4.4 Article

Dynamic Stabilization of DNA Assembly by Using Pyrrole-Imidazole Polyamide

Journal

CHEMBIOCHEM
Volume 21, Issue 20, Pages 2912-2915

Publisher

WILEY-V C H VERLAG GMBH
DOI: 10.1002/cbic.202000245

Keywords

DNA nanotechnology; DNA stabilization; hybridization; hybridization chain reaction; polyamides

Funding

  1. Singapore Ministry of Education Academic Research Fund Tier 2 [MOE2019-T2-1-116]

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We usedN-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.

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