title: DNA Three-Way Junctions Stabilized by Hydrophobic Interactions for Creation of Functional Nanostructures.
abstract: The construction of nanomaterials from oligonucleotides by modular assembly invariably requires the use of branched nucleic acid architectures such as three- and four-way junctions (3WJ and 4WJ). We describe the stabilization of DNA 3WJ by using non-nucleotide lipophilic spacers to create a hydrophobic pocket within the junction space. Stabilization of nucleic acid junctions is of particular importance when constructing nanostructures in the "ultra-nano" size range (<20 nm) with shorter double-stranded regions. UV thermal melting studies show that lipophilic spacers strategically placed within the junction space significantly increased thermal stability. For a 3WJ with eight base pair arms, thermal stability was increased from 30.5 °C for the unmodified junction to a maximum stability of 55.0 °C. The stability of the junction can be modulated within this temperature range by using the appropriate combinations of spacers.
authors.affiliation: Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599 (USA).
authors.forename: Brian M
authors.initials: BM
authors.lastname: Laing
authors.affiliation: Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599 (USA). arjay@med.unc.edu.
authors.forename: Rudolph L
authors.initials: RL
authors.lastname: Juliano
mesh_terms: D004247:DNA / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008055:Lipids / Q000737:chemistry*; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000737:chemistry; D013696:Temperature
chemical_list: D008055:Lipids; D009841:Oligonucleotides; D004247:DNA
keywords: DNA junctions; DNA nanotechnology; lipid oligonucleotide conjugates; nanomedicine