Reply to “Comment on ‘Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays’”

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Abstract
In their Comment, Carlon et al. correctly observe that hybridization experiments in solution have shown an asymmetry which we failed to notice. However, contrary to their statement, the stacking free energies of unlabeled nucleic acids in solution are not compatible with our (and other authors’) measurements, even qualitatively. Furthermore, to bolster our paper’s assertion that labeling of the nucleic acids materially modifies the observed affinities, we present experimental data in which a change of labeling protocol results in a clear change in the affinities in question. We must therefore agree with extant studies suggesting that the energies of hybridization in solution are a superficial approximation to the much more complex physicochemical process of hybridization of labeled nucleic acids in high-density oligonucleotide arrays.