dynamics: Perspectives from site-directed spin labeling Electron Paramagnetic Resonance. 24: 122-147. DOI: 10.1039/9781782620280-00122  0.413
2014 Ding Y, Zhang X, Tham KW, Qin PZ. Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe. Nucleic Acids Research. 42: e140. PMID 25092920 DOI: 10.1093/Nar/Gku695  0.492
2014 Zhang X, Dantas Machado AC, Ding Y, Chen Y, Lu Y, Duan Y, Tham KW, Chen L, Rohs R, Qin PZ. Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. Nucleic Acids Research. 42: 2789-97. PMID 24293651 DOI: 10.1093/Nar/Gkt1219  0.464
2013 Nguyen P, Shi X, Sigurdsson ST, Herschlag D, Qin PZ. A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme. Chembiochem : a European Journal of Chemical Biology. 14: 1720-3. PMID 23900919 DOI: 10.1002/Cbic.201300376  0.486
2013 Chen Y, Zhang X, Dantas Machado AC, Ding Y, Chen Z, Qin PZ, Rohs R, Chen L. Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion. Nucleic Acids Research. 41: 8368-76. PMID 23836939 DOI: 10.1093/Nar/Gkt584  0.447
2013 Ding Y, Zhang X, Qin P. Sequence-Dependent Local Environment in P53 Response Element Probed by Site-Directed Spin Labeling Biophysical Journal. 104: 343a. DOI: 10.1016/J.Bpj.2012.11.1906  0.525
2013 Zhang X, Carolina A, Machado D, Chen Y, Ding Y, Chen L, Rohs R, Qin P. Deformation of a P53 Response Element Revealed by Site-Directed Spin Labeling Biophysical Journal. 104: 197a-198a. DOI: 10.1016/J.Bpj.2012.11.1115  0.489
2012 Popova AM, Hatmal MM, Frushicheva MP, Price EA, Qin PZ, Haworth IS. Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations. The Journal of Physical Chemistry. B. 116: 6387-96. PMID 22574834 DOI: 10.1021/Jp303303V  0.651
2012 Zhang X, Tung CS, Sowa GZ, Hatmal MM, Haworth IS, Qin PZ. Global structure of a three-way junction in a phi29 packaging RNA dimer determined using site-directed spin labeling. Journal of the American Chemical Society. 134: 2644-52. PMID 22229766 DOI: 10.1021/Ja2093647  0.471
2012 Nguyen P, Qin PZ. RNA dynamics: perspectives from spin labels. Wiley Interdisciplinary Reviews. Rna. 3: 62-72. PMID 21882345 DOI: 10.1002/Wrna.104  0.454
2010 Zhang X, Lee SW, Zhao L, Xia T, Qin PZ. Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling. Rna (New York, N.Y.). 16: 2474-83. PMID 20980674 DOI: 10.1016/J.Bpj.2010.12.1486  0.343
2010 Popova AM, Qin PZ. A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA. Biophysical Journal. 99: 2180-9. PMID 20923652 DOI: 10.1016/J.Bpj.2010.08.005  0.691
2010 Qin PZ, Niu CG, Ruan M, Zeng GM, Wang XY. A novel bifunctional europium complex as a potential fluorescent label for DNA detection Analyst. 135: 2144-2149. PMID 20585687 DOI: 10.1039/c0an00072h  0.31
2010 Popova A, Qin PZ. Sequence-Specific Stereomeric Environment in a DNA Duplex Revealed by a Nucleotide-Independent Nitroxide Probe Biophysical Journal. 98: 401a. DOI: 10.1016/J.Bpj.2009.12.2160  0.731
2010 Zhang X, Hatmal M, Haworth I, Qin PZ. Mapping the Global Conformation of the Phi29 Packaging RNA Dimer Using Deer Distance Constraints Biophysical Journal. 98: 264a. DOI: 10.1016/J.Bpj.2009.12.1436  0.444
2010 Grant GPG, Nguyen P, Boyd N, Herschlag D, Qin P. Nanosecond Motions of the Substrate-Recognition Duplex in a Group I Intron Assessed by Site-Directed Spin Labeling Biophysical Journal. 98: 263a-264a. DOI: 10.1016/j.bpj.2009.12.1435  0.312
2009 Zhang X, Cekan P, Sigurdsson ST, Qin PZ. Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy. Methods in Enzymology. 469: 303-328. PMID 20946796 DOI: 10.1016/S0076-6879(09)69015-7  0.529
2009 Popova AM, Kálai T, Hideg K, Qin PZ. Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes. Biochemistry. 48: 8540-50. PMID 19650666 DOI: 10.1021/Bi900860W  0.724
2009 Grant GP, Boyd N, Herschlag D, Qin PZ. Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling. Journal of the American Chemical Society. 131: 3136-7. PMID 19220053 DOI: 10.1021/Ja808217S  0.742
