Two-dimensional Ising model for microarray hybridization: cooperative interactions between bound target molecules

Abstract

The Langmuir adsorption model is widely used for description and quantification of microarray oligo-target hybridization. According to the model, the binding centers for adsorption of target molecules from solution are represented by oligo-probes. However, the Langmuir model does not consider the interactions between the targets adsorbed at the neighboring binding centers, which are possible due to high-density of array-bound probes. We have shown that the two-dimensional Ising model, which takes into account the nearest neighboring target molecules interactions, better describes the experimental data of oligo-target hybridization in comparison with the Langmuir model. Thus, we found an evidence for existence of positive cooperative interactions between adsorbed target molecules: so, binding of the first target molecules facilitates the binding of subsequent ones to the neighboring probes.

Communicated by Ramaswamy H. Sarma

Keywords:

• DNA microarray
• hybridization isotherm
• oligonucleotide probe
• probe-target duplex
• 2D-Ising model
• cooperative interactions

Acknowledgements

We thank Jeff Hooyberghs, who kindly provided the detailed experimental data published in paper (Hooyberghs et al., 2009) and helpful discussions, Alexander Pozhitkov for helpful discussions.

Additional information

Funding

The work was supported by the Presidium of the Russian Academy of Sciences Program “Molecular and cell biology” and by the Program of Fundamental research for State Academies for 2013–2020 years (grant number 01201363818).