ArticleNucleic acids research2009
The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters.
Article in Nucleic acids research, 2009. 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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21 citing papers in PubMed.
- Design and Validation of Specific Oligonucleotide Probes on Planar Magnetic Biosensors.Analytical chemistry · 2024Article
- Full pathogen characterisation: species identification including the detection of virulence factors and antibiotic resistance genes via multiplex DNA-assays.Scientific reports · 2021Article
- Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches.Chemical science · 2020Article
- Article
- ImtRDB: a database and software for mitochondrial imperfect interspersed repeats annotation.BMC genomics · 2019Article
- Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization.PloS one · 2019Article
- Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes.PloS one · 2018Article
- Enrichment of Viral Nucleic Acids by Solution Hybrid Selection with Genus Specific Oligonucleotides.Scientific reports · 2017Article
- Thermodynamic framework to assess low abundance DNA mutation detection by hybridization.PloS one · 2017Article
- Optimization of signal-to-noise ratio for efficient microarray probe design.Bioinformatics (Oxford, England) · 2016Article
- Targeted resequencing of HIV variants by microarray thermodynamics.Nucleic acids research · 2013Article
- Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond.Nucleic acids research · 2012Article
- Hybridization and amplification rate correction for affymetrix SNP arrays.BMC medical genomics · 2012Article
- Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics.PloS one · 2012Article
- From hybridization theory to microarray data analysis: performance evaluation.BMC bioinformatics · 2011Article
- Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes.BMC biotechnology · 2011Article
- Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.PloS one · 2011Article
- Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm.Nucleic acids research · 2010Article
- Application of equilibrium models of solution hybridization to microarray design and analysis.PloS one · 2010Article
- Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching (PM) complementary sequence and other spots with one or two mismatches (MM) : in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution. The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays.
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