{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T12:27:57Z","timestamp":1788870477645,"version":"build-2803163510"},"reference-count":45,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2005,11,1]],"date-time":"2005-11-01T00:00:00Z","timestamp":1130803200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2005,11,1]],"date-time":"2005-11-01T00:00:00Z","timestamp":1130803200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2005,11,1]],"date-time":"2005-11-01T00:00:00Z","timestamp":1130803200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2005,11,1]],"date-time":"2005-11-01T00:00:00Z","timestamp":1130803200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2005,11,1]],"date-time":"2005-11-01T00:00:00Z","timestamp":1130803200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2005,11,1]],"date-time":"2005-11-01T00:00:00Z","timestamp":1130803200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2005,11,1]],"date-time":"2005-11-01T00:00:00Z","timestamp":1130803200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100000070","name":"National Institute of Biomedical Imaging and Bioengineering","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000070","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P41-EB0001979"],"award-info":[{"award-number":["P41-EB0001979"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Molecular Biology"],"published-print":{"date-parts":[[2005,11]]},"DOI":"10.1016\/j.jmb.2005.09.032","type":"journal-article","created":{"date-parts":[[2005,10,3]],"date-time":"2005-10-03T09:40:34Z","timestamp":1128332434000},"page":"483-496","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":26,"title":["Perturbation of the Hierarchical Folding of a Large RNA by the Destabilization of its Scaffold's Tertiary Structure"],"prefix":"10.1016","volume":"354","author":[{"given":"Inna","family":"Shcherbakova","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Brenowitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jmb.2005.09.032_bib1","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1006\/jmbi.1994.1117","article-title":"GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain","volume":"236","author":"Murphy","year":"1994","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib2","doi-asserted-by":"crossref","first-page":"1678","DOI":"10.1126\/science.273.5282.1678","article-title":"Crystal structure of a group I ribozyme domain: principles of RNA packing [see comments]","volume":"273","author":"Cate","year":"1996","journal-title":"Science"},{"key":"10.1016\/j.jmb.2005.09.032_bib3","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1126\/science.8052848","article-title":"Kinetic intermediates in RNA folding","volume":"265","author":"Zarrinkar","year":"1994","journal-title":"Science"},{"key":"10.1016\/j.jmb.2005.09.032_bib4","doi-asserted-by":"crossref","first-page":"3159","DOI":"10.1021\/bi962428+","article-title":"The P4-P6 domain directs higher order folding of the Tetrahymena ribozyme core","volume":"36","author":"Doherty","year":"1997","journal-title":"Biochemistry"},{"key":"10.1016\/j.jmb.2005.09.032_bib5","doi-asserted-by":"crossref","first-page":"1940","DOI":"10.1126\/science.279.5358.1940","article-title":"RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting","volume":"279","author":"Sclavi","year":"1998","journal-title":"Science"},{"key":"10.1016\/j.jmb.2005.09.032_bib6","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1006\/jmbi.1999.3439","article-title":"Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA","volume":"296","author":"Pan","year":"2000","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib7","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/S0022-2836(03)00247-X","article-title":"Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme","volume":"328","author":"Uchida","year":"2003","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib8","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/S0968-0004(02)00012-9","article-title":"Is there a unifying mechanism for protein folding?","volume":"28","author":"Daggett","year":"2003","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/j.jmb.2005.09.032_bib9","doi-asserted-by":"crossref","first-page":"11555","DOI":"10.1073\/pnas.95.20.11555","article-title":"RNA folding causes secondary structure rearrangement","volume":"95","author":"Wu","year":"1998","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1016\/j.jmb.2005.09.032_bib10","doi-asserted-by":"crossref","first-page":"2342","DOI":"10.1093\/nar\/gkh537","article-title":"Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns","volume":"32","author":"Klosterman","year":"2004","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/j.jmb.2005.09.032_bib11","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1017\/S1355838201001716","article-title":"An early transition state for folding of the P4-P6 RNA domain","volume":"7","author":"Silverman","year":"2001","journal-title":"RNA"},{"key":"10.1016\/j.jmb.2005.09.032_bib12","doi-asserted-by":"crossref","first-page":"12465","DOI":"10.1021\/bi000828y","article-title":"Multiple folding pathways for the P4-P6 RNA domain","volume":"39","author":"Silverman","year":"2000","journal-title":"Biochemistry"},{"key":"10.1016\/j.jmb.2005.09.032_bib13","doi-asserted-by":"crossref","first-page":"5799","DOI":"10.1021\/bi020042v","article-title":"Linkage of monovalent and divalent ion binding in the folding of the p4-p6 domain of the Tetrahymena ribozyme","volume":"41","author":"Uchida","year":"2002","journal-title":"Biochemistry"},{"key":"10.1016\/j.jmb.2005.09.032_bib14","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/75139","article-title":"Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation","volume":"7","author":"Ralston","year":"2000","journal-title":"Nature Struct. