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Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jun;73(6 Pt 1):063901; author reply 063902. Epub 2006 Jun 26.

Comment on "Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays".

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  • 1Interdisciplinary Research Institute c/o IEMN, Cité Scientifique Boite Postale 60069, F-59652 Villeneuve d'Ascq, France.

Abstract

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.

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PMID:
16906888
[PubMed]

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