Complex DNA Nanostructure Assembly via Hybridization Chain Reaction


Laura Lanier


Laura Lanier, Harry Bermudez

Author Affiliation: 

Polymer Science and Engineering Department, University of Massachusetts Amherst


Complex DNA nanostructures were created with an isothermal self-assembly method called hybridization chain reaction (HCR). HCR is a supramolecular polymerization of DNA that proceeds as a cascade of strand displacement reactions. Two DNA monomers are kinetically trapped in hairpins until the addition of an initiator strand opens the hairpin of one monomer through a strand displacement reaction. The unhybridized end then opens the hairpin of the other monomer through a strand displacement reaction. This cascade of strand displacement reactions continues, producing a supramolecular DNA polymer. We have demonstrated that HCR produces supramolecular polymers of DNA through a living polymerization mechanism. Synthesizing DNA polymers by HCR yields supramolecular polymers with low dispersity whose molecular weight is controlled by the monomer to initiator stoichiometric ratio, consistent with a living polymerization mechanism. Additionally, HCR polymerization can be continued by the addition of further monomer, demonstrating its living nature by the absence of termination and chain transfer reactions. Identification of the living character of HCR presents new opportunities in macromolecular assembly of structural DNA nanotechnology. Utilizing the demonstrated living nature, complex nanostructures are created via HCR. Supramolecular star polymers are created by modifying a DNA star to initiate HCR from each arm. Asymmetric star polymers are created by independently controlling the growth of each arm. Bottlebrush structures are created by modifying the monomer to include an additional overhang that initiates a secondary HCR polymerization. The creation of these complex nanostructures is demonstrated by gel electrophoresis and atomic force microscopy. Independent control over bottlebrush mainchain and sidechain lengths allows for the easy creation of bottlebrushes with controlled aspect ratios, which has potential applications as a model bottlebrush system.