title: Triplex addressability as a basis for functional DNA nanostructures.
abstract: Here, we present the formation of a fully addressable DNA nanostructure that shows the potential to be exploited as, for example, an information storage device based on pH-driven triplex strand formation or nanoscale circuits based on electron transfer. The nanostructure is composed of two adjacent hexagonal unit cells (analogous to naphthalene) in which each of the eleven edges has a unique double-stranded DNA sequence, constructed using novel three-way oligonucleotides. This allows each ten base-pair side, just 3.4 nm in length, to be assigned a specific address according to its sequence. Such constructs are therefore an ideal precursor to a nonrepetitive two-dimensional grid on which the "addresses" are located at a precise and known position. Triplex recognition of these addresses could function as a simple yet efficient means of information storage and retrieval. Future applications that may be envisaged include nanoscale circuits as well as subnanometer precision in nanoparticle templating. Characterization of these precursor nanostructures and their reversible targeting by triplex strand formation is shown here using gel electrophoresis, atomic force microscopy, and fluorescence resonance energy transfer (FRET) measurements. The durability of the system to repeated cycling of pH switching is also confirmed by the FRET studies.
authors.affiliation: Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.
authors.forename: John
authors.initials: J
authors.lastname: Tumpane
authors.forename: Ravindra
authors.initials: R
authors.lastname: Kumar
authors.forename: Erik P
authors.initials: EP
authors.lastname: Lundberg
authors.forename: Peter
authors.initials: P
authors.lastname: Sandin
authors.forename: Nittaya
authors.initials: N
authors.lastname: Gale
authors.forename: Iris S
authors.initials: IS
authors.lastname: Nandhakumar
authors.forename: Bo
authors.initials: B
authors.lastname: Albinsson
authors.forename: Per
authors.initials: P
authors.lastname: Lincoln
authors.forename: L Marcus
authors.initials: LM
authors.lastname: Wilhelmsson
authors.forename: Tom
authors.initials: T
authors.lastname: Brown
authors.forename: Bengt
authors.initials: B
authors.lastname: Nordén
mesh_terms: D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry*; D009281:Naphthalenes / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D013053:Spectrophotometry
chemical_list: D009281:Naphthalenes; D009838:Oligodeoxyribonucleotides; C031721:naphthalene; D004247:DNA