2008 Sowa GZ, Qin PZ. Site-directed spin labeling studies on nucleic acid structure and dynamics. Progress in Nucleic Acid Research and Molecular Biology. 82: 147-97. PMID 18929141 DOI: 10.1016/S0079-6603(08)00005-6  0.538
2008 Fang Y, Shu D, Xiao F, Guo P, Qin PZ. Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging. Biochemical and Biophysical Research Communications. 372: 589-94. PMID 18514064 DOI: 10.1016/J.Bbrc.2008.05.094  0.415
2008 Grant GP, Popova A, Qin PZ. Diastereomer characterizations of nitroxide-labeled nucleic acids. Biochemical and Biophysical Research Communications. 371: 451-5. PMID 18442474 DOI: 10.1016/J.Bbrc.2008.04.088  0.777
2007 Qin PZ, Haworth IS, Cai Q, Kusnetzow AK, Grant GP, Price EA, Sowa GZ, Popova A, Herreros B, He H. Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nature Protocols. 2: 2354-65. PMID 17947978 DOI: 10.1038/Nprot.2007.308  0.74
2007 Price EA, Sutch BT, Cai Q, Qin PZ, Haworth IS. Computation of nitroxide-nitroxide distances in spin-labeled DNA duplexes. Biopolymers. 87: 40-50. PMID 17538992 DOI: 10.1002/Bip.20769  0.597
2007 Cai Q, Kusnetzow AK, Hideg K, Price EA, Haworth IS, Qin PZ. Nanometer distance measurements in RNA using site-directed spin labeling. Biophysical Journal. 93: 2110-7. PMID 17526583 DOI: 10.1529/Biophysj.107.109439  0.636
2007 Grant GP, Qin PZ. A facile method for attaching nitroxide spin labels at the 5' terminus of nucleic acids. Nucleic Acids Research. 35: e77. PMID 17517787 DOI: 10.1093/Nar/Gkm240  0.75
2006 Cai Q, Kusnetzow AK, Hubbell WL, Haworth IS, Gacho GP, Van Eps N, Hideg K, Chambers EJ, Qin PZ. Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nucleic Acids Research. 34: 4722-30. PMID 16966338 DOI: 10.1093/Nar/Gkl546  0.668
2006 Qin PZ, Iseri J, Oki A. A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling. Biochemical and Biophysical Research Communications. 343: 117-24. PMID 16530169 DOI: 10.1016/J.Bbrc.2006.02.138  0.456
2005 Qin PZ, Feigon J, Hubbell WL. Site-directed spin labeling studies reveal solution conformational changes in a GAAA tetraloop receptor upon Mg(2+)-dependent docking of a GAAA tetraloop. Journal of Molecular Biology. 351: 1-8. PMID 15993422 DOI: 10.1016/J.Jmb.2005.06.007  0.375
2005 Fang Y, Cai Q, Qin PZ. 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. PMID 15982001 DOI: 10.1021/Bi0475020  0.516
2004 Qin PZ, Dieckmann T. Application of NMR and EPR methods to the study of RNA. Current Opinion in Structural Biology. 14: 350-9. PMID 15193316 DOI: 10.1016/J.Sbi.2004.04.002  0.432
2003 Qin PZ, Hideg K, Feigon J, Hubbell WL. Monitoring RNA base structure and dynamics using site-directed spin labeling. Biochemistry. 42: 6772-83. PMID 12779332 DOI: 10.1021/Bi027222P  0.533
2001 Qin PZ, Butcher SE, Feigon J, Hubbell WL. Quantitative analysis of the isolated GAAA tetraloop/receptor interaction in solution: a site-directed spin labeling study. Biochemistry. 40: 6929-36. PMID 11389608 DOI: 10.1021/Bi010294G  0.408
2001 Su LJ, Qin PZ, Michels WJ, Pyle AM. Guiding ribozyme cleavage through motif recognition: the mechanism of cleavage site selection by a group ii intron ribozyme. Journal of Molecular Biology. 306: 655-68. PMID 11243778 DOI: 10.1006/Jmbi.2000.4323  0.395
1999 Qin PZ, Pyle AM. Site-specific labeling of RNA with fluorophores and other structural probes Methods: a Companion to Methods in Enzymology. 18: 60-70. PMID 10208817 DOI: 10.1006/Meth.1999.0757  0.486
1998 Qin PZ, Pyle AM. The architectural organization and mechanistic function of group II intron structural elements Current Opinion in Structural Biology. 8: 301-308. PMID 9666325 DOI: 10.1016/S0959-440X(98)80062-6  0.314
1998 Xiang Q, Qin PZ, Michels WJ, Freeland K, Pyle AM. Sequence specificity of a group II intron ribozyme: Multiple mechanisms for promoting unusually high discrimination against mismatched targets Biochemistry. 37: 3839-3849. PMID 9521704 DOI: 10.1021/Bi972661N  0.357
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