ArticleNucleic acids research2006
On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes.
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 28 papers.
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Who cites it
28 citing papers in PubMed.
- Towards Personalized Allele-Specific Antisense Oligonucleotide Therapies for Toxic Gain-of-Function Neurodegenerative Diseases.Pharmaceutics · 2022Review
- Low-Cost Platform for Multiplexed Electrochemical Melting Curve Analysis.ACS measurement science au · 2022Article
- Label-free detection of conformational changes in switchable DNA nanostructures with microwave microfluidics.Nature communications · 2019Article
- Modeling Hybridization Kinetics of Gene Probes in a DNA Biochip Using FEMLAB.Microarrays (Basel, Switzerland) · 2017Article
- 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
- Isothermal discrimination of single-nucleotide polymorphisms via real-time kinetic desorption and label-free detection of DNA using silicon photonic microring resonator arrays.Analytical chemistry · 2011Article
- Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays.PloS one · 2011Article
- Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties.BMC genomics · 2010Article
- Evaluating oligonucleotide properties for DNA microarray probe design.Nucleic acids research · 2010Article
- Washing scaling of GeneChip microarray expression.BMC bioinformatics · 2010Article
- Pooled RNAi Screens - Technical and Biological Aspects.Current genomics · 2010Article
- Large scale analysis of positional effects of single-base mismatches on microarray gene expression data.BioData mining · 2010Article
- An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays.BMC bioinformatics · 2009Article
- Article
- Position dependent mismatch discrimination on DNA microarrays - experiments and model.BMC bioinformatics · 2008Article
- Multi-stringency wash of partially hybridized 60-mer probes reveals that the stringency along the probe decreases with distance from the microarray surface.Nucleic acids research · 2008Article
- Design and analysis of mismatch probes for long oligonucleotide microarrays.BMC genomics · 2008Article
- Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays.BMC genomics · 2008Article
- An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays.Bioinformatics (Oxford, England) · 2008Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Nucleic acid hybridization serves as backbone for many high-throughput systems for detection, expression analysis, comparative genomics and re-sequencing. Specificity of hybridization between probes and intended targets is always critical. Approaches to ensure and evaluate specificity include use of mismatch probes, obtaining dissociation curves rather than single temperature hybridizations, and comparative hybridizations. In this study, we quantify effects of mismatch type and position on intensity of hybridization signals and provide a new approach based on dissociation rate constants to evaluate specificity of hybridized signals in complex target mixtures. Using an extensive set of 18mer oligonucleotide probes on an in situ synthesized biochip platform, we demonstrate that mismatches in the center of the probe are more discriminating than mismatches toward the extremities of the probe and mismatches toward the attached end are less discriminating than those toward the loose end. The observed destabilizing effect of a mismatch type agreed in general with predictions using the nearest neighbor model. Use of a new parameter, specific dissociation temperature (T(d-w), temperature of maximum specific dissociation rate constant), obtained from probe-target duplex dissociation profiles considerably improved the evaluation of specificity. These results have broad implications for hybridization data obtained from complex mixtures of nucleic acids.
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