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Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
Published on: May 8, 2015
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Sequence-dependent structural changes in a self-assembling DNA oligonucleotide
Maithili Saoji1, Paul J Paukstelis1
1Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
Acta Crystallographica. Section D, Biological Crystallography
|December 3, 2015
Summary
A single nucleotide addition dramatically alters DNA nanostructure formation. This study reveals how sequence dictates DNA folding through altered noncanonical base pairing, impacting crystallization outcomes.
Area of Science:
- Biochemistry
- Structural Biology
- Nanotechnology
Background:
- DNA's programmability enables complex 2D and 3D structure construction via Watson-Crick base pairing.
- DNA oligonucleotides display significant local structural diversity influenced by sequence and environment.
- The precise sequence-structure relationship in DNA remains incompletely understood.
Purpose of the Study:
- To investigate how a single-nucleotide addition affects the self-assembly and structure of DNA 13-mers.
- To elucidate the role of noncanonical base pairing in DNA nanostructure formation.
- To understand the interplay between sequence, noncanonical interactions, and crystallization fate.
Main Methods:
- Crystallization of self-assembling DNA 13-mers in the presence of Mg(2+).
- X-ray crystallography to determine high-resolution structures.
- Comparative analysis of structures with and without the single-nucleotide addition.
Main Results:
- Identical crystallization conditions yielded significantly different overall DNA structures upon single-nucleotide addition.
- All predicted Watson-Crick base pairs were maintained.
- A major rearrangement of noncanonical base pairs occurred, including sheared A-G pairs, base-triple junctions, and tertiary interactions.
- The altered noncanonical structure formation was sequence-dependent within the Watson-Crick duplex region.
Conclusions:
- Demonstrates a critical sequence-structure relationship in short DNA oligonucleotides.
- Highlights the significant impact of noncanonical base pairing on DNA nanostructure and crystallization.
- Reveals a unique interplay between Watson-Crick and noncanonical base pairs governing DNA folding outcomes.
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