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Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA
Author(s) -
Giro Andrea,
Bergia Anna,
Zuccheri Giampaolo,
Bink Hugo H.J.,
Pleij Cornelis W.A.,
Samorì Bruno
Publication year - 2004
Publication title -
microscopy research and technique
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.536
H-Index - 118
eISSN - 1097-0029
pISSN - 1059-910X
DOI - 10.1002/jemt.20123
Subject(s) - rna , molecule , turnip yellow mosaic virus , protein secondary structure , chemistry , population , crystallography , biophysics , atomic force microscopy , nucleic acid secondary structure , globular protein , nanotechnology , materials science , biology , biochemistry , organic chemistry , demography , sociology , gene
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. Microsc. Res. Tech. 65:235–245, 2004. © 2005 Wiley‐Liss, Inc.