title: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
abstract: 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.
authors.affiliation: Department of Biochemistry G. Moruzzi and National Institute for the Physics of the Matter, University of Bologna, Bologna 40126, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Giro
authors.forename: Anna
authors.initials: A
authors.lastname: Bergia
authors.forename: Giampaolo
authors.initials: G
authors.lastname: Zuccheri
authors.forename: Hugo H J
authors.initials: HH
authors.lastname: Bink
authors.forename: Cornelis W A
authors.initials: CW
authors.lastname: Pleij
authors.forename: Bruno
authors.initials: B
authors.lastname: Samorì
mesh_terms: D007091:Image Processing, Computer-Assisted; D018625:Microscopy, Atomic Force / Q000379:methods*; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D017806:Tymovirus / Q000737:chemistry* / Q000235:genetics
chemical_list: D012367:RNA, Viral