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Here, we show that ssDNA with chemical modifications in 12\u201319% of internal bases, which we denote as enhanced ssDNA (esDNA), improve knock-in (KI) by 2\u20133-fold compared to end-modified ssDNA in airway basal stem cells (ABCs), CD34\u00a0+\u00a0hematopoietic cells (CD34\u00a0+\u00a0cells), T-cells and endothelial cells. Over 50% of alleles showed KI in three clinically relevant loci (CFTR, HBB and CCR5) in ABCs using esDNA and up to 70% of alleles showed KI in the HBB locus in CD34\u00a0+\u00a0cells in the presence of a DNA-PKcs inhibitor. This level of correction is therapeutically relevant and is comparable to adeno-associated virus-based templates. The esDNA templates did not improve KI in induced pluripotent stem cells (iPSCs). This may be due to the absence of the nuclease TREX1 in iPSCs. Indeed, knocking out TREX1 in other cells improved KI using unmodified ssDNA. esDNA can be used to modify 20\u201330 bp regions in primary cells for therapeutic applications and biological modeling. The use of this approach for gene length insertions will require new methods to produce long chemically modified ssDNA in scalable quantities.<\/jats:p>","DOI":"10.1093\/nar\/gkae1069","type":"journal-article","created":{"date-parts":[[2024,10,22]],"date-time":"2024-10-22T07:18:05Z","timestamp":1729581485000},"page":"13561-13576","source":"Crossref","is-referenced-by-count":12,"title":["Single-stranded DNA with internal base modifications mediates highly efficient knock-in in primary cells using CRISPR-Cas9"],"prefix":"10.1093","volume":"52","author":[{"given":"Karen\u00a0L","family":"Kanke","sequence":"first","affiliation":[{"name":"Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH\u00a043215,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachael\u00a0E","family":"Rayner","sequence":"additional","affiliation":[{"name":"Department of Veterinary Biosciences, The Ohio State University , Columbus , OH 43210,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jack","family":"Bozik","sequence":"additional","affiliation":[{"name":"Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH\u00a043215,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eli","family":"Abel","sequence":"additional","affiliation":[{"name":"Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH\u00a043215,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aparna","family":"Venugopalan","sequence":"additional","affiliation":[{"name":"Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH\u00a043215,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ma","family":"Suu","sequence":"additional","affiliation":[{"name":"Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH\u00a043215,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reza","family":"Nouri","sequence":"additional","affiliation":[{"name":"Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH\u00a043215,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob\u00a0T","family":"Stack","sequence":"additional","affiliation":[{"name":"Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH\u00a043215,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gongbo","family":"Guo","sequence":"additional","affiliation":[{"name":"Institute for Genomic Medicine, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH 43215,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatyana\u00a0A","family":"Vetter","sequence":"additional","affiliation":[{"name":"Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH\u00a043215,","place":["USA"]},{"name":"Department of Pediatrics, The Ohio State University , Columbus , OH 43210,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Estelle","family":"Cormet-Boyaka","sequence":"additional","affiliation":[{"name":"Department of Veterinary Biosciences, The Ohio State University , Columbus , OH 43210,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark\u00a0E","family":"Hester","sequence":"additional","affiliation":[{"name":"Institute for Genomic Medicine, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH 43215,","place":["USA"]},{"name":"Department of Pediatrics, The Ohio State University , Columbus , OH 43210,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9167-3056","authenticated-orcid":false,"given":"Sriram","family":"Vaidyanathan","sequence":"additional","affiliation":[{"name":"Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children\u2019s Hospital , 700 Children's Drive,\u00a0 Columbus , OH\u00a043215,","place":["USA"]},{"name":"Department of Pediatrics, The Ohio State University , Columbus , OH 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