25 Citations (Scopus)

Abstract

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
Volume6
Issue number6
DOIs
StatePublished - Jun 26 2012

Fingerprint

crowding
Single-Stranded DNA
Nanostructures
DNA
deoxyribonucleic acid
Kinetics
kinetics
Tile
Rate constants
Nucleotides
tiles
nucleotides
Fluorophores
strands
Quantum yield
probes
Nanotechnology
Reaction kinetics
Chemical reactions
Nucleation

Keywords

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

ASJC Scopus subject areas

  • Engineering(all)
  • Materials Science(all)
  • Physics and Astronomy(all)

Cite this

Steric crowding and the kinetics of DNA hybridization within a DNA nanostructure system. / Pinheiro, Andre V.; Nangreave, Jeanette; Jiang, Shuoxing; Yan, Hao; Liu, Yan.

In: ACS Nano, Vol. 6, No. 6, 26.06.2012, p. 5521-5530.

Research output: Contribution to journalArticle

Pinheiro, Andre V. ; Nangreave, Jeanette ; Jiang, Shuoxing ; Yan, Hao ; Liu, Yan. / Steric crowding and the kinetics of DNA hybridization within a DNA nanostructure system. In: ACS Nano. 2012 ; Vol. 6, No. 6. pp. 5521-5530.
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