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Related Concept Videos

CRISPR01:59

CRISPR

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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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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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Homologous Recombination02:31

Homologous Recombination

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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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CRISPR and crRNAs02:53

CRISPR and crRNAs

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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.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
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Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
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The Antiviral System of Bacteria and Archaea: CRISPR01:23

The Antiviral System of Bacteria and Archaea: CRISPR

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CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats is a adaptive immune system found in bacteria and archaea that protects against viral infections. This system enables prokaryotic cells to identify, remember, and neutralize foreign genetic elements, primarily bacteriophages, by storing fragments of the invader’s DNA as a genetic memory.The CRISPR immune response begins during an initial infection. Cas (CRISPR-associated) proteins play a central role in this...
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Related Experiment Video

Updated: Jul 30, 2025

Efficient Generation of hiPSC Neural Lineage Specific Knockin Reporters Using the CRISPR/Cas9 and Cas9 Double Nickase System
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Hybrid Multitask Learning Reveals Sequence Features Driving Specificity in the CRISPR/Cas9 System.

Dhvani Sandip Vora1, Shashank Yadav1, Durai Sundar1,2

  • 1Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.

Biomolecules
|May 16, 2023
PubMed
Summary

CRISPR/Cas9 genome editing is advanced by a new model, CRISP-RCNN, that accurately predicts unintended DNA edits (off-target effects) and their severity. This deep learning approach improves the safety and reliability of gene editing technologies.

Keywords:
CNN-LSTMCRISPR/Cas9SHAPoff-targetsaliencysequence features

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • CRISPR/Cas9 gene editing offers precise genomic modification but is limited by unpredictable off-target effects.
  • Current methods for detecting off-target effects lack comprehensive predictive power for novel sequences.

Purpose of the Study:

  • To develop a robust method for predicting CRISPR/Cas9 off-target sites and their activity levels.
  • To identify sequence features crucial for determining Cas9 activity.

Main Methods:

  • A hybrid deep learning model, CRISP-RCNN (CNN-biLSTM), was developed for simultaneous off-target prediction and activity extent assessment.
  • Integrated gradients and weighting kernels were used for feature importance analysis, including nucleotide and position preferences and mismatch tolerance.

Main Results:

  • The CRISP-RCNN model effectively predicts both the likelihood of off-target activity and the degree of that activity.
  • Analysis revealed key sequence features and nucleotide preferences influencing Cas9 binding and cleavage efficiency.

Conclusions:

  • The developed deep learning approach enhances the prediction accuracy of CRISPR/Cas9 off-target effects.
  • CRISP-RCNN offers a valuable tool for improving the safety and efficacy of genome editing applications in research and therapy.