title: Coulomb blockage of hybridization in two-dimensional DNA arrays.
abstract: 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.
authors.affiliation: Department of Chemistry, University of Houston, Houston, TX 77204-5003, USA. vainrub@uh.edu
authors.forename: Arnold
authors.initials: A
authors.lastname: Vainrub
authors.forename: B Montgomery
authors.initials: BM
authors.lastname: Pettitt
mesh_terms: D055592:Biophysical Phenomena; D001703:Biophysics; D004247:DNA / Q000737:chemistry*; D015233:Models, Statistical; D009154:Mutation; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D013223:Statistics as Topic; D013696:Temperature; D013816:Thermodynamics
chemical_list: D004247:DNA