Coulomb blockage of hybridization in two-dimensional DNA arrays

Arnold Vainrub, B. Montgomery Pettitt

Research output: Contribution to journalArticlepeer-review

127 Scopus citations


Experiments on DNA microarrays have revealed substantial differences in hybridization thermodynamics between DNA free in solution and surface tethered DNA. Here we develop a mean field model of the Coulomb effects in two-dimensional DNA arrays to understand the binding isotherms and thermal denaturation of the double helix. We find that the electrostatic repulsion of the assayed nucleic acid from the array of DNA probes dominates the binding thermodynamics, and thus causes the Coulomb blockage of the hybridization. The results explain, observed in DNA microarrays, the dramatic decrease of the hybridization efficiency and the thermal denaturation curve broadening as the probe surface density grows. We demonstrate application of the theory for evaluation and optimization of the sensitivity, specificity, and the dynamic range of DNA array devices.

Original languageEnglish (US)
Pages (from-to)4
Number of pages1
JournalPhysical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics
Issue number4
StatePublished - Oct 17 2002
Externally publishedYes

ASJC Scopus subject areas

  • Statistical and Nonlinear Physics
  • Statistics and Probability
  • Condensed Matter Physics


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