dorsal/arxiv
View SchemaComment on: ``Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays"
| Authors | E. Carlon, T. Heim, J. Klein Wolterink, G. T. Barkema |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0607023 |
| URL | https://arxiv.org/abs/q-bio/0607023 |
| DOI | 10.1103/PhysRevE.73.063901 |
| Journal | Phys. Rev. E 73, 063901 (2006) |
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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"abstract": "In a recent paper [Phys. Rev. E 68, 011906 (2003)], Naef and Magnasco\nsuggested that the \"bright\" mismatches observed in Affymetrix microarray\nexperiments are caused by the fluorescent molecules used to label RNA target\nsequences, which would impede target-probe hybridization. Their conclusion is\nbased on the observation of \"unexpected\" asymmetries in the affinities obtained\nby fitting microarray data from publicly available experiments. We point out\nhere that the observed asymmetry is due to the inequivalence of RNA and DNA,\nand that the reported affinities are consistent with stacking free energies\nobtained from melting experiments of unlabeled nucleic acids in solution. The\nconclusion of Naef and Magnasco is therefore based on an unjustified\nassumption.",
"arxiv_id": "q-bio/0607023",
"authors": [
"E. Carlon",
"T. Heim",
"J. Klein Wolterink",
"G. T. Barkema"
],
"categories": [
"q-bio.BM",
"cond-mat.soft",
"physics.chem-ph"
],
"doi": "10.1103/PhysRevE.73.063901",
"journal_ref": "Phys. Rev. E 73, 063901 (2006)",
"title": "Comment on: ``Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays\"",
"url": "https://arxiv.org/abs/q-bio/0607023"
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