Breakdown of thermodynamic equilibrium for DNA hybridization in microarrays

TL;DR

This paper investigates why DNA hybridization in microarrays deviates from equilibrium predictions, proposing a kinetic model with a long-lived partially hybridized state that affects detection specificity.

Contribution

It introduces a kinetic model incorporating a long-lived hybridization state to explain deviations from equilibrium in DNA microarrays.

Findings

Deviations from equilibrium are due to a partially hybridized long-lived state.

The model accurately predicts intensity versus free energy behavior.

Slow relaxation impacts microarray specificity.

Abstract

Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic model. Experiments confirm the model predictions for the intensity vs. free energy behavior. The existence of slow relaxation phenomena has important consequences for the specificity of microarrays as devices for the detection of a target sequence from a complex mixture of nucleic acids.