ArticleNucleic acids research2005
Position of the fluorescent label is a crucial factor determining signal intensity in microarray hybridizations.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Sequence-dependent quenching of fluorescein fluorescence on single-stranded and double-stranded DNA.RSC advances · 2022Article
- A flow-proteometric platform for analyzing protein concentration (FAP): Proof of concept for quantification of PD-L1 protein in cells and tissues.Biosensors & bioelectronics · 2018Article
- A comprehensive analysis of predicted HLA binding peptides of JE viral proteins specific to north Indian isolates.Bioinformation · 2014Article
- Optimized light-directed synthesis of aptamer microarrays.Analytical chemistry · 2013Article
- Rapid genotyping of human papillomavirus by post-PCR array-based hybridization techniques.Journal of clinical microbiology · 2011Article
- Hybridization efficiency of molecular beacons bound to gold nanowires: effect of surface coverage and target length.Langmuir : the ACS journal of surfaces and colloids · 2010Article
- Identifying Fishes through DNA Barcodes and Microarrays.PloS one · 2010Article
- Washing scaling of GeneChip microarray expression.BMC bioinformatics · 2010Article
- Large scale analysis of positional effects of single-base mismatches on microarray gene expression data.BioData mining · 2010Article
- Beyond Affymetrix arrays: expanding the set of known hybridization isotherms and observing pre-wash signal intensities.Nucleic acids research · 2010Article
- Prevalence of betaproteobacterial sequences in nifH gene pools associated with roots of modern rice cultivars.Microbial ecology · 2009Article
- A competitive hybridization model predicts probe signal intensity on high density DNA microarrays.Nucleic acids research · 2008Article
- In situ-synthesized virulence and marker gene biochip for detection of bacterial pathogens in water.Applied and environmental microbiology · 2008Article
- Unravelling microbial communities with DNA-microarrays: challenges and future directions.Microbial ecology · 2007Review
- A nifH-based oligonucleotide microarray for functional diagnostics of nitrogen-fixing microorganisms.Microbial ecology · 2007Article
- Influence of dangling ends and surface-proximal tails of targets on probe-target duplex formation in 16S rRNA gene-based diagnostic arrays.Applied and environmental microbiology · 2007Article
- Technology development to explore the relationship between oral health and the oral microbial community.BMC oral health · 2006Article
- DNA microarrays for identifying fishes.Marine biotechnology (New York, N.Y.)Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A key issue in applications of short oligonucleotide-based microarrays is how to design specific probes with high sensitivity. Some details of the factors affecting microarray hybridization remain unclear, hampering a reliable quantification of target nucleic acids. We have evaluated the effect of the position of the fluorescent label [position of label (POL)] relative to the probe-target duplex on the signal output of oligonucleotide microarrays. End-labelled single-stranded DNA targets of different lengths were used for hybridization with perfect-match oligonucleotide probe sets targeting different positions of the same molecule. Hybridization results illustrated that probes targeting the labelled terminus of the target showed significantly higher signals than probes targeting other regions. This effect was independent of the target gene, the fluorophore and the slide surface chemistry. Comparison of microarray signal patterns of fluorescently end-labelled, fluorescently internally random-labelled and radioactively end-labelled target-DNAs with the same set of oligonucleotide probes identified POL as a critical factor affecting signal intensity rather than binding efficiency. Our observations define a novel determinant for large differences of signal intensities. Application of the POL effect may contribute to better probe design and data interpretation in microarray applications.
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