title: Flexibility of C3h -Symmetrical Linkers in Tris-oligonucleotide-Based Tetrahedral Scaffolds.
abstract: Flexibility of tris-oligonucleotides is determined by the length of their connecting hydrocarbon chains. Tris-oligonucleotides are branched DNA building blocks with three oligonucleotide arms attached to a C3h -symmetrical linker core at these chains. Four tris-oligonucleotides hybridise into a tetrahedral nanocage by sequence-determined self-assembly. The influence of methylene, ethylene and propylene chains was studied by synthesising sets of tris-oligonucleotides and analysing the relative stability of the hybridisation products against digestion by mung bean nuclease by using gel electrophoresis. Linkers with ethylene chains showed sufficient flexibility, whereas methylene-chain linkers were too rigid. Tris-oligonucleotides based on the latter still formed tetrahedral scaffolds in intermixing experiments with linkers of higher flexibility. Thus, a new generation of versatile isocyanurate-based linkers was established.
authors.affiliation: Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany. christos.panagiotidis@ruhr-uni-bochum.de.
authors.forename: Christos
authors.initials: C
authors.lastname: Panagiotidis
authors.affiliation: LIMES Institute, Chemical Biology and Medicinal Chemistry Unit, Universität Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Kath-Schorr
authors.affiliation: Lehrstuhl für Organische Chemie I, Bioorganische Chemie, Ruhr-Universität Bochum, Universitätsstrasse 150, 44780, Bochum, Germany.
authors.forename: Günter
authors.initials: G
authors.lastname: von Kiedrowski
mesh_terms: D004591:Electrophoresis, Polyacrylamide Gel; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D009943:Organophosphorus Compounds / Q000737:chemistry; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014227:Triazines / Q000737:chemistry
chemical_list: D009841:Oligonucleotides; D009943:Organophosphorus Compounds; D014227:Triazines; C509473:isocyanuric acid; C434331:phosphoramidite
keywords: DNA structures; isocyanurate; nanotechnology; self-assembly; tris-oligonucleotide