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Open Access Research article

Raman characterization of Avocado Sunblotch viroid and its response to external perturbations and self-cleavage

Gaston Hui-Bon-Hoa1*, Hussein Kaddour2, Jacques Vergne2, Sergei G Kruglik34 and Marie-Christine Maurel2*

Author Affiliations

1 Unité 779, INSERM, 78 rue du Général Leclerc, 94276 Le Kremlin Bicêtre, France

2 UMR 7205, Sorbonne Universités, UPMC Univ Paris 6, 4 place Jussieu, F-75005 Paris, France

3 Laboratoire Jean Perrin (UMR 8237), Sorbonne Universités, UPMC Univ Paris 6, 4 place Jussieu, F-75005 Paris, France

4 Laboratoire Jean Perrin (UMR 8237), CNRS, 4 place Jussieu, F-75005 Paris, France

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BMC Biophysics 2014, 7:2  doi:10.1186/2046-1682-7-2

Published: 21 March 2014

Abstract

Background

Viroids are the smallest pathogens of plants. To date the structural and conformational details of the cleavage of Avocado sunblotch viroid (ASBVd) and the catalytic role of Mg2+ ions in efficient self-cleavage are of crucial interest.

Results

We report the first Raman characterization of the structure and activity of ASBVd, for plus and minus viroid strands. Both strands exhibit a typical A-type RNA conformation with an ordered double-helical content and a C3′-endo/anti sugar pucker configuration, although small but specific differences are found in the sugar puckering and base-stacking regions. The ASBVd(-) is shown to self-cleave 3.5 times more actively than ASBVd(+). Deuteration and temperature increase perturb differently the double-helical content and the phosphodiester conformation, as revealed by corresponding characteristic Raman spectral changes. Our data suggest that the structure rigidity and stability are higher and the D2O accessibility to H-bonding network is lower for ASBVd(+) than for ASBVd(-). Remarkably, the Mg2+-activated self-cleavage of the viroid does not induce any significant alterations of the secondary viroid structure, as evidenced from the absence of intensity changes of Raman marker bands that, however exhibit small but noticeable frequency downshifts suggesting several minor changes in phosphodioxy, internal loops and hairpins of the cleaved viroids.

Conclusions

Our results demonstrate the sensitivity of Raman spectroscopy in monitoring structural and conformational changes of the viroid and constitute the basis for further studies of its interactions with therapeutic agents and cell membranes.

Keywords:
Viroid; RNA conformation; Self-cleavage activity; D2O perturbation; Temperature unfolding; Raman spectroscopy