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Atypical DNA secondary structures have been shown to trigger TR expansion: their characterization is important for a molecular understanding of TR disease. CD spectroscopy experiments in the last decade have unequivocally demonstrated that CGG runs adopt a left-handed Z-DNA conformation, whose features remain uncertain because it entails accommodating GG mismatches. In order to find this missing motif, we have carried out molecular dynamics (MD) simulations to explore all the possible Z-DNA helices that potentially form after the transition from B- to Z-DNA. Such helices combine either CpG or GpC Watson-Crick steps in Z-DNA form with GG-mismatch conformations set as either intrahelical or extrahelical; and participating in BZ or ZZ junctions or in alternately extruded conformations. Characterization of the stability and structural features (especially overall left-handedness, higher-temperature and steered MD simulations) identified two novel Z-DNA helices: the most stable one displays alternately extruded Gs, and is followed by a helix with symmetrically extruded ZZ junctions. The G-extrusion favors a seamless stacking of the Watson-Crick base pairs; extruded Gs favor syn conformations and display hydrogen-bonding and stacking interactions. Such conformations could have the potential to hijack the MMR complex, thus triggering further expansion.<\/jats:p>","DOI":"10.1093\/nar\/gkac339","type":"journal-article","created":{"date-parts":[[2022,5,6]],"date-time":"2022-05-06T11:36:33Z","timestamp":1651836993000},"page":"4860-4876","source":"Crossref","is-referenced-by-count":14,"title":["Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats"],"prefix":"10.1093","volume":"50","author":[{"given":"Ashkan","family":"Fakharzadeh","sequence":"first","affiliation":[{"name":"Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiahui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Roland","sequence":"additional","affiliation":[{"name":"Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2750-5186","authenticated-orcid":false,"given":"Celeste","family":"Sagui","sequence":"additional","affiliation":[{"name":"Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,10]]},"reference":[{"key":"2022052021514370500_B1","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1101\/gr.10.7.967","article-title":"Microsatellites in different eukaryotic genomes: survey and analysis","volume":"10","author":"Toth","year":"2000","journal-title":"Genome Res."},{"key":"2022052021514370500_B2","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/S0168-9525(97)01008-1","article-title":"Simple sequence repeats as a source of quantitative genetic variation","volume":"13","author":"Kashi","year":"1997","journal-title":"Trends Genet."},{"key":"2022052021514370500_B3","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1002\/bies.20248","article-title":"Coding repeats and evolutionary \u2018agility\u2019","volume":"27","author":"Caburet","year":"2005","journal-title":"BioEssays"},{"key":"2022052021514370500_B4","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1016\/0092-8674(91)90397-H","article-title":"Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome","volume":"65","author":"Verkerk","year":"1991","journal-title":"Cell"},{"key":"2022052021514370500_B5","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1126\/science.252.5009.1179","article-title":"Fragile X genotype characterized by an unstable region of DNA","volume":"00","author":"Yu","year":"1991","journal-title":"Science"},{"key":"2022052021514370500_B6","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1038\/352077a0","article-title":"Androgen receptor gene mutations in X-linked spinal and bulbar muscular atrophy","volume":"352","author":"La\u00a0Spada","year":"1991","journal-title":"Nature"},{"key":"2022052021514370500_B7","first-page":"76","article-title":"Molecular-basis of the fragile-X syndrome and diagnostic applications","volume":"49","author":"Oberle","year":"1991","journal-title":"Am. 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