Triple-Stranded DNA As a Structural Element in DNA Origami

Ken Sachenbacher, Ali Khoshouei, Maximilian Nicolas Honemann, Wouter Engelen, Elija Feigl, Hendrik Dietz

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

Molecular self-assembly with DNA origami offers an attractive route to fabricate arbitrary three-dimensional nanostructures. In DNA origami, B-form double-helical DNA domains (dsDNA) are commonly linked with covalent phosphodiester strand crossovers to build up three-dimensional objects. To expand the palette of structural motifs in DNA origami, here we describe hybrid duplex-triplex DNA motifs as pH-dependent building blocks in DNA origami. We investigate design rules for incorporating triplex forming oligonucleotides and noncanonical duplex-triplex crossovers in multilayer DNA origami objects. We use single-particle cryoelectron microscopy to elucidate the structural basis of triplex domains and of duplex-triplex crossovers. We find that duplex-triplex crossovers can complement and fully replace the canonical duplex-duplex crossovers within DNA origami objects, for example, to increase the crossover density for potentially greater rigidity and reduced interhelical spacing, and to create connections at sites where conventional crossovers may be undesirable. We also show the pH-induced formation of a DNA origami object stabilized entirely by triplex-mediated strand crossovers.

Original languageEnglish
Pages (from-to)9014-9024
Number of pages11
JournalACS Nano
Volume17
Issue number10
DOIs
StatePublished - 23 May 2023

Keywords

  • Cryo EM
  • DNA origami
  • DNA triplex
  • nanodevices
  • pH switching

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