ArticleNucleic acids research2006
Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics.Biophysical journal · 2024Article
- Application of next-generation sequencing to identify different pathogens.Frontiers in microbiology · 2023Review
- Article
- Hamming Distance as a Concept in DNA Molecular Recognition.ACS omega · 2017Article
- Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization.The Analyst · 2015Article
- Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.Nucleic acids research · 2013Review
- Identification of non-specific hybridization using an empirical equation fitted to non-equilibrium dissociation curves.Journal of microbiological methods · 2012Article
- Thermostable DNA immobilization and temperature effects on surface hybridization.Langmuir : the ACS journal of surfaces and colloids · 2012Article
- Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics.PloS one · 2012Article
- Molecular techniques for pathogen identification and fungus detection in the environment.IMA fungus · 2011Article
- Normalization and centering of array-based heterologous genome hybridization based on divergent control probes.BMC bioinformatics · 2011Article
- Was the Scanner Calibration Slide used for its intended purpose?BMC bioinformatics · 2011Article
- Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays.PloS one · 2011Article
- Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes.BMC biotechnology · 2011Article
- Identifying Fishes through DNA Barcodes and Microarrays.PloS one · 2010Article
- Large scale analysis of positional effects of single-base mismatches on microarray gene expression data.BioData mining · 2010Article
- Detection of tmRNA molecules on microarrays at low temperatures using helper oligonucleotides.BMC biotechnology · 2010Article
- Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities.Nucleic acids research · 2010Article
- Broad spectrum microarray for fingerprint-based bacterial species identification.BMC biotechnology · 2010Article
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8 authors.
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Abstract
Hybridization of rRNAs to microarrays is a promising approach for prokaryotic and eukaryotic species identification. Typically, the amount of bound target is measured by fluorescent intensity and it is assumed that the signal intensity is directly related to the target concentration. Using thirteen different eukaryotic LSU rRNA target sequences and 7693 short perfect match oligonucleotide probes, we have assessed current approaches for predicting signal intensities by comparing Gibbs free energy (DeltaG degrees) calculations to experimental results. Our evaluation revealed a poor statistical relationship between predicted and actual intensities. Although signal intensities for a given target varied up to 70-fold, none of the predictors were able to fully explain this variation. Also, no combination of different free energy terms, as assessed by principal component and neural network analyses, provided a reliable predictor of hybridization efficiency. We also examined the effects of single-base pair mismatch (MM) (all possible types and positions) on signal intensities of duplexes. We found that the MM effects differ from those that were predicted from solution-based hybridizations. These results recommend against the application of probe design software tools that use thermodynamic parameters to assess probe quality for species identification. Our results imply that the thermodynamic properties of oligonucleotide hybridization are by far not yet understood.
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