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Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
Published on: April 12, 2019
Three-dimensional DNA crystals with pH-responsive noncanonical junctions.
Stephanie E Muser1, Paul J Paukstelis
1Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, Maryland NanoCenter, College Park, Maryland 20742, United States.
Journal of the American Chemical Society
|July 10, 2012
Summary
Researchers designed novel three-dimensional (3D) DNA crystals using noncanonical base pairs. These DNA crystals exhibit pH-dependent structural changes and can form adaptive biomaterial scaffolds for molecular assembly.
Area of Science:
- Biomolecular Engineering
- Crystallography
- Synthetic Biology
Background:
- Three-dimensional (3D) DNA crystals are promising programmable biomaterial scaffolds.
- The linear nature of standard DNA structures limits complex 3D lattice design.
- Noncanonical base pairing offers a route to create junctions for intricate DNA architectures.
Purpose of the Study:
- To design and characterize 3D DNA crystals utilizing parallel-stranded noncanonical base pairs.
- To investigate the influence of pH on DNA crystal structure and stability.
- To explore the potential of these DNA crystals as adaptive biomaterial scaffolds.
Main Methods:
- Design of DNA sequences incorporating parallel-stranded noncanonical base pairs.
- X-ray crystallography for structure determination at different pH values.
- Analysis of conformational changes and crystal packing.
Main Results:
- Crystals exhibited designed secondary structure interactions, with some variations based on pH.
- A conformational change in the Watson-Crick duplex region led to unexpected crystal packing.
- The noncanonical motif remained predictable at pH 5.5, while a novel C-G•G-C quadruple base pair emerged at pH 7.0.
- Demonstrated interconversion between motif variants in response to pH changes.
Conclusions:
- Highlights critical factors for successful DNA crystal design.
- Presents the first 3D DNA lattice constructed from A-DNA helical sheets.
- Reveals an adaptive noncanonical DNA motif suitable for dynamic biomaterial assemblies.
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