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Structural Insights and Binding Site Analysis for Improved CRISPR-Cas13a Sensitivity and Efficiency
Document Type : Original Article
Author
Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
Abstract
CRISPR-Cas13a systems have revolutionized RNA detection and manipulation, with trans-cleavage activity playing a pivotal role in their diagnostic applications. Enhancing this activity is crucial for achieving greater sensitivity, speed, and versatility in both research and clinical settings. Targeting specific protein binding sites with organic chemical agents represents a promising approach for increasing trans-cleavage activity. This research utilized homology modelling alongside computational approaches, including InterProSurf, GHECOM, and eF-seek, to examine structural characteristics and identify high-confidence binding sites in Cas13a orthologs. These methods provided a comprehensive analysis of the protein's functional architecture, contributing to a deeper understanding of its mechanistic behaviour. Functional amino acids located on the protein surface, along with pockets exhibiting lower binding affinity scores, were identified as potential binding sites for small molecules. Key residues influencing ligand interactions were pinpointed, including residues 603, 605, and 606 in LbaCas13a; residues 1112 and 1145 in LbuCas13a; and residues 735, 784, and 787 in LshCas13a. The eF-seek analysis revealed more extensive residue interaction networks in LbaCas13a, which correlate with its enhanced trans-cleavage activity. These findings provide a comprehensive framework for optimizing CRISPR-Cas13a systems, offering valuable insights for improving their sensitivity and efficiency in precision diagnostics. Future research can refine Cas13a-based tools by focusing on their structural and functional details to unlock their full potential in biomedical applications.
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OPEN ACCESS
©2026 The author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit: http://creativecommons.org/licenses/by/4.0/
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Volume 14, Issue 1
January and February 2026Pages 90-103
- Receive Date 13 July 2025
- Revise Date 12 August 2025
- Accept Date 22 September 2025
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