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Terminal-Specific Interaction between Double-Stranded DNA Layers: Colloidal Dispersion Behavior and Surface Force.

Naoki Kanayama1,2, Taito Sekine3, Kazunari Ozasa2

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The pairing of outermost base pairs on double-stranded DNA-grafted nanoparticles dictates their aggregation behavior in high salt. Complementary pairs attract and aggregate, while mismatched pairs repel, revealing specific DNA interactions.

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Area of Science:

  • Nanotechnology
  • Biophysics
  • Materials Science

Background:

  • Double-stranded DNA-grafted nanoparticles (dsDNA-NPs) show salt-dependent dispersion.
  • This behavior is linked to the pairing status of outermost DNA base pairs.

Purpose of the Study:

  • Investigate how outermost base pairs influence interactions between dsDNA-grafted layers.
  • Characterize the surface forces governing dsDNA-NP behavior.

Main Methods:

  • Developed a method for homogenous dsDNA layer formation using hairpin DNAs on gold surfaces.
  • Employed colloidal probe atomic force microscopy to measure forces between dsDNA layers.
  • Analyzed force-distance curves in aqueous media across varying NaCl concentrations (10-1000 mM).

Main Results:

  • Surface forces between dsDNA layers are bilateral and controlled by outermost base pairs.
  • Complementary outermost base pairs induced attractive forces at high salt concentrations (10-1000 mM NaCl).
  • Mismatched outermost base pairs primarily exhibited repulsive forces within the same salt concentration range.

Conclusions:

  • The pairing status of outermost DNA base pairs significantly impacts surface forces.
  • Blunt-end stacking between complementary DNA terminals drives attraction under high-salt conditions.
  • This base-pair specific interaction explains the unique dispersion behavior of dsDNA-NPs.