Steric crowding and the kinetics of DNA hybridization within a DNA nanostructure system

Andre V. Pinheiro, Jeanette Nangreave, Shuoxing Jiang, Hao Yan, Yan Liu

Research output: Contribution to journalArticlepeer-review

33 Scopus citations


Figure Persented: The ability to generate precisely designed molecular networks and modulate the surrounding environment is vital for fundamental studies of chemical reactions. DNA nanotechnology simultaneously affords versatility and modularity for the construction of tailored molecular environments. We systematically studied the effects of steric crowding on the hybridization of a 20 nucleotide (nt) single-stranded DNA (ssDNA) target to a complementary probe strand extended from a rectangular six-helix tile, where the number and character of the surrounding strands influence the molecular environment of the hybridization site. The hybridization events were monitored through an increase in the quantum yield of a single reporter fluorophore (5-carboxyfluorescein) upon hybridization of the 20-nt ssDNA, an effect previously undocumented in similar systems. We observed that as the hybridization site moved from outer to inner positions along the DNA tile, the hybridization rate constant decreased. A similar rate decrease was observed when noncomplementary single- and double-stranded DNA flanked the hybridization site. However, base-pairing interactions between the hybridization site of the probe and the surrounding DNA resulted in a reduction in the reaction kinetics. The decreases in the hybridization rate constants can be explained by the reduced probability of successful nucleation of the invading ssDNA target to the complementary probe.

Original languageEnglish (US)
Pages (from-to)5521-5530
Number of pages10
JournalACS nano
Issue number6
StatePublished - Jun 26 2012


  • DNA nanotechnology
  • dynamic DNA nanostructures
  • hybridization kinetics
  • self-assembly
  • single-stranded DNA probe

ASJC Scopus subject areas

  • General Materials Science
  • General Engineering
  • General Physics and Astronomy


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