{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T02:24:55Z","timestamp":1790648695022,"version":"4.1.0"},"reference-count":58,"publisher":"American Chemical Society (ACS)","issue":"12","license":[{"start":{"date-parts":[[2020,10,27]],"date-time":"2020-10-27T00:00:00Z","timestamp":1603756800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/pubs.acs.org\/page\/policy\/authorchoice_termsofuse.html"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 EY027440"],"award-info":[{"award-number":["R01 EY027440"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CHE-1905374"],"award-info":[{"award-number":["CHE-1905374"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>CRISPR-Cas12a is a genome-editing system, recently also harnessed for nucleic acid detection, which is promising for the diagnosis of the SARS-CoV-2 coronavirus through the DETECTR technology. Here, a collective ensemble of multimicrosecond molecular dynamics characterizes the key dynamic determinants allowing nucleic acid processing in CRISPR-Cas12a. We show that DNA binding induces a switch in the conformational dynamics of Cas12a, which results in the activation of the peripheral REC2 and Nuc domains to enable cleavage of nucleic acids. The simulations reveal that large-amplitude motions of the Nuc domain could favor the conformational activation of the system toward DNA cleavages. In this process, the REC lobe plays a critical role. Accordingly, the joint dynamics of REC and Nuc shows the tendency to prime the conformational transition of the DNA target strand toward the catalytic site. Most notably, the highly coupled dynamics of the REC2 region and Nuc domain suggests that REC2 could act as a regulator of the Nuc function, similar to what was observed previously for the HNH domain in the CRISPR-associated nuclease Cas9. These mutual domain dynamics could be critical for the nonspecific binding of DNA and thereby for the underlying mechanistic functioning of the DETECTR technology. Considering that REC is a key determinant in the system\u2019s specificity, our findings provide a rational basis for future biophysical studies aimed at characterizing its function in CRISPR-Cas12a. Overall, our outcomes advance our mechanistic understanding of CRISPR-Cas12a and provide grounds for novel engineering efforts to improve genome editing and viral detection.<\/jats:p>","DOI":"10.1021\/acs.jcim.0c00929","type":"journal-article","created":{"date-parts":[[2020,10,27]],"date-time":"2020-10-27T08:00:30Z","timestamp":1603785630000},"page":"6427-6437","source":"Crossref","is-referenced-by-count":63,"title":["Molecular Dynamics Reveals a DNA-Induced Dynamic Switch\nTriggering Activation of CRISPR-Cas12a"],"prefix":"10.1021","volume":"60","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0776-9771","authenticated-orcid":true,"given":"Aakash","family":"Saha","sequence":"first","affiliation":[{"name":"University of California, Riverside , , 900 University Avenue , , ,","place":["Riverside, California, United States, 92521"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1946-2750","authenticated-orcid":true,"given":"Pablo R.","family":"Arantes","sequence":"additional","affiliation":[{"name":"University of California, Riverside , , 900 University Avenue , , ,","place":["Riverside, California, United States, 92521"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rohaine V.","family":"Hsu","sequence":"additional","affiliation":[{"name":"University of California, Riverside , , 900 University Avenue , , ,","place":["Riverside, California, United States, 92521"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yogesh B.","family":"Narkhede","sequence":"additional","affiliation":[{"name":"University of California, Riverside , , 900 University Avenue , , ,","place":["Riverside, California, United States, 92521"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Jinek","sequence":"additional","affiliation":[{"name":"University of Zurich , , Winterthurerstrasse 190 , ,","place":["Zurich, Switzerland, CH-8057"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1404-8737","authenticated-orcid":true,"given":"Giulia","family":"Palermo","sequence":"additional","affiliation":[{"name":"University of California, Riverside , , 900 University Avenue , , ,","place":["Riverside, California, United States, 92521"]},{"name":"University of California, Riverside , , 900 University Avenue , , ,","place":["Riverside, California, United States, 92521"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,10,27]]},"reference":[{"key":"2026092806075282700_cit1","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1126\/science.1225829","article-title":"A Programmable Dual-RNA-Guided DNA Endonuclease in\nAdaptive Bacterial Immunity","volume":"337","author":"Jinek","year":"2012","journal-title":"Science"},{"key":"2026092806075282700_cit2","doi-asserted-by":"publisher","first-page":"1258096","DOI":"10.1126\/science.1258096","article-title":"Genome Editing.