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RNA Editing02:23

RNA Editing

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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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RACE - Rapid Amplification of cDNA Ends02:35

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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CRISPR/Cas9 Genome Editing01:28

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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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Related Experiment Video

Updated: Nov 20, 2025

Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms
09:51

Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms

Published on: May 25, 2018

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Prime Editing Guide RNA Design Automation Using PINE-CONE.

Kylie Standage-Beier, Stefan J Tekel, David A Brafman

    ACS Synthetic Biology
    |January 19, 2021
    PubMed
    Summary
    This summary is machine-generated.

    Prime editing (PE) enables precise DNA edits without breaks. The PINE-CONE software tool automates prime editing guide RNA design, accelerating synthetic biology and biomedical research applications.

    Keywords:
    CRISPRautomationgenome engineeringprime editing

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    A Nonsequencing Approach for the Rapid Detection of RNA Editing
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    Area of Science:

    • Genetics and Genomics
    • Molecular Biology
    • Bioengineering

    Background:

    • CRISPR-based technologies are essential for genome engineering and synthetic biology.
    • Prime editing (PE) offers precise genomic modifications without double-stranded DNA breaks or donor DNA.
    • The design of prime editing guide RNAs (pegRNAs) is complex and limits the throughput of PE applications.

    Purpose of the Study:

    • To develop a high-throughput software tool for automated pegRNA design.
    • To facilitate the design of prime editing strategies and associated cloning workflows.
    • To demonstrate the utility of the software in generating disease-relevant genetic edits.

    Main Methods:

    • Development of the Prime Induced Nucleotide Engineering Creator of New Edits (PINE-CONE) software.
    • PINE-CONE translates edit coordinates and sequences into pegRNA designs, accessory guides, and oligonucleotides.
    • Application of PINE-CONE to design pegRNAs targeting Alzheimer's Disease single nucleotide polymorphisms (SNPs).

    Main Results:

    • PINE-CONE enables high-throughput, automated design of pegRNAs and prime editing strategies.
    • The software streamlines the creation of pegRNAs, accessory guides, and oligonucleotides for cloning.
    • A library of pegRNAs targeting Alzheimer's Disease SNPs was rapidly designed using PINE-CONE.

    Conclusions:

    • PINE-CONE significantly enhances the efficiency of pegRNA design.
    • The software accelerates the application of prime editing in synthetic biology.
    • PINE-CONE is a valuable tool for biomedical research, particularly for studying disease genotypes.