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Related Concept Videos

Mismatch Repair01:20

Mismatch Repair

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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
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Intersegmental transfers drive target search in an RNA-targeting CRISPR system.

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Related Experiment Video

Updated: Jul 10, 2025

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter
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Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

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RNA structure modulates Cas13 activity and enables mismatch detection.

Ofer Kimchi1, Benjamin B Larsen2, Owen R S Dunkley2

  • 1Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, 08544, USA.

Biorxiv : the Preprint Server for Biology
|November 21, 2023
PubMed
Summary

The CRISPR-Cas13 system targets RNA, but its interaction with structured RNAs was unclear. This study reveals two mechanisms by which RNA structure influences Cas13 activity, improving RNA detection and mutation identification.

Keywords:
CRISPRCas13RNA detectionRNA structurestrand displacement

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Area of Science:

  • Molecular Biology
  • Biotechnology
  • Genetics

Background:

  • The RNA-targeting CRISPR nuclease Cas13 is crucial for nucleic acid detection and transcriptome engineering.
  • Cas13 activation relies on CRISPR RNA (crRNA) binding to a target RNA protospacer.
  • The mechanism of Cas13 binding to highly structured RNAs remains largely unknown, limiting its applications.

Conclusions:

  • This research elucidates the mechanism of Cas13 binding to structured RNAs, crucial for its function.
  • The findings enable improved Cas13-based RNA detection, with enhanced mismatch discrimination and sequence-agnostic mutation identification.
  • This work advances CRISPR-based nucleic acid detection and guides future RNA targeting strategies.