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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 Mg 2+  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 D 2 O accessibility to H-bonding network is lower for ASBVd(+) than for ASBVd(-). Remarkably, the Mg 2+ -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.

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