Structural Transformation of Wireframe DNA Origami via DNA Polymerase Assisted Gap-Filling
Abstract
The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions. This reduced the number of staple strands needed to determine the shape and size of the final structure after gap filling. For this, several DNA polymerases and single-stranded binding (SSB) proteins were tested, with T4 DNA polymerase being the best fit. The structures could be folded in as little as 6 min, and the subsequent optimized gap-filling reaction was completed in less than 3 min. The introduction of flexible gap regions results in fully collapsed or partially bent structures due to entropic spring effects. Finally, we demonstrated structural transformations of such deformed wireframe DNA origami structures with DNA polymerases including the expansion of collapsed structures and the straightening of curved tubes. We anticipate that this approach will become a powerful tool to build DNA wireframe structures more material-efficiently, and to quickly prototype and test new wireframe designs that can be expanded, rigidified, or mechanically switched. Mechanical force generation and structural transitions will enable applications in structural DNA nanotechnology, plasmonics, or single-molecule biophysics.
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The main approaches in structural DNA nanotechnology can be divided into three groups: DNA origami, DNA tile assembly, and wireframe DNA structures.
“The main approaches in structural DNA nanotechnology can be divided into three groups: DNA origami, DNA tile assembly, and wireframe DNA structures,104”
From Emerging Approaches to DNA Data Storage: Challenges and Prospects (2022) · cites this paper as [104]
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Emerging Approaches to DNA Data Storage: Challenges and Prospects
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- Authors
- Agarwal, N. P., Matthies, M., Joffroy, B., & Schmidt, T. L.
- Affiliations
- Center for Advancing Electronics Dresden (DE)
- Corresponding author
- Schmidt, Thorsten L.
- Venue
- ACS Nano
- Publisher
- American Chemical Society (ACS)
- Published
- 2018-02-16
- Volume
- 12
- Issue
- 3
- Pages
- 2546-2553
- ISSN
- 1936-0851 (ISSN-L)
- 1936-086X
- OpenAlex
- W2786750391
- Cited by
- 52
- References
- 38
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 4 · 2023: 9 · 2022: 7 · 2021: 3 · 2020: 12 · 2019: 5 · 2018: 3
- FWCI
- 2.04
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- ACS Nano (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Deutsche Forschungsgemeinschaft (043_2615A6)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Biological Computing
- Keywords
- DNA origami, T4 DNA polymerase, single-stranded DNA binding protein, structural change, DNA nanotechnology, DNA nanotubes, mechanical switching
- MeSH terms
- DNA, DNA-Directed DNA Polymerase, DNA, Single-Stranded, Kinetics, Models, Molecular, Nucleic Acid Conformation, Thermodynamics, Viral Proteins, Bacteriophage T4, Nanotechnology, Nanostructures
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