\nThe New Frontier of Genome Engineering\nwith CRISPR-Cas9","volume":"346","author":"Doudna","year":"2014","journal-title":"Science"},{"key":"2026092806075282700_cit3","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1016\/j.cell.2015.09.038","article-title":"Cpf1 Is a\nSingle RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System","volume":"163","author":"Zetsche","year":"2015","journal-title":"Cell"},{"key":"2026092806075282700_cit4","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1126\/science.aar6245","article-title":"CRISPR-Cas12a Target Binding Unleashes\nIndiscriminate Single-Stranded DNase Activity","volume":"360","author":"Chen","year":"2018","journal-title":"Science"},{"key":"2026092806075282700_cit5","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1038\/s41587-020-0513-4","article-title":"CRISPR\u2013Cas12-Based\nDetection of SARS-CoV-2","volume":"38","author":"Broughton","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"2026092806075282700_cit6","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1038\/nature13011","article-title":"DNA Interrogation\nby the CRISPR RNA-Guided Endonuclease Cas9","volume":"507","author":"Sternberg","year":"2014","journal-title":"Nature"},{"key":"2026092806075282700_cit7","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1016\/j.sbi.2017.10.015","article-title":"Molecular\nArchitectures and Mechanisms of Class 2 CRISPR-Associated\nNucleases","volume":"47","author":"Garcia-Doval","year":"2017","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2026092806075282700_cit8","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1038\/nsmb.3486","article-title":"Class 2 CRISPR\u2013Cas RNA-Guided\nEndonucleases: Swiss Army Knives of Genome Editing","volume":"24","author":"Stella","year":"2017","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026092806075282700_cit9","doi-asserted-by":"publisher","first-page":"169","DOI":"10.1038\/nrmicro.2016.184","article-title":"Diversity and Evolution\nof Class 2 CRISPR\u2013Cas Systems","volume":"15","author":"Shmakov","year":"2017","journal-title":"Nat. Rev.\nMicrobiol."},{"key":"2026092806075282700_cit10","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1038\/nature17944","article-title":"The Crystal Structure\nof Cpf1 in Complex with CRISPR RNA","volume":"532","author":"Dong","year":"2016","journal-title":"Nature"},{"key":"2026092806075282700_cit11","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1038\/cr.2016.88","article-title":"Type V\nCRISPR-Cas Cpf1 Endonuclease Employs a Unique Mechanism for CrRNA-Mediated\nTarget DNA Recognition","volume":"26","author":"Gao","year":"2016","journal-title":"Cell Res."},{"key":"2026092806075282700_cit12","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1016\/j.cell.2016.04.003","article-title":"Crystal Structure of\nCpf1 in Complex with Guide RNA and Target DNA","volume":"165","author":"Yamano","year":"2016","journal-title":"Cell"},{"key":"2026092806075282700_cit13","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1016\/j.molcel.2017.03.016","article-title":"Structural Basis for Guide RNA Processing\nand Seed-Dependent DNA Targeting by CRISPR-Cas12a","volume":"66","author":"Swarts","year":"2017","journal-title":"Mol. Cell"},{"key":"2026092806075282700_cit14","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1038\/nature22398","article-title":"Structure of the Cpf1\nEndonuclease\nR-Loop Complex after Target DNA Cleavage","volume":"546","author":"Stella","year":"2017","journal-title":"Nature"},{"key":"2026092806075282700_cit15","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1016\/j.molcel.2018.11.021","article-title":"Mechanistic Insights\ninto the Cis- and Trans-Acting DNase Activities\nof Cas12a","volume":"73","author":"Swarts","year":"2019","journal-title":"Mol. Cell"},{"key":"2026092806075282700_cit16","doi-asserted-by":"publisher","first-page":"1856","DOI":"10.1016\/j.cell.2018.10.045","article-title":"Conformational Activation\nPromotes CRISPR-Cas12a Catalysis\nand Resetting of the Endonuclease Activity","volume":"175","author":"Stella","year":"2018","journal-title":"Cell"},{"key":"2026092806075282700_cit17","doi-asserted-by":"publisher","first-page":"756","DOI":"10.1021\/acscentsci.6b00218","article-title":"Striking\nPlasticity of CRISPR-Cas9 and Key Role of Non-Target DNA, as Revealed\nby Molecular Simulations","volume":"2","author":"Palermo","year":"2016","journal-title":"ACS Cent. Sci."