Development of a Novel Photochemical Detection Technique for the Analysis of Polyamide-Binding Sites

  • Abhijit Saha
Part of the Springer Theses book series (Springer Theses)


We demonstrated sequence-specific electron injection using pyrene-conjugated pyrrole–imidazole polyamide (PIP) on 5-bromouracil (BrU)-substituted DNA. BrU is a good electron acceptor and is able to trap an electron from pyrene-conjugated polyamides after irradiation at 365 nm. This results in strand cleavage of the DNA by generating uracil-5-yl radical from BrU after eliminating the bromide anion. Using this exciting photochemical tool, we have analyzed the binding affinity, specificity, and binding orientation of four pyrene PIPs (1–4) using two long BrU-substituted DNAs (298 and 381 bp). The electron injection sites of 1–2 confirm very low sequence specificity, whereas 3, 4 exhibited high sequence specificity; moreover, electron injection by 2 also confirms its preference for reverse binding site. The binding affinity was further validated by SPR. Thus, these results suggest that it can be a useful tool for detecting binding sites of small molecules.


Pyrene polyamide Strand cleavage Intermolecular electron transfer BrU-substituted DNA Binding affinity 


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© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.Institute CurieOrsayFrance

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