{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,21]],"date-time":"2025-09-21T10:29:32Z","timestamp":1758450572699,"version":"3.44.0"},"reference-count":2,"publisher":"Turkish Computational and Theoretical Chemistry","issue":"3","funder":[{"DOI":"10.13039\/501100018968","name":"University of Jember","doi-asserted-by":"crossref","award":["3791\/UN25.3.1\/LT\/2023"],"award-info":[{"award-number":["3791\/UN25.3.1\/LT\/2023"]}],"id":[{"id":"10.13039\/501100018968","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2024,9,19]]},"abstract":"<jats:p xml:lang=\"en\">In this study, we conducted an in-silico study of single guide RNA (sgRNA) construction as the initial stage of CRISPR-Cas9-based genome editing on Salmonella bacteriophage SSE-121 to broaden its host range. The results of the study discovered 188 sgRNA candidates using CHOPCHOP prediction. All selected candidates were docked using free website-based docking tools HNADOCK, therefore the top seven candidates of sgRNAs were docked using HDOCK with the Cas9 protein. The molecular dynamics simulation of the most optimum sgRNA-Cas9 protein (docking score -387.43) and sgRNA-Cas9-DNA (docking score -431.58) were calculated using AMBER14 forcefield in YASARA Dynamics. Based on the in-silico evaluation, the gRNA6 was obtained as the optimum single guide RNA. The docking score with DNA targets was -592.23 and Cas9 protein was -387.43. The comparison between the Cas9 and Cas9-sgRNA complex showed that the binding effect of sgRNA could maintain better conformational stability than in the single form.<\/jats:p>","DOI":"10.33435\/tcandtc.1531868","type":"journal-article","created":{"date-parts":[[2024,12,29]],"date-time":"2024-12-29T17:09:58Z","timestamp":1735492198000},"page":"25-37","source":"Crossref","is-referenced-by-count":0,"title":["CRISPR-Cas Single-Guide RNA Construction for Tail Fiber Gene Gp0047 of Salmonella Phage SSE-121"],"prefix":"10.33435","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3448-3587","authenticated-orcid":true,"given":"Erlia","family":"Narulita","sequence":"first","affiliation":[{"name":"University of Jember"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-6971-8942","authenticated-orcid":true,"given":"Annisyah Nurmitha","family":"Oktarina","sequence":"additional","affiliation":[{"name":"University of Jember"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5761-8253","authenticated-orcid":true,"given":"Rina B.","family":"Opulencia","sequence":"additional","affiliation":[{"name":"University of the Philippines Los Ba\u00f1os"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2624-3241","authenticated-orcid":true,"given":"Agung Haris","family":"Widianto","sequence":"additional","affiliation":[{"name":"Monash University"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0834-007X","authenticated-orcid":true,"given":"Riska Ayu","family":"Febrianti","sequence":"additional","affiliation":[{"name":"University of Jember"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7823-0859","authenticated-orcid":true,"given":"Hardian Susilo","family":"Addy","sequence":"additional","affiliation":[{"name":"University of Jember"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"19061","published-online":{"date-parts":[[2025,9,15]]},"reference":[{"key":"ref1","unstructured":"[1] mc\u00f6mvnx\u00f6dnvlkjsl\u015fkcvsd"},{"key":"ref2","unstructured":"[2]m \u00e7mcx\u00e7v\u00f6xl\u015fmvlm d v"}],"container-title":["Turkish Computational and Theoretical Chemistry"],"original-title":[],"deposited":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T21:41:41Z","timestamp":1758404501000},"score":1,"resource":{"primary":{"URL":"https:\/\/dergipark.org.tr\/en\/doi\/10.33435\/tcandtc.1531868"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,15]]},"references-count":2,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2025,9,15]]}},"URL":"https:\/\/doi.org\/10.33435\/tcandtc.1531868","relation":{},"ISSN":["2587-1722"],"issn-type":[{"type":"print","value":"2587-1722"}],"subject":[],"published":{"date-parts":[[2025,9,15]]}}}