Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond.
In this article, it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is shown to break down for a mismatch distance below 5 nt. The behavior of mismatches in the vicinity of the helix edges, and the behavior of tandem mismatches are also investigated. Finally, some thermodynamic outlying sequences are observed and highlighted. These sequences contain combinations of GA mismatches. The analysis of the microarray data reported in this article provides new insights on the DNA hybridization parameters and can help to increase the accuracy of hybridization-based technologies.
Flemish Institute for Technological Research, VITO, Boeretang 200, B-2400 Mol, Belgium.
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Hadiwikarta
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Walter
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Hooyberghs
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Carlon
D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry; D016014:Linear Models; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D013816:Thermodynamics
D004247:DNA