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

ABSTRACT: 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.

SUBMITTER: Lee S

PROVIDER: S-EPMC6182132 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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

Lee Seonghyun S Kawamoto Yusuke Y Vaijayanthi Thangavel T Park Jihyun J Bae Jaeyoung J Kim-Ha Jeongsil J Sugiyama Hiroshi H Jo Kyubong K

Nucleic acids research 20181001 18

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 D ...[more]

PMID: 29931115

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Dataset Information

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

Publications

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

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