DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.

DNA hat viele physikalische und chemische Eigenschaften, die sie zu einem leistungsfähigen Material für molekulare Konstruktionen im Nanometer‐Maßstab machen. Insbesondere ihre Fähigkeit, Duplexe und andere Sekundärstrukturen durch vorhersagbare, Nucleotidsequenz‐gesteuerte Hybridisierung zu bilden, ermöglicht den Entwurf programmierbarer Strukturmotive, die wiederum zu großen supramolekularen Anordnungen, Gerüsten und sogar zu mechanischen und logischen Funktionseinheiten zusammengefügt werden können. Trotz der breiten Vielfalt solcher Strukturmotive, die als Bausteine beim programmierten Zusammenbau von supramolekularen DNA‐Nanoarchitekturen verwendet werden, sind den unterschiedlichen Modulen einige grundlegende Prinzipien des Entwurfs ihrer hierarchischen Konfiguration und der eingesetzten Nucleotidsequenzen gemein. Dieser Aufsatz gibt einen Überblick über dieses faszinierende und schnell wachsende Forschungsgebiet unter besonderer Berücksichtigung strukturchemischer Aspekte.

Since its pioneering description in 1982 by Seeman, [1] DNAbased nanotechnology has undergone a rapid development, such that the self-assembly of synthetic oligonucleotides is nowadays almost routinely applied for the fabrication of superlattices with nanometer-scaled features.[2] Despite these advances, the characterization of the self-assembled nanostructures is still limited to only a few physicochemical methodologies, mainly, gel electrophoresis, atomic force microscopy (AFM) or, more recently, cryo-transmission electron microscopy (cryo-TEM).[2] All these methods are usually destructive and allow only for end-point analysis of the final product, thereby precluding the possibility to detect and optimize the assembly process through manipulation of the same sample. To overcome these obstacles, we report herein a novel method based on Förster resonance energy transfer (FRET) spectroscopy to monitor in real time and with high throughput the self-assembly of DNA tiles and nanoarrays.[3] As demonstrated for several DNA nanostructures of different sequence design, this approach allows the complete thermodynamic characterization of the assembly process.As schematically illustrated in Figure 1 a, we chose a set of nine oligomers which self-assemble into a cross-shaped DNA motif, a 4 4 tile composed of four four-arm DNA branched junctions.[4] Five individual tiles, denoted A, A 2 , B, B 2 , and B 3( Figure S1 a-e in the Supporting Information) [5] were designed bearing distinct differences in oligonucleotide composition. Tiles A 2 and B 3 were designed such that they associate specifically with each other to form a two-dimensional nanoscaled lattice (A 2 B 3 ) with an internal periodicity of approximately 19.3 nm (Figure 2 a, and Figure S3 in the Supporting Information).To enable the in situ monitoring of the self-assembly process by FRET spectroscopy, the two oligomers of the "east" arm of the tile (NE and SE) were labeled at terminal positions with fluorescein (Fsc) as the donor and tetramethylrhodamine (TAMRA) as the acceptor. The distance between the two fluorophores in the final superstructures (ca. 4-5 nm) and their relative positioning within all the various constructs allowed us to analyze the superstructures formation and their thermodynamic properties.[6] The selfassembly of an equimolar mixture comprising all the oligomers necessary for a distinct superstructure (0.4 mm each) was then monitored online using a real-time PCR thermocycler.[5]The FRET efficiency was measured as the decrease of the Fsc donor emission owing to energy transfer to the TAMRA acceptor, [7] and its variation with temperature was monitored in the range between 29 and 80 8C (both heating and cooling rates were 0.1 8C min À1 ). A typical example of the obtained assembly/disassembly curves is shown in Figure 1 b. The superimposition of the heating and cooling profiles, as well as the rapid variation of the assembled fraction (q) in a relatively narrow temperature range around T m , revealed reversibility and cooperativity of superstructur...

We report on the microarray-based in vitro evaluation of two libraries of DNA oligonucleotide sequences, designed in silico for applications in supramolecular self-assembly, such as DNA computing and DNA-based nanosciences. In this first study which is devoted to the comparison of sequence motif properties theoretically predicted with their performance in real-life, the DNA-directed immobilization (DDI) of proteins was used as an example of DNA-based self-assembly. Since DDI technologies, DNA computing, and DNA nanoconstruction essentially depend on similar prereguisites, in particular, large and uniform hybridization efficiencies combined with low nonspecific cross-reactivity between individual sequences, we anticipate that the microarray approach demonstrated here will enable rapid evaluation of other DNA sequence libraries.

Abstract. In DNA Computing and DNA nanotechnology the design of proper DNA sequences turned out to be an elementary problem [1−9]. We here present a software program for the construction of sets ("pools") of DNA sequences. The program can create DNA sequences to meet logical and physical parameters such as uniqueness, melting temperature and GC ratio as required by the user. It can create sequences de novo, complete sequences with gaps and allows import and recycling of sequences that are still in use. The program always creates sequences that are − in terms of uniqueness, GC ratio and melting temperature − "compatible" to those already in the pool, no matter whether those were added manually or created or completed by the program itself. The software comes with a GUI and a Sequence Wizard. In vitro tests of the program's output were done by generating a set of oligomers designed for self−assembly. The software is available for download under