title: Intercalators as molecular chaperones in DNA self-assembly.
abstract: DNA intercalation has found many diagnostic and therapeutic applications. Here, we propose the use of simple DNA intercalators, such as ethidium bromide, as tools to facilitate the error-free self-assembly of DNA nanostructures. We show that ethidium bromide can influence DNA self-assembly, decrease the formation of oligomeric side products, and cause libraries of multiple equilibrating structures to converge into a single product. Using a variety of 2D- and 3D-DNA systems, we demonstrate that intercalators present a powerful alternative for the adjustment of strand-end alignment, favor the formation of fully duplexed "closed" structures, and create an environment where the smallest, most stable structure is formed. A new 3D-DNA motif, the ninja star, was self-assembled in quantitative yield with this method. Moreover, ethidium bromide can be readily removed using isoamyl alcohol extractions combined with intercalator-specific spin columns, thereby yielding the desired ready-to-use DNA structure.
authors.affiliation: Department of Chemistry and Center for Self-Assembled Chemical Structures (CSACS), McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 0B8, Canada.
authors.forename: Andrea A
authors.initials: AA
authors.lastname: Greschner
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Bujold
authors.forename: Hanadi F
authors.initials: HF
authors.lastname: Sleiman
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004996:Ethidium / Q000737:chemistry*; D007364:Intercalating Agents / Q000737:chemistry*; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation
chemical_list: D007364:Intercalating Agents; D004247:DNA; D004996:Ethidium