DNA nanotechnology has broad applications in biomedical drug delivery and pro- grammable materials. Characterization of the self-assembly of DNA origami and quan- tum dots (QDs) is necessary for the development of new DNA-based nanostructures. We use computation and experiment to show that the self-assembly of 3D hierarchi- cal nanostructures can be controlled by programming the binding site number and their positions on DNA origami. Using biotinylated pentagonal pyramid wireframe DNA origamis and streptavidin capped QDs, we demonstrate that DNA origami with 1 binding site at the outer vertex can assemble multi-meric origamis with up to 6 DNA origamis on 1 QD, and DNA origami with 1 binding site at the inner center can only assemble monomeric and dimeric origamis. Meanwhile, the yield percentages of differ- ent multi-meric origamis are controlled by the QD:DNA-origami stoichiometric mixing ratio. DNA origamis with 2 binding sites at the αγ positions (of the pentagon) make larger nanostructures than those with binding sites at the αβ positions. In general, increasing the number of binding sites leads to increases in the nanostructure size. At high DNA origami concentration, the QD number in each cluster becomes the limiting factor for the growth of nanostructures. We find that reducing the QD size can also affect the self-assembly because of the reduced access to the binding sites from more densely packed origamis.
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This content will become publicly available on May 28, 2025
Characterization of DNA Origami Nanostructures for Size and Concentration by Dynamic Light Scattering and Nanoparticle Tracking Analysis
Nucleic acids self-assembly has rapidly advanced to produce multi-dimensional nanostructures with precise sizes and shapes. DNA nanostructures hold great potential for a wide range of applications, including biocatalysis, smart materials, molecular diagnosis, and therapeutics. Here, we present a study of using dynamic light scattering (DLS) and nanoparticles tracking analysis (NTA) to analyze DNA origami nanostructures for their size distribution and particles concentrations. Compared to DLS, NTA demonstrated higher resolution of size measurement with a smaller FWHM and was well suited for characterizing multimerization of DNA nanostructures. We future used intercalation dye to enhance the fluorescence signals of DNA origami to increase the detection sensitivity. By optimizing intercalation dyes and the dye-to-DNA origami ratio, fluorescent NTA was able to accurately quantify the concentration of dye-intercalated DNA nanostructures, closely matching with values obtained by UV absorbance at 260 nm. This optimized fluorescent NTA method offers an alternative approach for determining the concentration of DNA nanostructures based on their size distribution, in addition to commonly used UV absorbance quantification. This detailed information of size and concentration is not only crucial for production and quality control but could also provide mechanistic insights in various applications of DNA nanomaterials.
more » « less- Award ID(s):
- 2141141
- PAR ID:
- 10518665
- Publisher / Repository:
- ChemRxiv
- Date Published:
- Subject(s) / Keyword(s):
- DNA origami nucleic acids self-assembly dynamic light scattering nanoparticle tracking analysis size distribution and concentration
- Format(s):
- Medium: X
- Institution:
- Rutgers University-Camden
- Sponsoring Org:
- National Science Foundation
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