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Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures
Vladimir A Brylev1, Alexey V Ustinov1,2, Vladimir B Tsvetkov3,4,5
1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
Langmuir : the ACS Journal of Surfaces and Colloids
|December 2, 2020
Summary
Researchers developed a new method for creating unique DNA nanostructures called "nanoethylenes" and "nano-methylcyclobutanes." This advance simplifies the synthesis of complex branched oligodeoxynucleotide conjugates for DNA nanotechnology.
Area of Science:
- Biotechnology
- Nanotechnology
- Synthetic Biology
Background:
- Reliable synthesis of branched oligodeoxynucleotide (ODN) conjugates is crucial for producing discrete DNA nanostructures with covalent junctions.
- Existing methods face challenges in assembling complex branched structures.
Purpose of the Study:
- To develop a facile and scalable approach for synthesizing primitive discrete DNA nanostructures, specifically "nanoethylenes" and cyclic DNA tetragon structures.
- To expand the toolkit for DNA origami and related nanotechnology applications.
Main Methods:
- Synthesis of V-shaped oligonucleotide conjugates using pentaerythritol-based diazide and alkyne-modified oligonucleotides via copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC).
- Optimization of "nanoethylene" formation conditions.
- Design of nanoethylene-based "nanomonomers" with pendant adapters for self-assembly.
- Characterization using native polyacrylamide gel electrophoresis (PAGE), atomic force microscopy (AFM), and molecular modeling.
Main Results:
- Successfully scaled up the synthesis of V-shaped oligonucleotide conjugates.
- Achieved optimized conditions for "nanoethylene" formation.
- Demonstrated high-yield spontaneous conversion of nanoethylene-based nanomonomers into the smallest cyclic DNA product, the DNA tetragon ("nano-methylcyclobutane").
- Confirmed DNA nanostructure formation and assembly via PAGE, AFM, and molecular modeling.
Conclusions:
- The proposed method offers a straightforward and efficient route to discrete DNA nanostructures.
- Adapter-directed association provides precise control over self-assembly processes.
- This approach broadens the capabilities for constructing complex DNA nanostructures for various applications.