},{"key":"2026092806075282700_cit18","doi-asserted-by":"publisher","first-page":"7260","DOI":"10.1073\/pnas.1707645114","article-title":"CRISPR-Cas9\nConformational Activation as Elucidated from Enhanced Molecular Simulations","volume":"114","author":"Palermo","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026092806075282700_cit19","doi-asserted-by":"publisher","first-page":"e9","DOI":"10.1017\/S0033583518000070","article-title":"Key Role of the\nREC Lobe during CRISPR\u2013Cas9 Activation by \u2018Sensing\u2019,\n\u2018Regulating\u2019, and \u2018Locking\u2019 the Catalytic\nHNH Domain","volume":"51","author":"Palermo","year":"2018","journal-title":"Q. Rev. Biophys."},{"key":"2026092806075282700_cit20","doi-asserted-by":"publisher","first-page":"e46500","DOI":"10.7554\/eLife.46500","article-title":"Structural and Functional\nInsights into the Bona Fide Catalytic State of Streptococcus Pyogenes\nCas9 HNH Nuclease Domain","volume":"8","author":"Zuo","year":"2019","journal-title":"eLife"},{"key":"2026092806075282700_cit21","doi-asserted-by":"publisher","first-page":"37584","DOI":"10.1038\/srep37584","article-title":"Cas9-Catalyzed DNA\nCleavage Generates Staggered Ends: Evidence from\nMolecular Dynamics Simulations","volume":"6","author":"Zuo","year":"2016","journal-title":"Sci. Rep."},{"key":"2026092806075282700_cit22","doi-asserted-by":"publisher","DOI":"10.1021\/acscatal.0c03566","article-title":"Catalytic Mechanism\nof Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab-Initio Molecular\nDynamics","author":"Casalino","year":"2020","journal-title":"ACS Catal."},{"key":"2026092806075282700_cit23","doi-asserted-by":"publisher","first-page":"eaao0027","DOI":"10.1126\/sciadv.aao0027","article-title":"A Conformational\nCheckpoint between DNA Binding and Cleavage by CRISPR-Cas9","volume":"3","author":"Dagdas","year":"2017","journal-title":"Sci. Adv."},{"key":"2026092806075282700_cit24","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1038\/s41594-019-0258-2","article-title":"Cryo-EM Structures\nReveal Coordinated Domain Motions That Govern DNA Cleavage by Cas9","volume":"26","author":"Zhu","year":"2019","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026092806075282700_cit25","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1038\/nature24268","article-title":"Enhanced\nProofreading Governs CRISPR\u2013Cas9 Targeting\nAccuracy","volume":"550","author":"Chen","year":"2017","journal-title":"Nature"},{"key":"2026092806075282700_cit26","doi-asserted-by":"publisher","first-page":"794","DOI":"10.1016\/j.molcel.2020.02.023","article-title":"Highly Parallel\nProfiling of Cas9 Variant Specificity","volume":"78","author":"Schmid-Burgk","year":"2020","journal-title":"Mol.\nCell"},{"key":"2026092806075282700_cit27","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1016\/j.celrep.2017.12.048","article-title":"The Conformational Dynamics of Cas9 Governing DNA Cleavage Are Revealed\nby Single-Molecule FRET","volume":"22","author":"Yang","year":"2018","journal-title":"Cell Rep."},{"key":"2026092806075282700_cit28","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1038\/nature16526","article-title":"High-Fidelity CRISPR\u2013Cas9\nNucleases with No Detectable Genome-Wide off-TargetEffects","volume":"529","author":"Kleinstiver","year":"2016","journal-title":"Nature"},{"key":"2026092806075282700_cit29","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1038\/nbt.4066","article-title":"A Highly Specific SpCas9\nVariant Is Identified by in Vivo Screening in Yeast","volume":"36","author":"Casini","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"2026092806075282700_cit30","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1038\/s41587-018-0011-0","article-title":"Engineered CRISPR\u2013Cas12a Variants with Increased\nActivities and Improved Targeting Ranges for Gene, Epigenetic and\nBase Editing","volume":"37","author":"Kleinstiver","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"2026092806075282700_cit31","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/S0969-2126(01)00142-3","article-title":"Recombining the\nStructures of HIV Integrase, RuvC and\nRNase H","volume":"3","author":"Yang","year":"1995","journal-title":"Structure"},{"key":"2026092806075282700_cit32","doi-asserted-by":"publisher","first-page":"762","DOI":"10.1002\/wcms.1099","article-title":"Essential Dynamics:\nFoundation and Applications","volume":"2","author":"Daidone","year":"2012","journal-title":"WIREs Comput. Mol.