arXiv subjects

J. Klein Wolterink

Publications and source records attributed to J. Klein Wolterink.

3 recordsLinked to original sources

arXiv2006

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

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.

q-bio.BM↗

arXiv2006

Effective affinities in microarray data

In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between different studies are evident. For instance, some authors have fitted the hybridization affinities from the microarray fluorescent intensities, while others used affinities obtained from melting experiments in solution. The former approach yields fitted affinities that at first sight are only partially consistent with solution values. In this paper we show that this discrepancy exists only superficially: a sufficiently complete model provides effective affinities which are fully consistent with those fitted to experimental data. This link provides new insight on the relevant processes underlying the functioning of DNA microarrays.

q-bio.BM↗

arXiv2006

Spinodal decomposition in polymer mixtures via surface diffusion

We present experimental results for spinodal decomposition in polymer mixtures of gelatin and dextran. The domain growth law is found to be consistent with t^1/4-growth over extended time-regimes. Similar results are obtained from lattice simulations of a polymer mixture. This slow growth arises due to the suppression of the bulk mobility of polymers. In that case, spinodal decomposition is driven by the diffusive transport of material along domain interfaces, which gives rise to a t^1/4-growth law.

cond-mat.soft↗