ArticleBMC biotechnology2003
Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios.
Article in BMC biotechnology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Nanoparticle-assisted detection of nucleic acids in a polymeric nanopore with a large pore size.Biosensors & bioelectronics · 2022Article
- Hamming Distance as a Concept in DNA Molecular Recognition.ACS omega · 2017Article
- Article
- Nonvolatile copolymer compositions for fabricating gel element microarrays.Analytical biochemistry · 2012Article
- SERCA2a superinhibition by human phospholamban triggers electrical and structural remodeling in mouse hearts.Physiological genomics · 2011Article
- Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays.PloS one · 2011Article
- Sizing up the future of microRNA analysis.Analytical and bioanalytical chemistry · 2010Review
- Application of equilibrium models of solution hybridization to microarray design and analysis.PloS one · 2010Article
- An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays.BMC bioinformatics · 2009Article
- 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
- 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
- Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction.Nucleic acids research · 2008Review
- Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays.BMC genomics · 2007Article
- Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer.Nucleic acids research · 2007Article
- Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray.BMC genomics · 2006Article
- Using RNA sample titrations to assess microarray platform performance and normalization techniques.Nature biotechnology · 2006Article
- Prognostic gene expression signatures can be measured in tissues collected in RNAlater preservative.The Journal of molecular diagnostics : JMD · 2006Article
- Competitive hybridization kinetics reveals unexpected behavior patterns.Biophysical journal · 2005Article
- Specific and nonspecific hybridization of oligonucleotide probes on microarrays.Biophysical journal · 2005Article
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10 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA microarrays are now routinely used to monitor the transcript levels of thousands of genes simultaneously. However, the array fabrication method, hybridization conditions, and oligodeoxyribonucleotide probe length can impact the performance of a DNA microarray platform.
resultsWe demonstrate solution-phase hybridization behavior of probe:target interactions by showing a strong correlation between the effect of mismatches in probes attached to a three dimensional matrix of a microarray and solution-based, thermodynamic duplex melting studies. The effects of mismatches in the probes attached to the microarray also demonstrate that most, if not all, of the oligodeoxyribonucleotide is available for hybridization. Kinetic parameters were also investigated. As anticipated, hybridization signals increased in a transcript concentration-dependent manner, and mismatch specificity increased with hybridization time. Unexpectedly, hybridization time increased the accuracy of fold changes by relieving the compression observed in expression ratios, and this effect may be more dramatic for larger fold changes.
conclusionsTaken together, these studies demonstrate that a three-dimensional surface may enable use of shorter oligodeoxyribonucleotide probes and that hybridization time may be critical in improving the accuracy of microarray data.
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