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

Y V Stirmanov1, O V Matveeva1, Y D Nechipurenko1

  • 1a Engelhardt Institute of Molecular Biology , Russian Academy of Sciences , Moscow , Russia.

Journal of Biomolecular Structure & Dynamics
|August 8, 2018
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Summary
This summary is machine-generated.

The two-dimensional Ising model better describes microarray oligo-target hybridization than the Langmuir model. This study reveals cooperative interactions between target molecules during hybridization, where initial binding facilitates subsequent binding events.

Keywords:
2D-Ising modelDNA microarraycooperative interactionshybridization isothermoligonucleotide probeprobe-target duplex

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Biology

Background:

  • The Langmuir adsorption model is standard for analyzing microarray oligo-target hybridization.
  • This model assumes independent binding events and does not account for interactions between bound targets.
  • High probe density on microarrays suggests potential for inter-target interactions.

Purpose of the Study:

  • To evaluate the suitability of the two-dimensional Ising model for microarray oligo-target hybridization.
  • To investigate the influence of interactions between adsorbed target molecules on hybridization.
  • To compare the descriptive power of the Ising model against the Langmuir model.

Main Methods:

  • Utilized the two-dimensional Ising model to incorporate nearest-neighbor interactions.
  • Analyzed experimental data from oligo-target hybridization experiments.
  • Compared model predictions with experimental results.

Main Results:

  • The two-dimensional Ising model provided a better fit to experimental hybridization data compared to the Langmuir model.
  • Evidence of positive cooperative interactions between adsorbed target molecules was observed.
  • Initial target binding was found to facilitate the binding of subsequent targets to neighboring probes.

Conclusions:

  • The Langmuir model is insufficient for describing oligo-target hybridization at high probe densities.
  • The two-dimensional Ising model offers a more accurate representation by including inter-target interactions.
  • Positive cooperative interactions play a significant role in the hybridization process on microarrays.