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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