ArticlePloS one2010
Application of equilibrium models of solution hybridization to microarray design and analysis.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 7 citations in OpenAlex.
- Re-Evaluating the Conventional Wisdom about Binding Assays.Trends in biochemical sciences · 2020Review
- The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization.BMC research notes · 2013Article
- ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.BMC bioinformatics · 2011Article
- Accurate estimates of microarray target concentration from a simple sequence-independent Langmuir model.PloS one · 2010Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe probe percent bound value, calculated using multi-state equilibrium models of solution hybridization, is shown to be useful in understanding the hybridization behavior of microarray probes having 50 nucleotides, with and without mismatches. These longer oligonucleotides are in widespread use on microarrays, but there are few controlled studies of their interactions with mismatched targets compared to 25-mer based platforms. PRINCIPAL
findings50-mer oligonucleotides with centrally placed single, double and triple mismatches were spotted on an array. Over a range of target concentrations it was possible to discriminate binding to perfect matches and mismatches, and the type of mismatch could be predicted accurately in the concentration midrange (100 pM to 200 pM) using solution hybridization modeling methods. These results have implications for microarray design, optimization and analysis methods.
conclusionsOur results highlight the importance of incorporating biophysical factors in both the design and the analysis of microarrays. Use of the probe "percent bound" value predicted by equilibrium models of hybridization is confirmed to be important for predicting and interpreting the behavior of long oligonucleotide arrays, as has been shown for short oligonucleotide arrays.
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