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.

Small-Molecule Binding Aptamers: Selection Strategies, Characterization, and Applications

“…The aptamers for each monosaccharide had high specificity as a result of the counter-selections that were performed against the receptor alone and the other sugars with the receptor. Furthermore, counter-selections were run against a mixture of steroids to remove any hydrophobic three-way junctions which are known to dominate selection experiments (Kato et al, 2000 ; Laing and Juliano, 2015 ). These methods were found to be successful in the selection of aptamers for monosaccharides that lack suitable epitopes for aptamer binding.…”

Metal-Mediated Coordination Cages: Endohedral Functionalization and Oligonucleotide Embedding

“…As a reference a second sequence was synthesized, where the ligand was replaced by a single thymine nucleobase, which should form T-T mismatches at the central position in the HJ, simulating a disorder within the structure, as it is caused by the incorporated ligands. This behavior can be explained by a stacking of the polyaromatic ligands within the HJ structure, comparable to the effect described in a three-way junction by Laing et al [179] Either the ligands intercalate into the nearby double helices or more likely, they do interact with each other, forming an aggregate. This aggregation is indicated by a significant bathochromic shift, observable for the ligand-specific UV-vis band, caused by the assembly of HJ and is known from molecules forming so called J-aggregates or excimers.…”

Supramolecular DNA Three-Way Junction Motifs With a Bridging Metal Center

“…These stabilization effects can be explained by the additional stacking interaction with the base pairs facing the central cavity. Stabilization based on the hydrophobic effect was also demonstrated by the incorporation of lipophilic spacers or side chains into three strands forming 3WJs (Laing and Juliano, 2015).…”