Rational Design of DNA Nanoarchitectures Feldkamp, Udo; Niemeyer, Christof M.
Angewandte Chemie (International ed.),
March 13, 2006, Letnik:
45, Številka:
12
Journal Article
Recenzirano
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.
In the past 20 years, DNA has been established as a powerful material for molecular constructions at the nanometer scale. The ability to design building blocks from DNA containing well‐defined secondary structure motifs (a–f, in the scheme) allows the assembly of large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices.
Tiles and arrays: The self‐assembly of DNA nanostructures can be monitored in real time and with high throughput by FRET spectroscopy. A van't Hoff analysis of the fluorescence data allows for a ...complete thermodynamic characterization of the tile formation as well as array formation (see picture).
The design of nucleic acid sequences for a highly specific and efficient hybridization is a crucial step in DNA computing and DNA-based nanotechnology applications. The CANADA package contains ...software tools for designing DNA sequences that meet these and other requirements, as well as for analyzing and handling sequences. CANADA is freely available, including a detailed manual and example input files, at http://ls11-www.cs.uni-dortmund.de/molcomp/downloads.
DNA branches out: Recent advances in the assembly of dendritic DNA structures enable applications in biosensing of pathogens and the generation of novel pads of DNA hydrogel biomaterials (see scheme, ...left). These pads are immersed in a cell extract containing RNA polymerase (red), ribosomes (yellow), and other components for in vitro protein biosynthesis, where they can be used as templates for cell‐free protein production.
Rational Engineering of Dynamic DNA Systems Feldkamp, Udo; Niemeyer, Christof M
Angewandte Chemie (International ed.),
May 13, 2008, Letnik:
47, Številka:
21
Journal Article
Recenzirano
Opening time: A method for the systematic and automatable design of DNA hybridization networks was recently introduced, which was based on the catalytic opening of metastable hairpin loops (see ...scheme). This technique has various applications in nanobiotechnology, such as the stepwise self‐assembly of DNA scaffolds and the engineering of dynamic DNA devices.
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.
Software Tools for DNA Sequence Design Feldkamp, Udo; Rauhe, Hilmar; Banzhaf, Wolfgang
Genetic programming and evolvable machines,
06/2003, Letnik:
4, Številka:
2
Journal Article
Recenzirano
The design of DNA sequences is a key problem for implementing molecular self-assembly with nucleic acid molecules. These molecules must meet several physical, chemical and logical requirements, ...mainly to avoid mishybridization. Since manual selection of proper sequences is too time-consuming for more than a handful of molecules, the aid of computer programs is advisable. In this paper two software tools for designing DNA sequences are presented, the DNASequenceGenerator and the DNASequenceCompiler. Both employ an approach of sequence dissimilarity based on the uniqueness of overlapping subsequences and a graph based algorithm for sequence generation. Other sequence properties like melting temperature or forbidden subsequences are also regarded, but not secondary structure errors or equilibrium chemistry. Fields of application are DNA computing and DNA-based nanotechnology. In the second part of this paper, sequences generated with the DNASequenceGenerator are compared to those from several publications of other groups, an example application for the DNASequenceCompiler is presented, and the advantages and disadvantages of the presented approach are discussed.
Schleife auf: Vor kurzem wurde eine Methode zum systematischen und automatisierbaren Entwurf von DNA‐Hybridisierungsnetzwerken vorgestellt, die auf dem katalytischen Öffnen von metastabilen ...Haarnadelschleifen basiert (siehe Schema). Diese Technik ermöglicht sehr unterschiedliche Anwendungen in der Nanobiotechnologie, etwa die schrittweise Selbstorganisation von DNA‐Gerüsten oder die Konstruktion dynamischer DNA‐Funktionseinheiten.
Verzweigte DNA: Fortschritte beim Aufbau dendritischer DNA‐Strukturen ermöglichen Anwendungen zum Nachweis von Pathogenen sowie die Herstellung von Plättchen aus DNA‐Hydrogel‐Biomaterialien (links im ...Schema), die als Matrize für die Proteinproduktion in einem Zellextrakt fungieren, der RNA‐Polymerase (rot), Ribosomen (gelb) und andere Komponenten enthält (rechts).
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