Structural analysis of long single-stranded RNA molecules with atomic force microscopy imaging

Jamie L. Gilmore, Aiko Yoshida, Katashi Deguchi, Suguru Asai, Hideki Aizaki, Masahiro Kumeta, Kiwamu Hyodo, Tetsuro Okuno, Takaji Wakita, Kunio Takeyasu

Research output: Chapter in Book/Report/Conference proceedingConference contribution


Characterization of the structure of long RNA molecules (>1 kb) is usually a time-consuming and tedious process. In this study, we have developed an imaging procedure for obtaining images of the extended secondary structures of long RNA molecules combined with automated MATLAB-based data processing algorithms for identification of the domain architecture of the molecules in these images. These algorithms include a molecule autoselection procedure based on height and area thresholding, a morphological thinning procedure to generate skeletons of the molecule in order to analyze the branched structure of the molecules, and a procedure to generate local volume profiles along the main chain of the molecule for identification of domains and prediction of the number of nucleotides comprising each domain. The single-molecule nature of this technique also allows for the identification of varying conformations of the molecule and assessment of the conformational flexibility of the identified domain organization.

Original languageEnglish
Title of host publication3rd International Multidisciplinary Microscopy and Microanalysis Congress (InterM) - Proceedings
EditorsZehra Banu Bahsi Oral, Ahmet Yavuz Oral
PublisherSpringer Science and Business Media, LLC
Number of pages7
ISBN (Print)9783319466002
Publication statusPublished - 2017
Externally publishedYes
Event3rd International Multidisciplinary Microscopy Congress, InterM2015 - Oludeniz, Turkey
Duration: Oct 19 2015Oct 23 2015

Publication series

NameSpringer Proceedings in Physics
ISSN (Print)0930-8989
ISSN (Electronic)1867-4941


Other3rd International Multidisciplinary Microscopy Congress, InterM2015

ASJC Scopus subject areas

  • Physics and Astronomy(all)


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