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There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the pathogenic (A2G3)n and nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in vitro reveals triplex H-DNA formation by only the pathogenic repeat. Consistently, bioinformatic analysis of S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs. Finally, the pathogenic, but not the nonpathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that the CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication.<\/jats:p>","DOI":"10.1093\/nar\/gkae124","type":"journal-article","created":{"date-parts":[[2024,2,21]],"date-time":"2024-02-21T19:31:05Z","timestamp":1708543865000},"page":"4361-4374","source":"Crossref","is-referenced-by-count":13,"title":["Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures"],"prefix":"10.1093","volume":"52","author":[{"given":"Julia A","family":"Hisey","sequence":"first","affiliation":[{"name":"Department of Biology, Tufts University , Medford , MA\u00a0 02155 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elina A","family":"Radchenko","sequence":"additional","affiliation":[{"name":"Department of Biology, Tufts University , Medford , MA\u00a0 02155 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas H","family":"Mandel","sequence":"additional","affiliation":[{"name":"Department of Biology, Tufts University , Medford , MA\u00a0 02155 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryan\u00a0J","family":"McGinty","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston , MA 02115, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel","family":"Matos-Rodrigues","sequence":"additional","affiliation":[{"name":"Laboratory of Genome Integrity, National Cancer Institute NIH , Bethesda , MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anastasia","family":"Rastokina","sequence":"additional","affiliation":[{"name":"Department of Biology, Tufts University , Medford , MA\u00a0 02155 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3414-6369","authenticated-orcid":false,"given":"Chiara","family":"Masnovo","sequence":"additional","affiliation":[{"name":"Department of Biology, Tufts University , Medford , MA\u00a0 02155 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Ceschi","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical and Pharmacological Sciences, University of Padova , Padova\u00a0 35131 , Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfredo","family":"Hernandez","sequence":"additional","affiliation":[{"name":"Department of Biology, Tufts University , Medford , MA\u00a0 02155 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9","family":"Nussenzweig","sequence":"additional","affiliation":[{"name":"Laboratory of Genome Integrity, National Cancer Institute NIH , Bethesda , MD 20892, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4576-7582","authenticated-orcid":false,"given":"Sergei\u00a0M","family":"Mirkin","sequence":"additional","affiliation":[{"name":"Department of Biology, Tufts University , Medford , MA\u00a0 02155 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,2,21]]},"reference":[{"key":"2024050805492386200_B1","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1038\/s41588-019-0372-4","article-title":"Biallelic expansion of an intronic repeat in RFC1 is a common cause of late-onset ataxia","volume":"51","author":"Cortese","year":"2019","journal-title":"Nat. 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