TAMRA-polypyrrole for A/T sequence visualization on DNA molecules

조회수 : 432 등록일 : 2018.12.05 00:00

Lee, S (Lee, Seonghyun) ; Jo, K (Jo, Kyubong) 2018.10.12

TAMRA-polypyrrole for A/T sequence visualization on DNA molecules

Lee, S (Lee, Seonghyun)1,2 ] Kawamoto, Y (Kawamoto, Yusuke)3 ] Vaijayanthi, T (Vaijayanthi, Thangavel)3 ] Park, J (Park, Jihyun)1,2 ] Bae, J (Bae, Jaeyoung)1,2 ] Kim-Ha, J (Kim-Ha, Jeongsil)4 ] Sugiyama, H (Sugiyama, Hiroshi)3 ] Jo, K (Jo, Kyubong)1,2 ]

[ 1 ] Sogang Univ, Dept Chem, Seoul 04107, South Korea
[ 2 ] Sogang Univ, Program Integrated Biotechnol, Seoul 04107, South Korea
[ 3 ] Kyoto Univ, Grad Sch Sci, Dept Chem, Sakyo Ku, Kyoto 6068502, Japan
[ 4 ] Sejong Univ, Dept Integrat Biosci & Biotechnol, Coll Life Sci, Seoul 05006, South Korea

Fluorophore-linked, sequence-specific DNA binding reagents can visualize sequence information on a large DNA molecule. In this paper, we synthesized newly designed TAMRA-linked polypyrrole to visualize adenine and thymine base pairs. A fluorescent image of the stained DNA molecule generates an intensity profile based on A/T frequency, revealing a characteristic sequence composition pattern. Computer-aided comparison of this intensity pattern with the genome sequence allowed us to determine the DNA sequence on a visualized DNA molecule from possible intensity profile pattern candidates for a given genome. Moreover, TAMRA-polypyrrole offers robust advantages for single DNA molecule detection: no fluorophore-mediated photocleavage and no structural deformation, since it exhibits a sequence-specific pattern alone without the use of intercalating dyes such as YOYO-1. Accordingly, we were able to identify genomic DNA fragments from Escherichia coli cells by aligning them to the genomic A/T frequency map based on TAMRA-polypyrrole-generated intensity profiles. Furthermore, we showed band and interband patterns of polytene chromosomal DNA stained with TAMRA-polypyrrole because it prefers to bind AT base pairs.

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