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib15","doi-asserted-by":"crossref","first-page":"12271","DOI":"10.1021\/bi0264869","article-title":"The GAAA tetraloop-receptor interaction contributes differentially to folding thermodynamics and kinetics for the P4-P6 RNA domain","volume":"41","author":"Young","year":"2002","journal-title":"Biochemistry"},{"key":"10.1016\/j.jmb.2005.09.032_bib16","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1006\/jmbi.2000.4253","article-title":"Concerted kinetic folding of a multidomain ribozyme with a disrupted loop-receptor interaction","volume":"305","author":"Treiber","year":"2001","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib17","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1006\/jmbi.1996.0775","article-title":"Time-resolved synchrotron X-ray \u201cfootprinting\u201d, a new approach to the study of nucleic acid structure and function: application to protein\u2013DNA interactions and RNA folding","volume":"266","author":"Sclavi","year":"1997","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib18","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1016\/S0076-6879(00)17024-7","article-title":"Time-resolved synchrotron X-ray footprinting and its application to RNA folding","volume":"317","author":"Ralston","year":"2000","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.jmb.2005.09.032_bib19","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/S0958-1669(97)80155-3","article-title":"Quantitative nucleic acids footprinting: thermodynamic and kinetic approaches","volume":"8","author":"Petri","year":"1997","journal-title":"Curr. Opin. Biotechnol."},{"key":"10.1016\/j.jmb.2005.09.032_bib20","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1006\/jmbi.2001.5303","article-title":"Concerted binding and bending of DNA by Escherichia coli integration host factor","volume":"315","author":"Dhavan","year":"2002","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib21","doi-asserted-by":"crossref","first-page":"10975","DOI":"10.1021\/bi0010118","article-title":"Folding mechanism of the Tetrahymena ribozyme P4-P6 domain","volume":"39","author":"Deras","year":"2000","journal-title":"Biochemistry"},{"key":"10.1016\/j.jmb.2005.09.032_bib22","doi-asserted-by":"crossref","first-page":"1195","DOI":"10.1016\/j.jmb.2004.08.080","article-title":"Principles of RNA compaction: insights from the equilibrium folding pathway of the p4-p6 RNA domain in monovalent cations","volume":"343","author":"Takamoto","year":"2004","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib23","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1016\/j.jmb.2004.07.092","article-title":"Monovalent Ion-mediated folding of the Tetrahymena thermophila ribozyme","volume":"342","author":"Shcherbakova","year":"2004","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib24","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1126\/science.279.5358.1943","article-title":"Kinetic intermediates trapped by native interactions in RNA folding","volume":"279","author":"Treiber","year":"1998","journal-title":"Science"},{"key":"10.1016\/j.jmb.2005.09.032_bib25","doi-asserted-by":"crossref","first-page":"5291","DOI":"10.1021\/bi00071a003","article-title":"An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme","volume":"32","author":"Murphy","year":"1993","journal-title":"Biochemistry"},{"key":"10.1016\/j.jmb.2005.09.032_bib26","doi-asserted-by":"crossref","first-page":"8518","DOI":"10.1073\/pnas.142288399","article-title":"The rate-limiting step in the folding of a large ribozyme without kinetic traps","volume":"99","author":"Fang","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1016\/j.jmb.2005.09.032_bib27","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/S0022-2836(03)00854-4","article-title":"The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme","volume":"332","author":"Das","year":"2003","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib28","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/S0959-440X(03)00066-6","article-title":"RNA folding: models and perspectives","volume":"13","author":"Sosnick","year":"2003","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib29","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1038\/nsb871","article-title":"Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme","volume":"9","author":"Takamoto","year":"2002","journal-title":"Nature Struct. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib30","doi-asserted-by":"crossref","first-page":"3695","DOI":"10.1073\/pnas.051608598","article-title":"Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme","volume":"98","author":"Zheng","year":"2001","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1016\/j.jmb.2005.09.032_bib31","first-page":"351","article-title":"Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site","volume":"16","author":"Guo","year":"2004","journal-title":"Mol. Cell."