Abstract
Fluorophore-conjugated, sequence specific DNA binding small synthetic molecules can visualize sequence information on a large DNA molecule. In this study, we synthesized fluorophore-linked pyrrole polyamide to visualize adenine and thymine base pairs on fluorescent microscope. A fluorescent image of the stained DNA molecule generates an intensity profile based on A/T frequency, revealing a characteristic sequence composition pattern of DNA. Computer-aided comparison of the intensity patterns with the genome sequence allowed us to distinguish the DNA sequence on a visualized DNA molecule from intensity profile pattern candidates for a given genome. Moreover, TAMRA-polypyrrole practically offers robust advantages for single DNA molecule observation: no fluorophore-mediated photocleavage and no structural deformations 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 E. coli cells by aligning them to the genomic A/T frequency map based on TAMRA-polypyrrole-generated intensity profiles, as well as bacteriophage DNA and purified yeast chromosome.
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