Gengo Kashiwazaki1,2, Anandhakumar Chandran1,2, Sefan Asamitsu1, Takashi Kawase3, Yusuke Kawamoto1, Yoshito Sawatani1, Kaori Hashiya1, Toshikazu Bando1, Hiroshi Sugiyama1,4
1Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
2these authors contributed equally to this work
3Department of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-Honmachi 36-1, Sakyo, Kyoto 606-8501, Japan
4Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto 606-8501, Japan
Tóm tắt
AbstractMany long pyrrole‐imidazole polyamides (PIPs) have been synthesized in the search for higher specificity, with the aim of realizing the great potential of such compounds in biological and clinical areas. Among several types of PIPs, we designed and synthesized hairpin and cyclic PIPs targeting identical sequences. Bind‐n‐Seq analysis revealed that both bound to the intended sequences. However, adenines in the data analyzed by the previously reported Bind‐n‐Seq method appeared to be significantly higher in the motif ratio than thymines, even though the PIPs were not expected to distinguish A from T. We therefore examined the experimental protocol and analysis pipeline in detail and developed a new method based on Bind‐n‐Seq motif identification with a reference sequence (Bind‐n‐Seq‐MR). High‐throughput sequence analysis of the PIP‐enriched DNA data by Bind‐n‐Seq‐MR presented A and T comparably. Surface plasmon resonance assays were performed to validate the new method.
