Coulomb blockage of hybridization in two-dimensional DNA arrays

Arnold Vainrub, B. Montgomery Pettitt

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)41905
Number of pages1
JournalPhysical review. E, Statistical, nonlinear, and soft matter physics
Volume66
Issue number4
StatePublished - Oct 1 2002
Externally publishedYes

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Oligonucleotide Array Sequence Analysis
DNA Microarray
deoxyribonucleic acid
Thermodynamics
Probe
Mean-field Model
Hot Temperature
Dynamic Range
Helix
biopolymer denaturation
Electrostatics
Specificity
DNA
DNA Probes
Static Electricity
Nucleic Acids
Decrease
Curve
Optimization
Evaluation

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Coulomb blockage of hybridization in two-dimensional DNA arrays. / Vainrub, Arnold; Pettitt, B. Montgomery.

In: Physical review. E, Statistical, nonlinear, and soft matter physics, Vol. 66, No. 4, 01.10.2002, p. 41905.

Research output: Contribution to journalArticle

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