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Related Concept Videos

CRISPR/Cas9 Genome Editing01:28

CRISPR/Cas9 Genome Editing

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The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...
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Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...
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RNA Interference01:23

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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CRISPR and crRNAs02:53

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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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Types of RNA01:23

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Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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Protein-protein Interfaces02:04

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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In silico optimization of RNA-protein interactions for CRISPR-Cas13-based antimicrobials.

Ho-Min Park1,2, Yunseol Park1, Urta Berani1

  • 1Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon, South Korea.

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|October 7, 2022
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Summary

Researchers optimized RNA-protein interactions for CRISPR-Cas13 systems to develop novel antimicrobials. This study identified new crRNA candidates for improved CRISPR-Cas13-based antibacterial therapies targeting specific bacteria.

Keywords:
CRISPR-based antimicrobialsDrug designIn silico dockingRNA secondary structureRNA tertiary structureRNA–protein interactionStructural biology

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Biotechnology

Background:

  • CRISPR-Cas systems provide adaptive immunity in prokaryotes via RNA-protein interactions.
  • CRISPR-based antimicrobials offer targeted bacterial destruction with minimal microbiome impact.
  • Current CRISPR-Cas13 tools may have suboptimal RNA-protein interactions due to lack of direct crRNA-Cas protein association.

Purpose of the Study:

  • To optimize RNA-protein interactions within CRISPR-Cas13 systems for enhanced antimicrobial applications.
  • To investigate and improve the design of CRISPR-Cas13 based antimicrobials by focusing on crRNA and Cas13 protein interactions.

Main Methods:

  • Validated 3-D structure prediction of crRNAs against experimental structures.
  • Tested multiple RNA-protein interaction programs for in silico docking of crRNAs with Cas13 proteins.
  • Curated validation and candidate datasets of Cas13 proteins and interacting CRISPR repeats.

Main Results:

  • Identified candidate crRNAs with improved in silico docking compared to current tools.
  • Developed an automated pipeline for in silico optimization of RNA-protein interactions.
  • Demonstrated potential for enhanced CRISPR-Cas13 system design.

Conclusions:

  • Optimized in silico screening of RNA-protein interactions is an efficient preliminary step for designing effective CRISPR-Cas13 antimicrobials.
  • This work facilitates the development of next-generation, highly specific antibacterial agents.
  • The findings pave the way for more precise and effective CRISPR-based therapeutic strategies.