ArticleNucleic acids research2012
Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- High-throughput DNA melt measurements enable improved models of DNA folding thermodynamics.Nature communications · 2025Article
- Bioanalytical sensors using the heat-transfer method HTM and related techniques.Technisches Messen : TM · 2023Article
- Full pathogen characterisation: species identification including the detection of virulence factors and antibiotic resistance genes via multiplex DNA-assays.Scientific reports · 2021Article
- Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization.PloS one · 2019Article
- A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray.BMC genomics · 2017Article
- Thermodynamic framework to assess low abundance DNA mutation detection by hybridization.PloS one · 2017Article
- Influence of the length of target DNA overhang proximal to the array surface on discrimination of single-base mismatches on a 25-mer oligonucleotide array.BMC research notes · 2014Article
- Targeted resequencing of HIV variants by microarray thermodynamics.Nucleic acids research · 2013Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
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4 authors.
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Abstract
In this article, it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is shown to break down for a mismatch distance below 5 nt. The behavior of mismatches in the vicinity of the helix edges, and the behavior of tandem mismatches are also investigated. Finally, some thermodynamic outlying sequences are observed and highlighted. These sequences contain combinations of GA mismatches. The analysis of the microarray data reported in this article provides new insights on the DNA hybridization parameters and can help to increase the accuracy of hybridization-based technologies.
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