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Rational Design of DNA Nanoarchitectures Udo Feldkamp* and Christof M

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Rational Design of DNA Nanoarchitectures Udo Feldkamp* and Christof M Reviews U. Feldkamp and C. M. Niemeyer DOI: 10.1002/anie.200502358 Nanoscience Rational Design of DNA Nanoarchitectures Udo Feldkamp* and Christof M. Niemeyer* Keywords: DNA · materials science · nanostructures · self-assembly · supramolecular chemistry Angewandte Chemie 1856 www.angewandte.org 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Angew. Chem. Int. Ed. 2006, 45, 1856 – 1876 Angewandte DNANanoarchitectures Chemie DNA has many physical and chemical properties that make it a From the Contents powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other 1. Introduction 1857 secondary structures through predictable nucleotide-sequence- 2. General Considerations of DNA- directed hybridization allows for the design of programmable Sequence Design 1858 structural motifs which can self-assemble to form large supra- molecular arrays, scaffolds, and even mechanical and logical 3. One-Dimensional DNA Strands for nanodevices. Despite the large variety of structural motifs used Assembly and Immobilization of Non- Nucleic Acid Compounds 1859 as building blocks in the programmed assembly of supra- molecular DNA nanoarchitectures, the various modules share 4. Design and Assembly of DNA Motifs 1860 underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This 5. Three-Dimensional Structures from DNA 1866 Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design 6. Applications of DNA Nanoarchitectures 1868 point of view. 7. Conclusions and Perspectives 1872 1. Introduction combination of distinct ssDNA and dsDNA elements within an artificial DNA motif allows structural building blocks to be Biomolecules, such as proteins and nucleic acids, possess designed with tailored flexibility and rigidity. As we will perfect binding properties which have been optimized over describe in this Review, the rigidity of artificial DNA motifs billions of years of evolution. Hence, biomolecules are can even exceed that of dsDNA. currently intensively investigated for their use as building An additional advantage of using DNA as a construction blocks and structure-directing components in the so-called material is its relatively high physicochemical stability, which “bottom-up” approach to generate materials and devices with is much higher than that of proteins. Hence, nanostructured precise control at the nanometer length scale. Nucleic acids materials which are constructed from DNA can be synthe- have preferentially been used in the self-assembly of func- sized, processed, and stored under a broad range of environ- tional nanomaterials since they are more readily available by mental conditions without the necessity of special precautions synthetic chemical means and are more convenient to handle to avoid decomposition of this biological material. Moreover, than proteins.[1–4] it is particularly noteworthy that nature provides us with a DNA is a particularly promising candidate to serve as a variety of highly specific enzymes which allow the processing construction material in nanosciences. Despite its simplicity, of DNA materials with atomic precision and accuracy at the the outstanding specificity of the A-T and G-C Watson–Crick ngström level. For example, the backbone of DNA mole- hydrogen-bonding interaction allows the convenient pro- cules produced by either chemical or biological processes can gramming of artificial DNA receptor moieties through the be cleaved specifically at a known site by restriction simple four-letter alphabet. The power of DNA as a endonucleases, thereby opening up the possibility to produce molecular tool is enhanced by our ability to synthesize monodisperse solutions containing DNA molecules of pre- virtually any DNA sequence by automated methods,[5] and to cisely known size and chemical composition. No other amplify any DNA sequence from microscopic to macroscopic (polymeric) material offers these advantages, which are quantities by the polymerase chain reaction (PCR).[6] ideal for molecular constructions in the range of about Another very attractive feature of DNA is its memory of 5 nanometers up to the micrometer scale. These advantages chain direction. Although a DNA double helix is actually a have already been utilized in the extensive application of flexible polymer, as impressively demonstrated by the very DNA for rational constructions on the nanometer length compact shape of chromosomes, this flexibility is negligible scale,[1] and recent advances have demonstrated its applic- for short double strands. The persistence length, that is, the length up to which polymers can be considered essentially rigid and straight, is about 50 nm, which corresponds to 150 base pairs in the double helix.[7] Below this size, double- [*] Dr. U. Feldkamp, Prof. Dr. C. M. Niemeyer stranded DNA (dsDNA) behaves as a rather rigid polymer, Fachbereich Chemie and can, therefore, be used as a rigid spacer between two Biologisch-Chemische Mikrostrukturtechnik Universität Dortmund tethered functional molecular components at the two ends. Otto-Hahn Strasse 6, 44227 Dortmund (Germany) On the other hand, single-stranded DNA (ssDNA) is very Fax : (+49)231-755-7082 flexible and is, therefore, capable of forming tight loop E-mail: [email protected] structures or even directional turns of about 1808. Hence, the [email protected] Angew. Chem. Int. Ed. 2006, 45, 1856 – 1876 2006 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 1857 Reviews U. Feldkamp and C. M. Niemeyer ability for fabricating arrays of colloidal components, pro- sional elements. This Review is intended to summarize the teins, and even nanomechanical devices.[1, 3,4,8–11] construction principles so far applied to the rational fabrica- Further developments in this field, however, require tion of DNA nanoarchitectures. General construction princi- elaborate tools for tailoring sequences of the DNA nucleo- ples will be discussed as well as the underlying rules for bases of short synthetic oligonucleotides which encode the designing the base sequences of the building blocks. Finally, primary structure of supramolecular DNA architecture in an overview will be presented on the current state-of-the-art one, two, and three dimensions. This primary structure and conclusions drawn on future perspectives of DNA-based determines the ability of an oligonucleotide to hybridize nanomaterials. with other (partially) complementary oligomers, thereby allowing the formation of distinct motifs, such as tiles which comprise DNA helices, junctions, crossovers, and loops 2. General Considerations of DNA-Sequence Design (Figure 1). These motifs are then used as building blocks which can self-assemble by hybridization of pendent single The design and construction process of DNA-based strands (sticky ends) to form larger, two- and three-dimen- nanoarchitecture comprises several major steps. Firstly, any requirements to be satisfied by the envisioned construct and its potential application should be identified. For example, it may eventually be wished to use the scaffold for the directed attachment of non-nucleic acid components, such as nano- particles or proteins. In this case it needs to be determined whether the DNA scaffold should be rigid or flexible. The next question might concern whether the construct is to be used as a static scaffold or as a dynamic mechanical device that undergoes reversible or irreversible transitions between distinct and predictable conformations. Depending on the demands, the individual building blocks should then either be comprised of just rigid scaffolding elements or else may contain distinct single-stranded regions, often termed “toe holds”, which can hybridize to effector oligomers or act as dynamic elements for strand replacement and, thereby, induce large conformational changes of the motif. It must also be determined whether symmetric or non- symmetric patterns are to be produced by the assembly of the array, what kind of periodicity is desired, in how many dimensions the scaffold should grow, and whether this growth Figure 1. The well-known DNA double helix (topleft) is comprisedof two antiparallel strands of oligonucleotides which are bound together is to be terminated or potentially infinite. by specific Watson–Crick hydrogen bonds, represented as the ladder- Depending on these requirements, suitable DNA motifs like structure (topright). The choice of suitable DNA sequences allows comprised of junctions, loops, crossovers, and single-stranded the generation of complex motifs which contain a) double-helical binding sites (“sticky ends”) need to be selected as building regions, b) sticky ends, c) bulge loops, d) hairpin loops, e) junctions, blocks for the desired scaffold architecture. These motifs may and f) crossovers (see schematic representation at the bottom). Note also contain additional chemical groups which can enable the that three-dimensional information, such as helices, grooves, and attachment of non-nucleic acid components, such as proteins angles between helices, are omitted in this schematic representation. The arrowheads indicate the 5’!3’ direction of individual oligonucleo- and nanoparticles. As discussed below, biotin-modified loop tides. elements and aptamer sequences have so far been successfully Udo Feldkamp is a research assistant at the Christof M. Niemeyer has been Professor of University of Dortmund (Germany). He
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