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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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Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
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Synthetic Pentatricopeptide Repeat Proteins: Building a Toolkit for Precise RNA Control.

Jose M Lombana1, Maureen R Hanson1, Stephane Bentolila1

  • 1Molecular Biology Department, Cornell University, Ithaca, NY 14853, USA.

International Journal of Molecular Sciences
|December 30, 2025
PubMed
Summary

Synthetic PPR proteins offer programmable RNA editing for C-to-U and U-to-C conversions. These engineered enzymes show potential in biotechnology and treating RNA-mediated diseases.

Keywords:
RNA editingRNA engineeringpentatricopeptide repeat (PPR) proteinsprogrammable RNA recognitionsynthetic biology

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Biotechnology

Background:

  • Pentatricopeptide repeat (PPR) proteins naturally direct RNA editing (cytidine-to-uridine and uridine-to-cytidine) in plants via a specific recognition code.
  • This code allows for the rational design of synthetic PPR (synPPR) proteins with programmable RNA-binding specificity and stability.

Purpose of the Study:

  • To review the structural and mechanistic principles of PPR-mediated RNA editing.
  • To highlight advances in the design and application of synthetic PPR proteins as RNA engineering tools.

Main Methods:

  • Leveraging the amino acid-nucleotide recognition code of PPR proteins to design synthetic variants.
  • Fusing synthetic PPR scaffolds to DYW deaminase domains to create active RNA editors.
  • Utilizing these engineered enzymes across bacteria, plants, and human cells.

Main Results:

  • Synthetic PPR proteins can be programmed for specific RNA binding and stability.
  • Fusions with DYW domains create customizable enzymes for precise C-to-U or U-to-C base conversion.
  • Applications include RNA stabilization, translational regulation, and targeted RNA editing.

Conclusions:

  • Synthetic PPR proteins are versatile RNA engineering tools with broad applications in research, biotechnology, and medicine.
  • Emerging therapeutic potential for RNA-mediated diseases is significant.
  • Further refinements in specificity, efficiency, and modularity will enhance their utility in synthetic biology and RNA therapeutics.