# Hammerhead Ribozymes: Structural Insights, Catalytic Mechanisms, and Cutting-Edge Applications in Synthetic Biology

**Authors:** Liangliang Wang, Yan Liu, Xuemin Xian, Haitao Zhang

PMC · DOI: 10.3390/ijms26125624 · International Journal of Molecular Sciences · 2025-06-12

## TL;DR

This paper reviews hammerhead ribozymes, small RNA molecules used in synthetic biology for RNA manipulation and gene regulation.

## Contribution

The paper offers new insights into the structural and catalytic properties of hammerhead ribozymes and their biomedical applications.

## Key findings

- Hammerhead ribozymes are compact and efficient RNA tools for gene regulation.
- They have shown promise in disease therapy and biosensing applications.
- The paper outlines current challenges and future directions in their development.

## Abstract

Hammerhead ribozymes are a class of small RNA molecules with catalytic activity. Their compact size, high catalytic efficiency, structural simplicity, and modular design flexibility make them ideal tools for RNA manipulation and gene regulation. In recent years, these ribozymes have demonstrated tremendous application potential across diverse fields, including gene regulation, disease therapy, and biosensing, significantly advancing related research. This article provides a comprehensive review of recent progress in hammerhead ribozyme research within synthetic biology, thoroughly examines the current challenges, and outlines future development directions, aiming to offer valuable perspectives and insights for their biomedical applications.

## Full-text entities

- **Genes:** MIR155 (microRNA 155) [NCBI Gene 406947] {aka MIRN155, miRNA155, mir-155}, Mgmt (O-6-methylguanine-DNA methyltransferase) [NCBI Gene 17314] {aka AGT, Agat}, Plk1 (polo like kinase 1) [NCBI Gene 18817] {aka Plk, STPK13}, Mutyh (mutY DNA glycosylase) [NCBI Gene 70603] {aka 5730495A01Rik, Mutyha, Mutyhalpha, Mutyhb, Mutyhbeta, Mutyhc}
- **Diseases:** cancer (MESH:D009369), injury to (MESH:D014947), coronavirus (MESH:D018352), genetic disorder (MESH:D030342)
- **Chemicals:** tobramycin (MESH:D014031), O6-MeG (MESH:C008449), theophylline (MESH:D013806), Tetracycline (MESH:D013752), heavy metal (MESH:D019216), Mn2+ (-), Morpholino (MESH:D060172), spermidine (MESH:D013095), tetrapentylammonium (MESH:C027435), phosphate (MESH:D010710), tren (MESH:C099539), acids (MESH:D000143), polyA (MESH:D011061), 8-oxoG (MESH:C024829), D-ribose (MESH:D012266), metal (MESH:D008670), ATP (MESH:D000255), melamine (MESH:C011907), sugar (MESH:D000073893), lipid (MESH:D008055)
- **Species:** Dengue virus (no rank) [taxon 12637], Sus scrofa (pig, species) [taxon 9823], Mus musculus (house mouse, species) [taxon 10090], Schistosoma (genus) [taxon 6181], Caenorhabditis elegans (species) [taxon 6239], Hepatitis B virus (no rank) [taxon 10407], hepatitis C virus [taxon 11103], Human immunodeficiency virus 1 (no rank) [taxon 11676], Senecavirus A (no rank) [taxon 390157], Homo sapiens (human, species) [taxon 9606], Human immunodeficiency virus (species) [taxon 12721], Severe acute respiratory syndrome coronavirus 2 (no rank) [taxon 2697049], Chikungunya virus (no rank) [taxon 37124]
- **Mutations:** A6C

## Full text

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## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12192606/full.md

## References

98 references — full list in the complete paper: https://tomesphere.com/paper/PMC12192606/full.md

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Source: https://tomesphere.com/paper/PMC12192606