ArticleNucleic acids research2008
Multi-stringency wash of partially hybridized 60-mer probes reveals that the stringency along the probe decreases with distance from the microarray surface.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Visual detection of bacterial DNA using activated paper stripe.Mikrochimica acta · 2019Article
- Sensitive Genotyping of Foodborne-Associated Human Noroviruses and Hepatitis A Virus Using an Array-Based Platform.Sensors (Basel, Switzerland) · 2017Article
- Magnetoresistive sensors for measurements of DNA hybridization kinetics - effect of TINA modifications.Scientific reports · 2017Article
- SPR Detection and Discrimination of the Oligonucleotides Related to the Normal and the Hybrid bcr-abl Genes by Two Stringency Control Strategies.Nanoscale research letters · 2016Article
- Current Technologies and Recent Developments for Screening of HPV-Associated Cervical and Oropharyngeal Cancers.Cancers · 2016Review
- Direct immobilization of DNA probes on non-modified plastics by UV irradiation and integration in microfluidic devices for rapid bioassay.Analytical and bioanalytical chemistry · 2012Article
- Maize microarray annotation database.Plant methods · 2011Article
- A sensitive alternative for microRNA in situ hybridizations using probes of 2'-O-methyl RNA + LNA.The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2011Article
- Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays.PloS one · 2011Article
- Facile DNA immobilization on surfaces through a catecholamine polymer.Angewandte Chemie (International ed. in English) · 2011Article
- Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties.BMC genomics · 2010Article
- Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities.Nucleic acids research · 2010Article
- An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays.BMC bioinformatics · 2009Article
- Real-time DNA microarrays: reality check.Biochemical Society transactions · 2009Review
- Microfludic device for creating ionic strength gradients over DNA microarrays for efficient DNA melting studies and assay development.PloS one · 2009Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we describe a multi-parametric study of DNA hybridization to probes with 20-70% G + C content. Probes were designed towards 71 different sites/mutations in the phenylalanine hydroxylase gene. Seven probe lengths, three spacer lengths and six stringencies were systematically varied. The three spacer lengths were obtained by placing the gene-specific sequence in discrete steps along the 60-mer probes. The study was performed using Agilent 8 x 15 000 probes custom-made arrays and a home-built array washer providing different stringencies to each of the eight sub-arrays on the slides. Investigation of hybridization signals, specificity and dissociation curves indicated that probes close to the surface were influenced by an additional stringency provided by the microarray surface. Consistent with this, probes close to the surface required 4 x SSC, while probes placed away from the surface required 0.35 x SSC wash buffers in order to give accurate genotyping results. Multiple step dissociation was frequently observed for probes placed furthest away from surface, but not for probes placed proximal to the surface, which is consistent with the hypothesis that there is different stringency along the 60-mer. The results have impact on design of probes for genotyping, gene expression and comparative genome hybridization analysis.
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