{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T21:02:22Z","timestamp":1787000542936,"version":"build-2736575974"},"reference-count":119,"publisher":"American Chemical Society (ACS)","issue":"43","license":[{"start":{"date-parts":[[2022,10,24]],"date-time":"2022-10-24T00:00:00Z","timestamp":1666569600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM118508"],"award-info":[{"award-number":["R01GM118508"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Friedreich\u2019s ataxia is associated with noncanonical nucleic acid structures that emerge when GAA:TTC repeats in the first intron of the FXN gene expand beyond a critical number of repeats. Specifically, the noncanonical repeats are associated with both triplexes and R-loops. Here, we present an in silico investigation of all possible triplexes that form by attaching a third RNA strand to an RNA:RNA or DNA:DNA duplex, complementing previous DNA-based triplex studies. For both new triplexes results are similar. For a pyridimine UUC+ third strand, the parallel orientation is stable while its antiparallel counterpart is unstable. For a neutral GAA third strand, the parallel conformation is stable. A protonated GA+A third strand is stable in both parallel and antiparallel orientations. We have also investigated Na+ and Mg2+ ion distributions around the triplexes. The presence of Mg2+ ions helps stabilize neutral, antiparallel GAA triplexes. These results (along with previous DNA-based studies) allow for the emergence of a complete picture of the stability and structural characteristics of triplexes based on the GAA and TTC\/UUC sequences, thereby contributing to the field of trinucleotide repeats and the associated unusual structures that trigger expansion.<\/jats:p>","DOI":"10.1021\/acsomega.2c04358","type":"journal-article","created":{"date-parts":[[2022,10,24]],"date-time":"2022-10-24T09:18:58Z","timestamp":1666603138000},"page":"38728-38743","source":"Crossref","is-referenced-by-count":8,"title":["RNA as a Major-Groove\nLigand: RNA\u2013RNA and RNA\u2013DNA\nTriplexes Formed by GAA and UUC or TTC Sequences"],"prefix":"10.1021","volume":"7","author":[{"given":"Jiahui","family":"Zhang","sequence":"first","affiliation":[{"name":"North Carolina State University , , , ,","place":["Raleigh, North Carolina, United States, 27695-8202"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashkan","family":"Fakharzadeh","sequence":"additional","affiliation":[{"name":"North Carolina State University , , , ,","place":["Raleigh, North Carolina, United States, 27695-8202"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Roland","sequence":"additional","affiliation":[{"name":"North Carolina State University , , , ,","place":["Raleigh, North Carolina, United States, 27695-8202"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2750-5186","authenticated-orcid":true,"given":"Celeste","family":"Sagui","sequence":"additional","affiliation":[{"name":"North Carolina State University , , , ,","place":["Raleigh, North Carolina, United States, 27695-8202"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2022,10,24]]},"reference":[{"key":"2026081709211458400_cit1","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1073\/pnas.74.2.457","article-title":"Cell-free translation\nof simian virus 40 early messenger RNA coding for viral T-antigen","volume":"74","author":"Prives","year":"1977","journal-title":"Proc. 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U.S.A."},{"key":"2026081709211458400_cit40","doi-asserted-by":"publisher","first-page":"3785","DOI":"10.1093\/nar\/gki697","article-title":"Advances in mechanisms of genetic\ninstability related to hereditary\nneurological diseases","volume":"33","author":"Wells","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2026081709211458400_cit41","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1002\/biof.1060","article-title":"Expanded complexity\nof unstable repeat diseases","volume":"39","author":"Polak","year":"2013","journal-title":"Biofactors"},{"key":"2026081709211458400_cit42","doi-asserted-by":"publisher","first-page":"142","DOI":"10.3109\/10409238.2014.999192","article-title":"Repeat\ninstability during DNA repair:\nInsights from model systems","volume":"50","author":"Usdin","year":"2015","journal-title":"Crit. Rev. Biochem.\nMol. Biol."},{"key":"2026081709211458400_cit43","doi-asserted-by":"publisher","first-page":"9899","DOI":"10.1093\/nar\/gkaa665","article-title":"Atypical structures\nof GAA\/TTC trinucleotide repeats underlying Friedreich\u2019s ataxia:\nDNA triplexes and RNA\/DNA hybrids","volume":"48","author":"Zhang","year":"2020","journal-title":"Nucl. Acids\nRes."},{"key":"2026081709211458400_cit44","volume-title":"Biochemical Nomenclature\nand Related Documents","author":"Liebecq","year":"1992","edition":"2"},{"key":"2026081709211458400_cit45","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1093\/nar\/28.12.2369","article-title":"Regulation of the RNA-dependent protein kinase by triple\nhelix formation","volume":"28","author":"Vuyisich","year":"2000","journal-title":"Nucleic acids research"},{"key":"2026081709211458400_cit46","doi-asserted-by":"publisher","first-page":"1468","DOI":"10.1093\/nar\/gky1171","article-title":"Finely tuned conformational\ndynamics regulate the protective function of the lncRNA MALAT1 triple\nhelix","volume":"47","author":"Ageeli","year":"2019","journal-title":"Nucleic acids research"},{"key":"2026081709211458400_cit47","doi-asserted-by":"publisher","first-page":"1302","DOI":"10.1021\/ar200098t","article-title":"The molecular interactions\nthat stabilize RNA tertiary\nstructure: RNA motifs, patterns, and networks","volume":"44","author":"Butcher","year":"2011","journal-title":"Accounts of chemical research"},{"key":"2026081709211458400_cit48","doi-asserted-by":"publisher","first-page":"427","DOI":"10.4161\/rna.8.3.14999","article-title":"Potential in vivo roles of nucleic\nacid triple-helices","volume":"8","author":"Buske","year":"2011","journal-title":"RNA biology"},{"key":"2026081709211458400_cit49","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1002\/wrna.1194","article-title":"The emerging\nrole of triple helices in RNA biology","volume":"5","author":"Conrad","year":"2014","journal-title":"Wiley\nInterdisciplinary Reviews: RNA"},{"key":"2026081709211458400_cit50","doi-asserted-by":"publisher","first-page":"10970","DOI":"10.1073\/pnas.1309590110","article-title":"Pyrimidine motif triple\nhelix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential\nfor function in vivo","volume":"110","author":"Cash","year":"2013","journal-title":"Proc. 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Biol. Chem."},{"key":"2026081709211458400_cit61","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1017\/S0033583512000078","article-title":"Structure\nand mechanism of purine binding riboswitches","volume":"45","author":"Batey","year":"2012","journal-title":"Q. Rev. Biophys."},{"key":"2026081709211458400_cit62","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1038\/nchembio.1231","article-title":"Structure of a class\nII preQ 1 riboswitch reveals ligand recognition by a new fold","volume":"9","author":"Liberman","year":"2013","journal-title":"Nat. Chem. 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