Functional DNA origami nanoparticles (DNA-NPs) are used
as nanocarriers
in a variety of biomedical applications including targeted drug delivery
and vaccine development. DNA-NPs can be designed into a broad range
of nanoarchitectures in one, two, and three dimensions with high structural
fidelity. Moreover, the addressability of the DNA-NPs enables the
precise organization of functional moieties, which improves targeting,
actuation, and stability. DNA-NPs are usually functionalized via chemically
modified staple strands, which can be further conjugated with additional
polymers and proteins for the intended application. Although this
method of functionalization is extremely efficient to control the
stoichiometry and organization of functional moieties, fewer than
half of the permissible sites are accessible through staple modifications.
In addition, DNA-NP functionalization rapidly becomes expensive when
a high number of functionalizations such as fluorophores for tracking
and chemical modifications for stability that do not require spatially
precise organization are used. To facilitate the synthesis of functional
DNA-NPs, we propose a simple and robust strategy based on an asymmetric
polymerase chain reaction (aPCR) protocol that allows direct synthesis
of custom-length scaffolds that can be randomly modified and/or precisely
modified via sequence design. We demonstrated the potential of our
strategy by producing and characterizing heavily modified scaffold
strands with amine groups for dye functionalization, phosphorothioate
bonds for stability, and biotin for surface immobilization. We further
validated our sequence design approach for precise conjugation of
biomolecules by synthetizing scaffolds including binding loops and
aptamer sequences that can be used for direct hybridization of nucleic
acid tagged biomolecules or binding of protein targets.