Identifying DNA methylation in a nanochannel

Xiaoyin Sun; Takao Yasui; Takeshi Yanagida; Noritada Kaji; Sakon Rahong; Masaki Kanai; Kazuki Nagashima; Tomoji Kawai; Yoshinobu Baba

doi:10.1080/14686996.2016.1223516

Identifying DNA methylation in a nanochannel

Sci Technol Adv Mater. 2016 Oct 11;17(1):644-649. doi: 10.1080/14686996.2016.1223516. eCollection 2016.

Authors

Xiaoyin Sun¹, Takao Yasui², Takeshi Yanagida³, Noritada Kaji¹, Sakon Rahong¹, Masaki Kanai⁴, Kazuki Nagashima⁴, Tomoji Kawai⁵, Yoshinobu Baba⁶

Affiliations

¹ Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Nagoya, Japan; ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Nagoya, Japan.
² Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Nagoya, Japan; ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Nagoya, Japan; Japan Science and Technology Agency (JST), PRESTO, Saitama, Japan.
³ Institute of Materials Chemistry and Engineering, Kyushu University, Fukuoka, Japan; Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan.
⁴ Institute of Materials Chemistry and Engineering, Kyushu University , Fukuoka , Japan.
⁵ Institute of Scientific and Industrial Research, Osaka University , Osaka , Japan.
⁶ Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, Nagoya, Japan; ImPACT Research Center for Advanced Nanobiodevices, Nagoya University, Nagoya, Japan; Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Japan.

Abstract

DNA methylation is a stable epigenetic modification, which is well known to be involved in gene expression regulation. In general, however, analyzing DNA methylation requires rather time consuming processes (24-96 h) via DNA replication and protein modification. Here we demonstrate a methodology to analyze DNA methylation at a single DNA molecule level without any protein modifications by measuring the contracted length and relaxation time of DNA within a nanochannel. Our methodology is based on the fact that methylation makes DNA molecules stiffer, resulting in a longer contracted length and a longer relaxation time (a slower contraction rate). The present methodology offers a promising way to identify DNA methylation without any protein modification at a single DNA molecule level within 2 h.

Keywords: 102 Porous / Nanoporous / Nanostructured materials; 30 Bio-inspired and biomedical materials; DNA contraction; DNA methylation; nanochannel; single DNA molecule.