ArticleBiophysical journal2005
Competitive hybridization kinetics reveals unexpected behavior patterns.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Biofunctionalized nanoslits for wash-free and spatially resolved real-time sensing with full target capture.Biomicrofluidics · 2015Article
- Numerical modeling of DNA-chip hybridization with chaotic advection.Biomicrofluidics · 2013Article
- Article
- Thermostable DNA immobilization and temperature effects on surface hybridization.Langmuir : the ACS journal of surfaces and colloids · 2012Article
- Hybridization kinetics between immobilized double-stranded DNA probes and targets containing embedded recognition segments.Nucleic acids research · 2011Article
- Rapid genotyping of human papillomavirus by post-PCR array-based hybridization techniques.Journal of clinical microbiology · 2011Article
- Salt concentration effects on equilibrium melting curves from DNA microarrays.Biophysical journal · 2010Article
- An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays.BMC bioinformatics · 2009Article
- Direct calibration of PICKY-designed microarrays.BMC bioinformatics · 2009Article
- Microarray analysis of cytoplasmic versus whole cell RNA reveals a considerable number of missed and false positive mRNAs.RNA (New York, N.Y.) · 2009Article
- Real-time DNA microarrays: reality check.Biochemical Society transactions · 2009Review
- Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model.BMC genomics · 2008Article
- A competitive hybridization model predicts probe signal intensity on high density DNA microarrays.Nucleic acids research · 2008Article
- Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction.Nucleic acids research · 2008Review
- Kinetics of multiplex hybridization: mechanisms and implications.Biophysical journal · 2008Article
- Multiplex SNP discrimination.Biophysical journal · 2007Article
- Heteropolymeric triplex-based genomic assay to detect pathogens or single-nucleotide polymorphisms in human genomic samples.PloS one · 2007Article
- Revision of the nonequilibrium thermal dissociation and stringent washing approaches for identification of mixed nucleic acid targets by microarrays.Nucleic acids research · 2007Article
- Competitive displacement of DNA during surface hybridization.Biophysical journal · 2007Article
- Statistical thermodynamics and kinetics of DNA multiplex hybridization reactions.Biophysical journal · 2006Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although the kinetics of hybridization between a soluble polynucleotide and an immobilized complementary sequence have been studied by others, it is almost universally assumed that the interaction between each probe/target pair can be treated as a separate event. This simplifies the mathematics considerably, but it can give a false picture of the extent of hybridization that one achieves at equilibrium as well as the relative quantities of each hybridized pair during the approach to equilibrium. Here we solve the relevant kinetics equations simultaneously using Mathematica as a simulation language. Among the interesting results of this study are that, for certain circumstances, the relative ratio of incorrect to correct hybrids can change dramatically with time; that the relative abundances of two pairs are not what one would expect based on their equilibrium dissociation constants; that the volume of a wash solution after hybridization can have a large effect on results; and the fact that a short wash is typically better than a long one. We show that an optimum wash time exists for a given set of conditions. In addition, the ratio of soluble to insoluble (spotted) molecules can influence results substantially. Finally, the true levels of rare transcripts can be masked by the presence of highly abundant ones. Code is supplied to enable others to study conditions beyond those presented in this article.
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