Department of Bioengineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.
Information and Computer Science Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.
Int J Mol Sci. 2023 Mar 27;24(7):6261. doi: 10.3390/ijms24076261.
The CRISPR-Cas system has evolved into a cutting-edge technology that has transformed the field of biological sciences through precise genetic manipulation. CRISPR/Cas9 nuclease is evolving into a revolutionizing method to edit any gene of any species with desirable outcomes. The swift advancement of CRISPR-Cas technology is reflected in an ever-expanding ecosystem of bioinformatics tools designed to make CRISPR/Cas9 experiments easier. To assist researchers with efficient guide RNA designs with fewer off-target effects, nuclease target site selection, and experimental validation, bioinformaticians have built and developed a comprehensive set of tools. In this article, we will review the various computational tools available for the assessment of off-target effects, as well as the quantification of nuclease activity and specificity, including web-based search tools and experimental methods, and we will describe how these tools can be optimized for gene knock-out (KO) and gene knock-in (KI) for model organisms. We also discuss future directions in precision genome editing and its applications, as well as challenges in target selection, particularly in predicting off-target effects.
CRISPR-Cas 系统已发展成为一种尖端技术，通过精确的基因操作彻底改变了生物科学领域。CRISPR/Cas9 核酸酶正在发展成为一种革命性的方法，可以编辑任何物种的任何基因，并获得理想的结果。CRISPR-Cas 技术的快速发展反映在不断扩展的生物信息学工具生态系统中，这些工具旨在使 CRISPR/Cas9 实验更加容易。为了帮助研究人员设计具有更少脱靶效应的高效向导 RNA、核酸酶靶位选择和实验验证，生物信息学家已经构建和开发了一套全面的工具。在本文中，我们将回顾用于评估脱靶效应、以及定量核酸酶活性和特异性的各种计算工具，包括基于网络的搜索工具和实验方法，并将描述如何针对模式生物的基因敲除 (KO) 和基因敲入 (KI) 对这些工具进行优化。我们还讨论了精确基因组编辑及其应用的未来方向，以及靶位选择方面的挑战，特别是在预测脱靶效应方面。
