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TAMRA-polypyrrole for A/T sequence visualization on DNA molecules
Lee, Seonghyun,Kawamoto, Yusuke,Vaijayanthi, Thangavel,Park, Jihyun,Bae, Jaeyoung,Kim-Ha, Jeongsil,Sugiyama, Hiroshi,Jo, Kyubong Oxford University Press 2018 Nucleic acids research Vol.46 No.18
<P><B>Abstract</B></P><P>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 <I>Escherichia coli</I> 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.</P>