ArticleNucleic acids research2007
DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison.
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 19 papers.
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Who cites it
19 citing papers in PubMed.
- Peptide Nucleic Acid Probes for MicroRNA Detection: MgACS measurement science au · 2025Article
- Constant Temperature Electrochemical Biosensor for SNP Detection in Human Genomic DNA Based on DNA Melting Analysis.ACS sensors · 2025Article
- Applications of Surface Plasmon Resonance for Advanced Studies Involving Nucleic Acids.RNA nanomed · 2024Article
- Ionic Strength and Hybridization Position near Gold Electrodes Can Significantly Improve Kinetics in DNA-Based Electrochemical Sensors.ACS applied materials & interfaces · 2023Article
- ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation.BMC genomics · 2019Article
- Amplified single base-pair mismatch detection via aggregation of exonuclease-sheared gold nanoparticles.Analytical chemistry · 2014Article
- Hybridization kinetics between immobilized double-stranded DNA probes and targets containing embedded recognition segments.Nucleic acids research · 2011Article
- Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.PloS one · 2011Article
- Shielding effect of monovalent and divalent cations on solid-phase DNA hybridization: surface plasmon resonance biosensor study.Nucleic acids research · 2010Article
- Application of equilibrium models of solution hybridization to microarray design and analysis.PloS one · 2010Article
- Evaluating oligonucleotide properties for DNA microarray probe design.Nucleic acids research · 2010Article
- Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches.Biosensors & bioelectronics · 2010Article
- Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Article
- The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters.Nucleic acids research · 2009Article
- Conformational equilibria of bulged sites in duplex DNA studied by EPR spectroscopy.The journal of physical chemistry. B · 2009Article
- Position dependent mismatch discrimination on DNA microarrays - experiments and model.BMC bioinformatics · 2008Article
- Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays.BMC genomics · 2008Article
- Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: comparison of single base mismatches and base bulges.BMC biotechnology · 2008Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Hybridization intensities of 30 distinct short duplex DNAs measured on spotted microarrays, were directly compared with thermodynamic stabilities measured in solution. DNA sequences were designed to promote formation of perfect match, or hybrid duplexes containing tandem mismatches. Thermodynamic parameters DeltaH degrees , DeltaS degrees and DeltaG degrees of melting transitions in solution were evaluated directly using differential scanning calorimetry. Quantitative comparison with results from 63 multiplex microarray hybridization experiments provided a linear relationship for perfect match and most mismatch duplexes. Examination of outliers suggests that both duplex length and relative position of tandem mismatches could be important factors contributing to observed deviations from linearity. A detailed comparison of measured thermodynamic parameters with those calculated using the nearest-neighbor model was performed. Analysis revealed the nearest-neighbor model generally predicts mismatch duplexes to be less stable than experimentally observed. Results also show the relative stability of a tandem mismatch is highly dependent on the identity of the flanking Watson-Crick (w/c) base pairs. Thus, specifying the stability contribution of a tandem mismatch requires consideration of the sequence identity of at least four base pair units (tandem mismatch and flanking w/c base pairs). These observations underscore the need for rigorous evaluation of thermodynamic parameters describing tandem mismatch stability.
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