title: Microarray-based in vitro evaluation of DNA oligomer libraries designed in silico.
abstract: 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.
authors.affiliation: Universität Dortmund, Fachbereich Informatik, LS 11 44221 Dortmund, Germany. udo.feldkamp@cs.uni-dortmund.de
authors.forename: Udo
authors.initials: U
authors.lastname: Feldkamp
authors.forename: Ron
authors.initials: R
authors.lastname: Wacker
authors.forename: Hendrik
authors.initials: H
authors.lastname: Schroeder
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Banzhaf
authors.forename: Christof M
authors.initials: CM
authors.lastname: Niemeyer
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D019992:Databases as Topic; D015723:Gene Library; D007091:Image Processing, Computer-Assisted; D008856:Microscopy, Fluorescence; D008954:Models, Biological; D036103:Nanotechnology / Q000379:methods*; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000032:analysis* / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D009838:Oligodeoxyribonucleotides