CANADA: designing nucleic acid sequences for nanobiotechnology applications.

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.

Design and evaluation of single-stranded DNA carrier molecules for DNA-directed assembly.

Due to the exceptional molecular recognition properties of nucleic acids, the computational design of DNA sequence motifs is of paramount interest for a wide variety of applications, ranging from DNA-based nanotechnology and DNA computing to the broad field of DNA microarray technologies. These applications rely on the specificity of Watson-Crick base-pairing, and thus, are highly sensitive to non-specific interactions and the formation of any undesired secondary structures, which contradict an efficient intermolecular hybridization. Here we report on the in silico design and in vitro evaluation of single-stranded DNA (ssDNA) carrier strands for the directional DNA-based positioning of streptavidin (STV) conjugates covalently tagged with short ssDNA oligonucleotides.

Rational design of DNA nanoarchitectures.

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.

Microarray-based in vitro evaluation of DNA oligomer libraries designed in silico.

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.