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

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dc.creatorCarlon, E.
dc.creatorHeim, T.
dc.creatorWolterink, J. Klein
dc.creatorBarkema, G. T.
dc.date2006-07-18
dc.date.accessioned2026-07-07T07:22:49Z
dc.date.available2026-07-07T07:22:49Z
dc.descriptionIn 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.
dc.description2 pages
dc.identifierhttps://arxiv.org/abs/q-bio/0607023
dc.identifierhttp://arxiv.org/abs/q-bio/0607023
dc.identifierPhys. Rev. E 73, 063901 (2006)
dc.identifierdoi:10.1103/PhysRevE.73.063901
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/115797
dc.subjectBiomolecules
dc.subjectSoft Condensed Matter
dc.subjectChemical Physics
dc.titleComment on: ``Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays"
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