Udo Feldkamp

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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(More)
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(More)
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(More)
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,(More)
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(More)
Various approaches to the self-assembly of molecules have been introduced already 2), 3), 4), 5), 6), . A step further toward flexible design and construction of precisely defined molecules are approaches to programmable self-assembly . In order to allow arbitrary programming, a sufficient solution of the negative design problem 5), 9) is needed. We present(More)
An approach based on programmable self-assembly of DNA oligonucleotides was used to create digital DNA molecules representing binary datastructures which are equivalent to those used in computers. Utilizing plasmids as a kind of computer memory, the digital molecules could be isolated, amplified and read out using common genetic techniques. Programmability(More)
In this study the advantages of statistical gene selection are combined with the power of Genetic Programming (GP) to build classifiers for assigning gene expression microarray data samples to categories characteristic of certain cell states. To that end we implemented different statistical measures in a program called GENEACTIVATOR and tested their(More)