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Related Concept Videos

RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Related Experiment Video

Updated: May 22, 2026

A Nonsequencing Approach for the Rapid Detection of RNA Editing
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A Nonsequencing Approach for the Rapid Detection of RNA Editing

Published on: April 21, 2022

Directed evolution of small RNA-stabilizing motifs that improve prime-editing efficiency.

Holt A Sakai1,2,3, Sarah E Pierce1,2,3, Allen Y Jiang1,2,3

  • 1Merkin Institute of Transformative Technologies in Healthcare, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Nature Biotechnology
|May 20, 2026
PubMed
Summary

Researchers developed PE-PRISM, a screening tool to optimize 3' RNA motifs for prime-editing (PE) guide RNAs (pegRNAs). Optimized motifs significantly enhanced PE efficiency for correcting genetic variants in cells and animal models.

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Area of Science:

  • Molecular Biology
  • Gene Editing Technologies
  • RNA Structure and Function

Background:

  • Prime-editing (PE) systems offer precise genome editing but their efficiency relies on guide RNA (pegRNA) stability and structure.
  • Structured RNA motifs at the 3' end of pegRNAs are crucial for performance but remain understudied.

Purpose of the Study:

  • To introduce PE-PRISM, a high-throughput screening platform for identifying and optimizing 3' RNA motifs in pegRNAs.
  • To systematically evaluate diverse RNA motifs, including pseudoknots and G-quadruplexes, for enhancing PE efficiency.

Main Methods:

  • Developed PE-PRISM, a pooled screening approach for analyzing thousands of 3' RNA motifs in human cells.
  • Employed structure-guided mutagenesis and combinatorial screening to refine promising RNA motifs.
  • Tested top-performing motifs, including engineered pseudoknots (tevo2.0, eHAV, eSBRMV1-A), against a panel of pathogenic variants.

Main Results:

  • Evaluated 2,858 RNA motifs across four iterative libraries, identifying novel functional elements.
  • Optimized motifs demonstrated superior PE efficiency compared to the standard tevopreQ1 motif for over 90% of tested pathogenic variants.
  • Enhanced PE efficiency was confirmed in primary human cells and in vivo models (mouse brain and liver).

Conclusions:

  • PE-PRISM is an effective tool for discovering and optimizing pegRNA 3' RNA motifs.
  • Engineered RNA motifs significantly improve prime-editing efficiency and broaden its applicability for therapeutic variant correction.
  • This work advances the engineering of RNA components to enhance gene editing technologies.