Design and Characterization of Compact, Programmable,
Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable
for Biomedical Applications
posted on 2024-01-25, 20:06authored byRoss Brumett, Leyla Danai, Abigail Coffman, Yasmine Radwan, Megan Teter, Hannah Hayth, Erwin Doe, Katelynn Pranger, Sable Thornburgh, Allison Dittmer, Zhihai Li, Tae Jin Kim, Kirill A. Afonin, Emil F. Khisamutdinov
We
report a thorough investigation of the role of single-stranded
thymidine (ssT) linkers in the stability and flexibility of minimal,
multistranded DNA nanostructures. We systematically explore the impact
of varying the number of ssTs in three-way junction motifs (3WJs)
on their formation and properties. Through various UV melting experiments
and molecular dynamics simulations, we demonstrate that while the
number of ssTs minimally affects thermodynamic stability, the increasing
ssT regions significantly enhance the structural flexibility of 3WJs.
Utilizing this knowledge, we design triangular DNA nanoparticles with
varying ssTs, all showing exceptional assembly efficiency except for
the 0T triangle. All triangles demonstrate enhanced stability in blood
serum and are nonimmunostimulatory and nontoxic in mammalian cell
lines. The 4T 3WJ is chosen as the building block for constructing
other polygons due to its enhanced flexibility and favorable physicochemical
characteristics, making it a versatile choice for creating cost-effective,
stable, and functional DNA nanostructures that can be stored in the
dehydrated forms while retaining their structures. Our study provides
valuable insights into the design and application of nucleic acid
nanostructures, emphasizing the importance of understanding stability
and flexibility in the realm of nucleic acid nanotechnology. Our findings
suggest the intricate connection between these ssTs and the structural
adaptability of DNA 3WJs, paving the way for more precise design and
engineering of nucleic acid nanosystems suitable for broad biomedical
applications.