Key result
Atomic force microscopy successfully mapped the secondary structure of Turnip Yellow Mosaic Virus RNA molecules, showing agreement with previously available evidence.
Atomic force microscopy is a viable method for mapping the secondary structure of RNA molecules and observing single molecule conformations.
Nowadays, the development of experimental procedures for the determination of the secondary structure of RNA molecules is taking advantage of the novel single-molecule probing and imaging techniques. We report a method for the mapping of the secondary structure of RNA molecules spread on a flat surface by means of the atomic force microscope. Globular domains comprising groups of RNA secondary and tertiary structure elements separated by unstructured domains can be discerned in the micrographs and their position along the molecule contour can be measured directly on unstained specimens. We have analyzed the morphology of a population of single molecules of 3' fragments of the Turnip Yellow Mosaic Virus RNA shorter than 1 kb in different temperature and electrolytic conditions. We found a satisfying agreement of the shape of the imaged structures with previously available evidence. The method we have developed can be used to map also different types of RNA molecules and has the advantage of showing the distribution of the single molecule conformations within the population.
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Giro et al. (2004) studied RNA secondary structure. Atomic force microscopy was evaluated on Morphology and secondary structure mapping of RNA molecules. Atomic force microscopy successfully mapped the secondary structure of Turnip Yellow Mosaic Virus RNA molecules, showing agreement with previously available evidence.
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