\nSci."},{"key":"2026092806075282700_cit33","doi-asserted-by":"publisher","first-page":"2777","DOI":"10.1038\/s41467-018-05245-x","article-title":"Direct Observation\nof DNA Target Searching and Cleavage by CRISPR-Cas12a","volume":"9","author":"Jeon","year":"2018","journal-title":"Nat. Commun."},{"key":"2026092806075282700_cit34","doi-asserted-by":"publisher","first-page":"16028","DOI":"10.1021\/jacs.7b05313","article-title":"Protospacer Adjacent\nMotif-Induced Allostery Activates CRISPR-Cas9","volume":"139","author":"Palermo","year":"2017","journal-title":"J. Am. Chem. Soc."},{"key":"2026092806075282700_cit35","doi-asserted-by":"publisher","first-page":"1477","DOI":"10.1126\/science.aab1452","article-title":"STRUCTURAL\nBIOLOGY. A Cas9-Guide RNA Complex Preorganized for Target DNA Recognition","volume":"348","author":"Jiang","year":"2015","journal-title":"Science"},{"key":"2026092806075282700_cit36","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1016\/j.celrep.2017.12.041","article-title":"DNA Unwinding Is\nthe Primary Determinant of CRISPR-Cas9 Activity","volume":"22","author":"Gong","year":"2018","journal-title":"Cell Rep."},{"key":"2026092806075282700_cit37","doi-asserted-by":"publisher","first-page":"3576","DOI":"10.1038\/s41467-020-17411-1","article-title":"Engineered\nCRISPR\/Cas9 Enzymes Improve Discrimination by Slowing DNA Cleavage\nto Allow Release of off-Target DNA","volume":"11","author":"Liu","year":"2020","journal-title":"Nat. Commun."},{"key":"2026092806075282700_cit38","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1002\/prot.20784","article-title":"Generalized\nCorrelation for Biomolecular Dynamics","volume":"62","author":"Lange","year":"2006","journal-title":"Proteins:\nStruct., Funct., Genet."},{"key":"2026092806075282700_cit39","doi-asserted-by":"publisher","first-page":"6584","DOI":"10.1073\/pnas.1802963115","article-title":"All-Atom Simulations Disentangle the Functional Dynamics\nUnderlying Gene Maturation in the Intron Lariat Spliceosome","volume":"115","author":"Casalino","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"2026092806075282700_cit40","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.1021\/jacs.9b10521","article-title":"Allosteric Motions\nof the CRISPR\u2013Cas9 HNH Nuclease\nProbed by NMR and Molecular Dynamics","volume":"142","author":"East","year":"2020","journal-title":"J. Am.\nChem. Soc."},{"key":"2026092806075282700_cit41","first-page":"e1503","article-title":"Establishing the Allosteric\nMecanism in CRISPR-Cas9","author":"Nierzwicki","year":"2020","journal-title":"WIREs Comput. Mol.\nSci."},{"key":"2026092806075282700_cit42","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1016\/j.sbi.2020.01.013","article-title":"Allosteric Regulation of CRISPR-Cas9 for DNA-Targeting and Cleavage","volume":"62","author":"Zuo","year":"2020","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2026092806075282700_cit43","doi-asserted-by":"publisher","first-page":"3927","DOI":"10.1021\/acs.jcim.9b00588","article-title":"Impact of Mutations\non NPAC Structural Dynamics: Mechanistic Insights from MD Simulations","volume":"59","author":"Montefiori","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"2026092806075282700_cit44","doi-asserted-by":"publisher","first-page":"4656","DOI":"10.1002\/chem.201904523","article-title":"Designing Molecular Spanners to Throw\nin the Protein\nNetworks","volume":"26","author":"Serapian","year":"2020","journal-title":"Chem. - Eur. J."},{"key":"2026092806075282700_cit45","doi-asserted-by":"publisher","first-page":"e55143","DOI":"10.7554\/eLife.55143","article-title":"CRISPR-Cas12a Exploits\nR-Loop Asymmetry to Form Double-Strand\nBreaks","volume":"9","author":"Cofsky","year":"2020","journal-title":"eLife"},{"key":"2026092806075282700_cit46","doi-asserted-by":"publisher","first-page":"2123","DOI":"10.1039\/C9CC08325A","article-title":"Direct Observation of the Formation\nof a CRISPR\u2013Cas12a R-Loop Complex at the Single-Molecule Level","volume":"56","author":"Cui","year":"2020","journal-title":"Chem. Commun."