Work

CRISPR-Cas Single-Guide RNA Construction for Tail Fiber Gene Gp0047 of Salmonella Phage SSE-121

Year: 2024

Type: article

Abstract: 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.

Source: Turkish computational and theoretical chemistry/Turkish computational and theoretical chemistry :

DOI: 10.33435/tcandtc.1531868

Authors: Erlia Narulita, Annisyah Nurmitha Oktarina, Rina B. Opulencia, Agung Haris Widianto, Riska Ayu Febrianti, Hardian Susilo Addy

Institutions: Universitas Jember, University of the Philippines Los Baños, Monash University

Language: English

Topic: CRISPR and Genetic Engineering

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: diamond

Funder: Universitas Jember

Award: G200782629