ArticleNucleic acids research2007
Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A Novel Method That Allows SNP Discrimination with 160:1 Ratio for Biosensors Based on DNA-DNA Hybridization.Biosensors · 2021Article
- A revised design for microarray experiments to account for experimental noise and uncertainty of probe response.PloS one · 2014Article
- 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
- Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics.PloS one · 2012Article
- Was the Scanner Calibration Slide used for its intended purpose?BMC bioinformatics · 2011Article
- Washing scaling of GeneChip microarray expression.BMC bioinformatics · 2010Article
- Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities.Nucleic acids research · 2010Article
- Kinetic and thermodynamic characterization of single-mismatch discrimination using single-molecule imaging.Nucleic acids research · 2009Article
- Real-time DNA microarrays: reality check.Biochemical Society transactions · 2009Review
- Microfludic device for creating ionic strength gradients over DNA microarrays for efficient DNA melting studies and assay development.PloS one · 2009Article
- Quantitative rRNA-targeted solution-based hybridization assay using peptide nucleic acid molecular beacons.Applied and environmental microbiology · 2008Article
- An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays.Bioinformatics (Oxford, England) · 2008Article
- Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays.Nucleic acids research · 2008Article
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4 authors.
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Abstract
Microarray experiments typically involve washing steps that remove hybridized nonspecific targets with the purpose of improving the signal-to-noise ratio. The quality of washing ultimately affects downstream analysis of the microarray and interpretation. The paucity of fundamental studies directed towards understanding the dissociation of mixed targets from microarrays makes the development of meaningful washing/dissociation protocols difficult. To fill the void, we examined activation energies and preexponential coefficients of 47 perfect match (PM) and double-mismatch (MM) duplex pairs to discover that there was no statistical difference between the kinetics of the PM and MM duplexes. Based on these findings, we evaluated the nonequilibrium thermal dissociation (NTD) approach, which has been used to identify specific microbial targets in mixed target samples. We found that the major premises for various washing protocols and the NTD approach might be seriously compromised because: (i) nonspecific duplexes do not always dissociate before specific ones, and (ii) the relationship between dissociation rates of the PM and MM duplexes depends on temperature and duplex sequence. Specifically for the NTD, we show that previously suggested use of reference curves, indices of curves and temperature ramps lead to erroneous conclusions.
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