Title: Comment on "Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays"
Authors: Carlon, Enrico ×
Heim, T
Wolterink, J. Klein
Barkema, G. T #
Issue Date: Jun-2006
Publisher: American physical soc
Series Title: Physical review e vol:73 issue:6
Article number: 063901
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.
ISSN: 1539-3755
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Theoretical Physics Section
× corresponding author
# (joint) last author

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