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Dynamic Stabilization of DNA Assembly by Using Pyrrole-Imidazole Polyamide
Authors:Dr. Yan Shan Ang  Dr. Toshikazu Bando  Prof. Hiroshi Sugiyama  Dr. Lin-Yue Lanry Yung
Affiliation:1. Department of Chemical & Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585 Singapore;2. Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502 Japan;3. Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502 Japan

Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University Yoshida-Ushinomiyacho, Sakyo,-ku, Kyoto, 606-8501 Japan

Abstract:We used N-methylpyrrole (Py)-N-methylimidazole-(Im) polyamide as an exogenous agent to modulate the formation of DNA assemblies at specific double-stranded sequences. The concept was demonstrated on the hybridization chain reaction that forms linear DNA. Through a series of melting curve analyses, we demonstrated that the binding of Py−Im polyamide positively influenced both the HCR initiation and elongation steps. In particular, Py−Im polyamide was found to drastically stabilize the DNA duplex such that its thermal stability approached that of an equivalent hairpin structure. Also, the polyamide served as an anchor between hairpin pairs in the HCR assembly, thus improving the originally weak interstrand stability. We hope that these proof-of-concept results can inspire future use of Py−Im polyamide as a molecular tool to modulate the formation of DNA assemblies.
Keywords:DNA nanotechnology  DNA stabilization  hybridization  hybridization chain reaction  polyamides
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