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Liposome membrane can induce self-cleavage of RNA that models the core fragments of hammerhead ribozyme

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Abstract

The hammerhead ribozyme (HHR) is one of smallest catalytic RNAs, composed of a catalytic core and three stems; it undergoes self-cleavage in the presence of divalent magnesium ions (Mg2+) or other cations. It is hypothesized that the function and metabolism of RNAs might be regulated via interaction with lipid membranes in the prebiotic world. Using synthetic RNAs that model the core fragment of hammerhead ribozyme-like assembly (HHR-a), we investigated the enhancement of the self-cleavage reaction of HHR-a induced by the liposomes, both in the absence and presence of Mg2+. The HHR-a activity was enhanced by 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DPPC) = 8/2 liposome with Mg2+, while other liposomes did not so significant. In the presence of DOPE/DPPC = 8/2 liposome, the HHR-a activity was observed without Mg2+, revealed by the conformational change of the HHR inhibitor complex induced by the interaction with the liposome. The UV resonance Raman spectroscopy analysis investigated the interaction between lipid molecules and nucleobases, suggesting that the ethanolamine group of DOPE molecules are assumed to act as monovalent cations alternative to Mg2+, depending on the liposome membrane characteristics.

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Abbreviations

HHR:

Hammerhead ribozyme

HHR-a:

Hammerhead ribozyme-like RNA assembly

HHR–IC:

HHR–inhibitor complex

MALDI TOF/MS:

Matrix-assisted laser desorption/ionization time-of-flight/mass spectrometry

CD:

Circular dichroism

UVRR:

UV resonance Raman

DOPE:

1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine

DPPE:

1,2-Dipalmitoyl-sn-glycero-3-phosphoethanolamine

DOPC:

1,2-Dioleoyl-sn-glycero-3-phosphocholine

DPPC:

1,2-Dipalmitoyl-sn-glycero-3-phosphocholine

DPH:

1,6-Diphenyl-1,3,5-hexatriene

Laurdan:

6-Lauroyl-2-dimethylaminonaphthalene

TNS:

2-(p-Toluidino)naphthalene-6-sulfonate

SGI:

SYBR Green I

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Acknowledgments

We thank Dr. Toshinori Shimanouchi (Graduate School of Environmental Science, Okayama University) for his constructive comments. This work was supported by the Funding Program for Next Generation World-Leading Researchers of the Council for Science and Technology Policy (CSTP) (GR066), JSPS Grant-in-Aid for Scientific Research A (26249116), and JSPS Grant-in-Aid for Research Activity Start-up (25889039). One of the authors (K.S.) also expresses his gratitude for the Japan Society for the Promotion of Science (JSPS) and GCOE scholarships.

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Authors and Affiliations

  1. Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyamacho, Toyonaka, Osaka, 560-8531, Japan

    Keishi Suga, Seishiro Tanaka & Hiroshi Umakoshi

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  1. Keishi Suga
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  2. Seishiro Tanaka
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  3. Hiroshi Umakoshi
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Correspondence to Hiroshi Umakoshi.

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Suga, K., Tanaka, S. & Umakoshi, H. Liposome membrane can induce self-cleavage of RNA that models the core fragments of hammerhead ribozyme. Eur Biophys J 45, 55–62 (2016). https://doi.org/10.1007/s00249-015-1076-z

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