Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures

Production
of small discrete DNA nanostructures containing covalent junctions
requires reliable methods for the synthesis and assembly of branched
oligodeoxynucleotide (ODN) conjugates. This study reports an approach
for self-assembly of hard-to-obtain primitive discrete DNA nanostructures“nanoethylenes”,
dimers formed by double-stranded oligonucleotides using V-shaped furcate
blocks. We scaled up the synthesis of V-shaped oligonucleotide conjugates
using pentaerythritol-based diazide and alkyne-modified oligonucleotides
using copper­(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and optimized
the conditions for “nanoethylene” formation. Next, we
designed nanoethylene-based “nanomonomers” containing
pendant adapters. They demonstrated smooth and high-yield spontaneous
conversion into the smallest cyclic product, DNA tetragon aka “nano-methylcyclobutane”. Formation of
DNA nanostructures was confirmed using native polyacrylamide gel electrophoresis
(PAGE) and atomic force microscopy (AFM) and additionally studied
by molecular modeling. The proposed facile approach to discrete DNA
nanostructures using precise adapter-directed association expands
the toolkit for the realm of DNA origami.