The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters

TL;DR

This study quantifies DNA hybridization free energies on microarrays, revealing their correlation with solution measurements and deviations from models at certain intensities, enhancing understanding of microarray interactions.

Contribution

It provides the first direct fitting of nearest-neighbor free energy parameters from microarray data, accounting for surface effects and deviations from solution thermodynamics.

Findings

Hybridization free energies correlate with solution data.

Deviations from the Langmuir model occur at intermediate intensities.

Surface effects influence hybridization thermodynamics.

Abstract

Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching complementary sequence and other spots with one or two mismatches: in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution. The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays.