TY - GEN
T1 - Structural analysis of long single-stranded RNA molecules with atomic force microscopy imaging
AU - Gilmore, Jamie L.
AU - Yoshida, Aiko
AU - Deguchi, Katashi
AU - Asai, Suguru
AU - Aizaki, Hideki
AU - Kumeta, Masahiro
AU - Hyodo, Kiwamu
AU - Okuno, Tetsuro
AU - Wakita, Takaji
AU - Takeyasu, Kunio
N1 - Funding Information:
This work has been supported by a Grant-in-Aid for Scientific Research on Innovative Areas “Molecular basis of host cell competency in virus infection” (#24115003) from MEXT Japan. We also thank Dr. James Hejna for access to the MATLAB software.
Publisher Copyright:
© Springer International Publishing AG 2017.
PY - 2017
Y1 - 2017
N2 - 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.
AB - 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.
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U2 - 10.1007/978-3-319-46601-9_1
DO - 10.1007/978-3-319-46601-9_1
M3 - Conference contribution
AN - SCOPUS:84996489231
SN - 9783319466002
T3 - Springer Proceedings in Physics
SP - 3
EP - 9
BT - 3rd International Multidisciplinary Microscopy and Microanalysis Congress (InterM) - Proceedings
A2 - Oral, Zehra Banu Bahsi
A2 - Oral, Ahmet Yavuz
PB - Springer Science and Business Media, LLC
T2 - 3rd International Multidisciplinary Microscopy Congress, InterM2015
Y2 - 19 October 2015 through 23 October 2015
ER -