Multifactorial modulation of binding and dissociation kinetics on Two-dimensional DNA nanostructures

Alexander Johnson-Buck, Jeanette Nangreave, Shuoxing Jiang, Hao Yan, Nils G. Walter

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

We use single-particle fluorescence resonance energy transfer (FRET) to show that organizing oligonucleotide probes into patterned two-dimensional arrays on DNA origami nanopegboards significantly alters the kinetics and thermodynamics of their hybridization with complementary targets in solution. By systematically varying the spacing of probes, we demonstrate that the rate of dissociation of a target is reduced by an order of magnitude in the densest probe arrays. The rate of target binding is reduced less dramatically, but to a greater extent than reported previously for one-dimensional probe arrays. By additionally varying target sequence and buffer composition, we provide evidence for two distinct mechanisms for the markedly slowed dissociation: direct hopping of targets between adjacent sequence-matched probes and nonsequence-specific, salt-bridged, and thus attractive electrostatic interactions with the DNA origami pegboard. This kinetic behavior varies little between individual copies of a given array design and will have significant impact on hybridization measurements and overall performance of DNA nanodevices as well as microarrays.

Original languageEnglish
Pages (from-to)2754-2759
Number of pages6
JournalNano Letters
Volume13
Issue number6
DOIs
Publication statusPublished - Jun 12 2013

Fingerprint

Nanostructures
DNA
deoxyribonucleic acid
Modulation
dissociation
modulation
Fluorescence Resonance Energy Transfer
Kinetics
Oligonucleotide Probes
probes
kinetics
Oligonucleotide Array Sequence Analysis
Static Electricity
Thermodynamics
Buffers
Salts
Microarrays
Coulomb interactions
oligonucleotides
Oligonucleotides

Keywords

  • DNA nanotechnology
  • DNA origami
  • kinetics
  • single molecule
  • single-particle FRET

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Bioengineering
  • Chemistry(all)
  • Materials Science(all)
  • Mechanical Engineering
  • Medicine(all)

Cite this

Multifactorial modulation of binding and dissociation kinetics on Two-dimensional DNA nanostructures. / Johnson-Buck, Alexander; Nangreave, Jeanette; Jiang, Shuoxing; Yan, Hao; Walter, Nils G.

In: Nano Letters, Vol. 13, No. 6, 12.06.2013, p. 2754-2759.

Research output: Contribution to journalArticle

Johnson-Buck, Alexander ; Nangreave, Jeanette ; Jiang, Shuoxing ; Yan, Hao ; Walter, Nils G. / Multifactorial modulation of binding and dissociation kinetics on Two-dimensional DNA nanostructures. In: Nano Letters. 2013 ; Vol. 13, No. 6. pp. 2754-2759.
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