},{"key":"2026092806075282700_cit47","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1016\/j.molcel.2018.06.043","article-title":"Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a","volume":"71","author":"Strohkendl","year":"2018","journal-title":"Mol. Cell"},{"key":"2026092806075282700_cit48","doi-asserted-by":"publisher","first-page":"5444","DOI":"10.1073\/pnas.1718686115","article-title":"Real-Time\nObservation\nof DNA Target Interrogation and Product Release by the RNA-Guided\nEndonuclease CRISPR Cpf1 (Cas12a)","volume":"115","author":"Singh","year":"2018","journal-title":"Proc. Natl.\nAcad. Sci. U. S. A."},{"key":"2026092806075282700_cit49","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/s41422-018-0022-x","article-title":"CRISPR-Cas12a Has Both Cis- and Trans-Cleavage Activities on Single-Stranded\nDNA","volume":"28","author":"Li","year":"2018","journal-title":"Cell Res."},{"key":"2026092806075282700_cit50","doi-asserted-by":"publisher","first-page":"3817","DOI":"10.1529\/biophysj.106.097782","article-title":"Refinement of the AMBER\nForce Field for Nucleic Acids: Improving the Description of Alpha\/Gamma\nConformers","volume":"92","author":"Perez","year":"2007","journal-title":"Biophys. J."},{"key":"2026092806075282700_cit51","doi-asserted-by":"publisher","first-page":"3836","DOI":"10.1021\/ct100481h","article-title":"Performance\nof Molecular Mechanics Force Fields for RNA Simulations: Stability\nof UUCG and GNRA Hairpins","volume":"6","author":"Banas","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"2026092806075282700_cit52","doi-asserted-by":"publisher","first-page":"2886","DOI":"10.1021\/ct200162x","article-title":"Refinement\nof the Cornell et Al.\nNucleic Acids Force Field Based on Reference Quantum Chemical Calculations\nof Glycosidic Torsion Profiles","volume":"7","author":"Zgarbova","year":"2011","journal-title":"J. Chem. Theory\nComput."},{"key":"2026092806075282700_cit53","doi-asserted-by":"publisher","first-page":"1493","DOI":"10.1021\/ct3000734","article-title":"Magnesium Ion\u2013Water Coordination\nand Exchange in Biomolecular Simulations","volume":"8","author":"Allne\u0301r","year":"2012","journal-title":"J.\nChem. Theory Comput."},{"key":"2026092806075282700_cit54","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison\nof Simple Potential Functions for Simulating Liquid Water","volume":"79","author":"Jorgensen","year":"1983","journal-title":"J. Chem. Phys."},{"key":"2026092806075282700_cit55","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1021\/acscentsci.9b00020","article-title":"Deciphering Off-Target Effects in\nCRISPR-Cas9 through Accelerated Molecular Dynamics","volume":"5","author":"Ricci","year":"2019","journal-title":"ACS Cent. Sci."},{"key":"2026092806075282700_cit56","doi-asserted-by":"publisher","first-page":"2394","DOI":"10.1021\/acs.jcim.8b00988","article-title":"Structure\nand Dynamics of the CRISPR\u2013Cas9 Catalytic Complex","volume":"59","author":"Palermo","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"2026092806075282700_cit57","doi-asserted-by":"publisher","first-page":"3684","DOI":"10.1063\/1.448118","article-title":"Molecular\nDynamics with Coupling to an External Bath","volume":"81","author":"Berendsen","year":"1984","journal-title":"J. Chem. Phys."},{"key":"2026092806075282700_cit58","unstructured":"Case, D. A.; Betz, R. M.; Botello-Smith, W.; Cerutti, D. S.; Cheatham, I. T. E.; Darden, T. A.; Duke, R. E.; Giese, T. J.; Gohlke, H.; Goetz, A. W.; Homeyer, N.; Izadi, S.; Janowski, P.; Kaus, J.; Kovalenko, A.; Lee, T. S.; LeGrand, S.; Li, P.; Lin, C.; Luchko, T.; Luo, R.; Madej, B.; Mermelstein, D.; Merz, K. M.; Monard, G.; Nguyen, H.; Nguyen, H. T.; Omelyan, I.; Onufriev, A.; Roe, D. R.; Roitberg, A.; Sagui, C.; Simmerling, C. L.; Swails, J.; Walker, R. C.; Wang, J.; Wolf, R. M.; Wu, X.; Xiong, Y.; Xue, Y.; York, D. M.; Kollman, P. A.\n          AMBER 2018; Univ. California: San Francisco, 2018."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.0c00929","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/60\/12\/6427\/9624460\/ci0c00929.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/60\/12\/6427\/9624460\/ci0c00929.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T10:30:16Z","timestamp":1790591416000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/60\/12\/6427\/891358\/Molecular-Dynamics-Reveals-a-DNA-Induced-Dynamic"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,10,27]]},"references-count":58,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2020,10,27]]},"published-print":{"date-parts":[[2020,12,28]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.0c00929","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,10,27]]}}}