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Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
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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
PubMed
Summary
This summary is machine-generated.

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.

Keywords:
DNA structurebase-triple interactionsself-assemblysequence–structure relationshipsheared G–A base pair

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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.