  In a recent paper [Phys. Rev. E 68, 011906 (2003)], Naef and Magnasco
suggested that the "bright" mismatches observed in Affymetrix microarray
experiments are caused by the fluorescent molecules used to label RNA target
sequences, which would impede target-probe hybridization. Their conclusion is
based on the observation of "unexpected" asymmetries in the affinities obtained
by fitting microarray data from publicly available experiments. We point out
here that the observed asymmetry is due to the inequivalence of RNA and DNA,
and that the reported affinities are consistent with stacking free energies
obtained from melting experiments of unlabeled nucleic acids in solution. The
conclusion of Naef and Magnasco is therefore based on an unjustified
assumption.
