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DNA Three‐Way Junctions Stabilized by Hydrophobic Interactions for Creation of Functional Nanostructures
Author(s) -
Laing Brian M.,
Juliano Rudolph L.
Publication year - 2015
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/cbic.201500034
Subject(s) - nucleic acid , thermal stability , oligonucleotide , dna , nucleotide , nanomaterials , nanotechnology , nanostructure , base pair , materials science , chemistry , biophysics , biochemistry , organic chemistry , biology , gene
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.