},{"key":"10.1016\/j.jmb.2005.09.032_bib32","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1006\/jmbi.1999.3298","article-title":"The effect of long-range loop\u2013loop interactions on folding of the Tetrahymena self-splicing RNA","volume":"294","author":"Pan","year":"1999","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib33","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1006\/jmbi.1998.1960","article-title":"Fast folding mutants of the Tetrahymena group I ribozyme reveal a rugged folding energy landscape","volume":"281","author":"Rook","year":"1998","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib34","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1006\/jmbi.2001.4660","article-title":"Role of counterion condensation in folding of the Tetrahymena ribozyme. II. Counterion-dependence of folding kinetics","volume":"309","author":"Heilman-Miller","year":"2001","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib35","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1038\/80691","article-title":"Small angle X-ray scattering reveals a compact intermediate in RNA folding [see comments]","volume":"7","author":"Russell","year":"2000","journal-title":"Nature Struct. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib36","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1038\/nsb0797-553","article-title":"A magnesium ion core at the heart of a ribozyme domain [see comments]","volume":"4","author":"Cate","year":"1997","journal-title":"Nature Struct. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib37","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1261\/rna.5205404","article-title":"A guide to ions and RNA structure","volume":"10","author":"Draper","year":"2004","journal-title":"RNA"},{"key":"10.1016\/j.jmb.2005.09.032_bib38","doi-asserted-by":"crossref","first-page":"12471","DOI":"10.1073\/pnas.96.22.12471","article-title":"An optimal Mg(2+) concentration for kinetic folding of the Tetrahymena ribozyme","volume":"96","author":"Rook","year":"1999","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1016\/j.jmb.2005.09.032_bib39","doi-asserted-by":"crossref","first-page":"8924","DOI":"10.1021\/bi00425a008","article-title":"Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes","volume":"27","author":"Zaug","year":"1988","journal-title":"Biochemistry"},{"key":"10.1016\/j.jmb.2005.09.032_bib40","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1006\/jmbi.1996.0252","article-title":"Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs","volume":"258","author":"Huang","year":"1996","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.jmb.2005.09.032_bib41","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1261\/rna.7214405","article-title":"SAFA: Semi-Automated Footprinting Analysis software for high-throughput quantification of nucleic acid footprinting experiments","volume":"11","author":"Das","year":"2005","journal-title":"RNA"},{"key":"10.1016\/j.jmb.2005.09.032_bib42","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/0076-6879(86)30011-9","article-title":"Quantitative DNase footprint titration: a method for studying protein\u2013DNA interactions","volume":"130","author":"Brenowitz","year":"1986","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.jmb.2005.09.032_bib43","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1016\/S0076-6879(98)95050-9","article-title":"Following the folding of RNA with time-resolved synchrotron X-ray footprinting","volume":"295","author":"Sclavi","year":"1998","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.jmb.2005.09.032_bib44","doi-asserted-by":"crossref","first-page":"4266","DOI":"10.1073\/pnas.072589599","article-title":"Rapid compaction during RNA folding","volume":"99","author":"Russell","year":"2002","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1016\/j.jmb.2005.09.032_bib45","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1016\/S0969-2126(96)00129-3","article-title":"Metal-binding sites in the major groove of a large ribozyme domain","volume":"4","author":"Cate","year":"1996","journal-title":"Structure"}],"container-title":["Journal of Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283605010971?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283605010971?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T20:55:53Z","timestamp":1758315353000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0022283605010971"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,11]]},"references-count":45,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2005,11]]}},"alternative-id":["S0022283605010971"],"URL":"https:\/\/doi.org\/10.1016\/j.jmb.2005.09.032","relation":{},"ISSN":["0022-2836"],"issn-type":[{"value":"0022-2836","type":"print"}],"subject":[],"published":{"date-parts":[[2005,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Perturbation of the Hierarchical Folding of a Large RNA by the Destabilization of its Scaffold's Tertiary Structure","name":"articletitle","label":"Article Title"},{"value":"Journal of Molecular Biology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmb.2005.09.032","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2005 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}]}}