Halothermophilic Cas9 and dCas9 Interaction with Variety sgRNA In-silico
Industrial bioprocesses often require microorganisms that can adapt to specific conditions, such as halothermophilic bacteria capable of producing biosurfactants with various applications. Enhancing production yield is important, and one approach genetic modification. Clustered Regularly Interspaced...
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Universitas Indonesia
2025-01-01
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| Series: | International Journal of Technology |
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| Online Access: | https://ijtech.eng.ui.ac.id/article/view/7367 |
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| author | Kenny Lischer Kholisoh Hayati Muhammad Haykal Fabian Fina Amreta Laksmi Yudhi Nugraha Hamdan Dwi Rizqi Riri Fauziyya Sarmoko Mohd Shukuri Mohamad Ali |
| author_facet | Kenny Lischer Kholisoh Hayati Muhammad Haykal Fabian Fina Amreta Laksmi Yudhi Nugraha Hamdan Dwi Rizqi Riri Fauziyya Sarmoko Mohd Shukuri Mohamad Ali |
| author_sort | Kenny Lischer |
| collection | DOAJ |
| description | Industrial bioprocesses often require microorganisms that can adapt to specific conditions, such as halothermophilic bacteria capable of producing biosurfactants with various applications. Enhancing production yield is important, and one approach genetic modification. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a highly effective method for genetic editing; however, its use in halothermophilic bacteria remains limited. So far, optimal genetic editing with Cas9 has only been achieved in thermophilic bacteria unsuitable for high-salt environments. For determining optimal CRISPR involves analyzing the binding interaction between sgRNA (single guide RNA) and Cas9 using Molecular Docking in halothermophilic bacteria. This includes preparing the structures of Cas9 and sgRNA, simulating them with HDOCK software, and data analysis. Molecular Docking has advantages such as cost-effectiveness and time efficiency in designing the optimal sgRNA length. Optimization of sgRNA is achieved by varying the lengths of repeat, spacer, and tracrRNA, aiming for the lowest binding energy values and visually feasible designs. For Cas9 from the selected bacterium, Klebsiella pneumoniae, the optimal sgRNA design for Cas9 involves a spacer of 10 nt. In contrast, dCas9 involves a spacer of 10 nt, a repeat of 36 nt, and tracrRNA of 63 nt. The native temperature of the bacteria did not significantly affect the optimal sgRNA length. |
| format | Article |
| id | doaj-art-62ebaca0199542cca391fda5bb66d2ee |
| institution | Kabale University |
| issn | 2086-9614 2087-2100 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Universitas Indonesia |
| record_format | Article |
| series | International Journal of Technology |
| spelling | doaj-art-62ebaca0199542cca391fda5bb66d2ee2025-01-31T14:13:03ZengUniversitas IndonesiaInternational Journal of Technology2086-96142087-21002025-01-0116132233110.14716/ijtech.v16i1.73677367Halothermophilic Cas9 and dCas9 Interaction with Variety sgRNA In-silicoKenny Lischer0Kholisoh Hayati1Muhammad Haykal Fabian2Fina Amreta Laksmi3Yudhi Nugraha4Hamdan Dwi Rizqi5Riri Fauziyya6Sarmoko7Mohd Shukuri Mohamad Ali81. Bioprocess Engineering, Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia, Depok, West Java, 16424, Indonesia 2. Research Centre of Biomedical Engineering, DepartmeChemical Engineering, Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia, Depok, West Java, 16424, IndonesiaBioprocess Engineering, Department of Chemical Engineering, Faculty of Engineering, Universitas Indonesia, Depok, West Java, 16424, IndonesiaNational Research and Innovation Agency, Cibinong, West Java, 16915, Indonesia1. Research Center for Molecular Biology Eijkman BRIN, National Research and Innovation Agency, Cibinong, West Java, 16915, Indonesia 2. Department of Molecular Medicine, University of Pavia, 27100,Department of Chemistry, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Surabaya, Jawa Timur, 60111, IndonesiaDepartment of Pharmacy, Sumatera Institute of Technology, Lampung, 35365, Indonesia.Department of Pharmacy, Sumatera Institute of Technology, Lampung, 35365, IndonesiaEnzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang 43400, Selangor, MalaysiaIndustrial bioprocesses often require microorganisms that can adapt to specific conditions, such as halothermophilic bacteria capable of producing biosurfactants with various applications. Enhancing production yield is important, and one approach genetic modification. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a highly effective method for genetic editing; however, its use in halothermophilic bacteria remains limited. So far, optimal genetic editing with Cas9 has only been achieved in thermophilic bacteria unsuitable for high-salt environments. For determining optimal CRISPR involves analyzing the binding interaction between sgRNA (single guide RNA) and Cas9 using Molecular Docking in halothermophilic bacteria. This includes preparing the structures of Cas9 and sgRNA, simulating them with HDOCK software, and data analysis. Molecular Docking has advantages such as cost-effectiveness and time efficiency in designing the optimal sgRNA length. Optimization of sgRNA is achieved by varying the lengths of repeat, spacer, and tracrRNA, aiming for the lowest binding energy values and visually feasible designs. For Cas9 from the selected bacterium, Klebsiella pneumoniae, the optimal sgRNA design for Cas9 involves a spacer of 10 nt. In contrast, dCas9 involves a spacer of 10 nt, a repeat of 36 nt, and tracrRNA of 63 nt. The native temperature of the bacteria did not significantly affect the optimal sgRNA length.https://ijtech.eng.ui.ac.id/article/view/7367biosurfactantcrispr-cas9 optimizationhalothermophilicmolecular dockingsgrna design |
| spellingShingle | Kenny Lischer Kholisoh Hayati Muhammad Haykal Fabian Fina Amreta Laksmi Yudhi Nugraha Hamdan Dwi Rizqi Riri Fauziyya Sarmoko Mohd Shukuri Mohamad Ali Halothermophilic Cas9 and dCas9 Interaction with Variety sgRNA In-silico International Journal of Technology biosurfactant crispr-cas9 optimization halothermophilic molecular docking sgrna design |
| title | Halothermophilic Cas9 and dCas9 Interaction with Variety sgRNA In-silico |
| title_full | Halothermophilic Cas9 and dCas9 Interaction with Variety sgRNA In-silico |
| title_fullStr | Halothermophilic Cas9 and dCas9 Interaction with Variety sgRNA In-silico |
| title_full_unstemmed | Halothermophilic Cas9 and dCas9 Interaction with Variety sgRNA In-silico |
| title_short | Halothermophilic Cas9 and dCas9 Interaction with Variety sgRNA In-silico |
| title_sort | halothermophilic cas9 and dcas9 interaction with variety sgrna in silico |
| topic | biosurfactant crispr-cas9 optimization halothermophilic molecular docking sgrna design |
| url | https://ijtech.eng.ui.ac.id/article/view/7367 |
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