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

doi:10.1007/978-3-319-46601-9_1

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 proceeding › Conference contribution

Abstract

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 language	English
Title of host publication	3rd International Multidisciplinary Microscopy and Microanalysis Congress (InterM) - Proceedings
Editors	Zehra Banu Bahsi Oral, Ahmet Yavuz Oral
Publisher	Springer Science and Business Media, LLC
Pages	3-9
Number of pages	7
ISBN (Print)	9783319466002
DOIs	https://doi.org/10.1007/978-3-319-46601-9_1
Publication status	Published - 2017
Externally published	Yes
Event	3rd International Multidisciplinary Microscopy Congress, InterM2015 - Oludeniz, Turkey Duration: Oct 19 2015 → Oct 23 2015

Publication series

Name	Springer Proceedings in Physics
Volume	186
ISSN (Print)	0930-8989
ISSN (Electronic)	1867-4941

Other

Other	3rd International Multidisciplinary Microscopy Congress, InterM2015
Country	Turkey
City	Oludeniz
Period	10/19/15 → 10/23/15

ASJC Scopus subject areas

Physics and Astronomy(all)

Access to Document

10.1007/978-3-319-46601-9_1

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Cite this

Gilmore, J. L., Yoshida, A., Deguchi, K., Asai, S., Aizaki, H., Kumeta, M., Hyodo, K., Okuno, T., Wakita, T., & Takeyasu, K. (2017). Structural analysis of long single-stranded RNA molecules with atomic force microscopy imaging. In Z. B. B. Oral, & A. Y. Oral (Eds.), 3rd International Multidisciplinary Microscopy and Microanalysis Congress (InterM) - Proceedings (pp. 3-9). (Springer Proceedings in Physics; Vol. 186). Springer Science and Business Media, LLC. https://doi.org/10.1007/978-3-319-46601-9_1

Structural analysis of long single-stranded RNA molecules with atomic force microscopy imaging. / Gilmore, Jamie L.; Yoshida, Aiko; Deguchi, Katashi; Asai, Suguru; Aizaki, Hideki; Kumeta, Masahiro; Hyodo, Kiwamu; Okuno, Tetsuro; Wakita, Takaji; Takeyasu, Kunio.

3rd International Multidisciplinary Microscopy and Microanalysis Congress (InterM) - Proceedings. ed. / Zehra Banu Bahsi Oral; Ahmet Yavuz Oral. Springer Science and Business Media, LLC, 2017. p. 3-9 (Springer Proceedings in Physics; Vol. 186).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Gilmore, JL, Yoshida, A, Deguchi, K, Asai, S, Aizaki, H, Kumeta, M, Hyodo, K, Okuno, T, Wakita, T & Takeyasu, K 2017, Structural analysis of long single-stranded RNA molecules with atomic force microscopy imaging. in ZBB Oral & AY Oral (eds), 3rd International Multidisciplinary Microscopy and Microanalysis Congress (InterM) - Proceedings. Springer Proceedings in Physics, vol. 186, Springer Science and Business Media, LLC, pp. 3-9, 3rd International Multidisciplinary Microscopy Congress, InterM2015, Oludeniz, Turkey, 10/19/15. https://doi.org/10.1007/978-3-319-46601-9_1

Gilmore JL, Yoshida A, Deguchi K, Asai S, Aizaki H, Kumeta M et al. Structural analysis of long single-stranded RNA molecules with atomic force microscopy imaging. In Oral ZBB, Oral AY, editors, 3rd International Multidisciplinary Microscopy and Microanalysis Congress (InterM) - Proceedings. Springer Science and Business Media, LLC. 2017. p. 3-9. (Springer Proceedings in Physics). https://doi.org/10.1007/978-3-319-46601-9_1

Gilmore, Jamie L. ; Yoshida, Aiko ; Deguchi, Katashi ; Asai, Suguru ; Aizaki, Hideki ; Kumeta, Masahiro ; Hyodo, Kiwamu ; Okuno, Tetsuro ; Wakita, Takaji ; Takeyasu, Kunio. / Structural analysis of long single-stranded RNA molecules with atomic force microscopy imaging. 3rd International Multidisciplinary Microscopy and Microanalysis Congress (InterM) - Proceedings. editor / Zehra Banu Bahsi Oral ; Ahmet Yavuz Oral. Springer Science and Business Media, LLC, 2017. pp. 3-9 (Springer Proceedings in Physics).

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