ArticleBMC genomics2007
Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Design of mismatch closure for enhanced specificity in DNA strand displacement reactions.Nucleic acids research · 2025Article
- Heteromultivalency enables enhanced detection of nucleic acid mutations.Nature chemistry · 2024Article
- Inference of transcriptome signatures of Escherichia coli in long-term stationary phase.Scientific reports · 2023Article
- Metagenomic investigation of gastrointestinal microbiome in cattle.Asian-Australasian journal of animal sciences · 2017Review
- Electrostatic melting in a single-molecule field-effect transistor with applications in genomic identification.Nature communications · 2017Article
- Sexual Dimorphism and Aging in the Human Hyppocampus: Identification, Validation, and Impact of Differentially Expressed Genes by Factorial Microarray and Network Analysis.Frontiers in aging neuroscience · 2016Article
- Bacterial transcriptome reorganization in thermal adaptive evolution.BMC genomics · 2015Article
- Influence of the length of target DNA overhang proximal to the array surface on discrimination of single-base mismatches on a 25-mer oligonucleotide array.BMC research notes · 2014Article
- An integrated lab-on-chip for rapid identification and simultaneous differentiation of tropical pathogens.PLoS neglected tropical diseases · 2014Article
- RNA transport and long-term memory storage.RNA biology · 2013Article
- Selective nucleic acid capture with shielded covalent probes.Journal of the American Chemical Society · 2013Article
- Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia coli transcriptome.BMC genomics · 2013Article
- VereFlu™: an integrated multiplex RT-PCR and microarray assay for rapid detection and identification of human influenza A and B viruses using lab-on-chip technology.Archives of virology · 2011Article
- Adaptation by stochastic switching of a monostable genetic circuit in Escherichia coli.Molecular systems biology · 2011Article
- Investigation of parameters that affect the success rate of microarray-based allele-specific hybridization assays.PloS one · 2011Article
- Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution.PLoS genetics · 2010Article
- Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress.BMC genomics · 2010Article
- Article
- A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities.BMC microbiology · 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
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-density oligonucleotide arrays are widely used for analysis of genome-wide expression and genetic variation. Affymetrix GeneChips - common high-density oligonucleotide arrays - contain perfect match (PM) and mismatch (MM) probes generated by changing a single nucleotide of the PMs, to estimate cross-hybridization. However, a fraction of MM probes exhibit larger signal intensities than PMs, when the difference in the amount of target specific hybridization between PM and MM probes is smaller than the variance in the amount of cross-hybridization. Thus, pairs of PM and MM probes with greater specificity for single nucleotide mismatches are desirable for accurate analysis.
resultsTo investigate the specificity for single nucleotide mismatches, we designed a custom array with probes of different length (14- to 25-mer) tethered to the surface of the array and all possible single nucleotide mismatches, and hybridized artificially synthesized 25-mer oligodeoxyribonucleotides as targets in bulk solution to avoid the effects of cross-hybridization. The results indicated the finite availability of target molecules as the probe length increases. Due to this effect, the sequence specificity of the longer probes decreases, and this was also confirmed even under the usual background conditions for transcriptome analysis.
conclusionOur study suggests that the optimal probe length for specificity is 19-21-mer. This conclusion will assist in improvement of microarray design for both transcriptome analysis and mutation screening.
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