{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T15:12:09Z","timestamp":1782486729979,"version":"3.54.5"},"reference-count":60,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,4,19]],"date-time":"2023-04-19T00:00:00Z","timestamp":1681862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000897","name":"Cystic Fibrosis Foundation","doi-asserted-by":"publisher","award":["XU19XX0"],"award-info":[{"award-number":["XU19XX0"]}],"id":[{"id":"10.13039\/100000897","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM149016"],"award-info":[{"award-number":["GM149016"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HL159900"],"award-info":[{"award-number":["HL159900"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HL147527"],"award-info":[{"award-number":["HL147527"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HL159871"],"award-info":[{"award-number":["HL159871"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["GM122181"],"award-info":[{"award-number":["GM122181"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007270","name":"University of Michigan","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007270","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The critical first step in Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)\u2013associated (CRISPR\u2013Cas) protein-mediated gene editing is recognizing a preferred protospacer adjacent motif (PAM) on target DNAs by the protein\u2019s PAM-interacting amino acids (PIAAs). Thus, accurate computational modeling of PAM recognition is useful in assisting CRISPR\u2013Cas engineering to relax or tighten PAM requirements for subsequent applications. Here, we describe a universal computational protein design framework (UniDesign) for designing protein\u2013nucleic acid interactions. As a proof of concept, we applied UniDesign to decode the PAM\u2013PIAA interactions for eight Cas9 and two Cas12a proteins. We show that, given native PIAAs, the UniDesign-predicted PAMs are largely identical to the natural PAMs of all Cas proteins. In turn, given natural PAMs, the computationally redesigned PIAA residues largely recapitulated the native PIAAs (74% and 86% in terms of identity and similarity, respectively). These results demonstrate that UniDesign faithfully captures the mutual preference between natural PAMs and native PIAAs, suggesting it is a useful tool for engineering CRISPR\u2013Cas and other nucleic acid-interacting proteins. UniDesign is open-sourced at https:\/\/github.com\/tommyhuangthu\/UniDesign.<\/jats:p>","DOI":"10.1093\/bib\/bbad133","type":"journal-article","created":{"date-parts":[[2023,3,16]],"date-time":"2023-03-16T19:28:46Z","timestamp":1678994926000},"source":"Crossref","is-referenced-by-count":16,"title":["Decoding CRISPR\u2013Cas PAM recognition with UniDesign"],"prefix":"10.1093","volume":"24","author":[{"given":"Xiaoqiang","family":"Huang","sequence":"first","affiliation":[{"name":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Zhou","sequence":"additional","affiliation":[{"name":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongshan","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jifeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaofeng","family":"Xia","sequence":"additional","affiliation":[{"name":"Research & Development, ATGC Inc. , 100 E Lancaster Avenue, LIMR Building Lab 129, Wynnewood, PA 19096 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuqing Eugene","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Xu","sequence":"additional","affiliation":[{"name":"Center for Advanced Models for Translational Sciences and Therapeutics, Department of Internal Medicine, University of Michigan Medical School , 2800 Plymouth Road, Ann Arbor, MI 48109 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,4,19]]},"reference":[{"key":"2023052022123024000_ref1","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1038\/nmeth.2649","article-title":"Cas9 as a versatile tool for engineering biology","volume":"10","author":"Mali","year":"2013","journal-title":"Nat 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genome engineering using CRISPR\/Cas systems","volume":"339","author":"Cong","year":"2013","journal-title":"Science"},{"key":"2023052022123024000_ref6","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/s41467-020-20633-y","article-title":"CRISPR technologies and the search for the PAM-free nuclease","volume":"12","author":"Collias","year":"2021","journal-title":"Nat Commun"},{"key":"2023052022123024000_ref7","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1126\/science.aba8853","article-title":"Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants","volume":"368","author":"Walton","year":"2020","journal-title":"Science"},{"key":"2023052022123024000_ref8","doi-asserted-by":"crossref","first-page":"1259","DOI":"10.1126\/science.aas9129","article-title":"Engineered CRISPR-Cas9 nuclease with expanded targeting 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Microbiol Biotechnol"},{"key":"2023052022123024000_ref12","doi-asserted-by":"crossref","first-page":"5484","DOI":"10.1039\/C8GC03420F","article-title":"Computational redesign of penicillin acylase for cephradine synthesis with high kinetic selectivity","volume":"20","author":"He","year":"2018","journal-title":"Green Chem"},{"key":"2023052022123024000_ref13","doi-asserted-by":"crossref","first-page":"eabc6378","DOI":"10.1126\/sciadv.abc6378","article-title":"Reengineering biocatalysts: computational redesign of chondroitinase ABC improves efficacy and stability","volume":"6","author":"Hettiaratchi","year":"2020","journal-title":"Sci Adv"},{"key":"2023052022123024000_ref14","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/s41586-022-04654-9","article-title":"Design of protein-binding proteins from the target structure 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