ArticleBiophysical journal2005
Specific and nonspecific hybridization of oligonucleotide probes on microarrays.
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 23 papers.
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Who cites it
23 citing papers in PubMed, 71 citations in OpenAlex.
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- Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data.Microarrays (Basel, Switzerland) · 2014Article
- A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat.Molecular pain · 2014Article
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- Washing scaling of GeneChip microarray expression.BMC bioinformatics · 2010Article
- G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration.BMC bioinformatics · 2010Article
- Identifying differentially methylated genes using mixed effect and generalized least square models.BMC bioinformatics · 2009Article
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- Linear model for fast background subtraction in oligonucleotide microarrays.Algorithms for molecular biology : AMB · 2009Article
- Thermodynamic scaling behavior in genechips.BMC bioinformatics · 2009Article
- Specific mutation screening of TP53 gene by low-density DNA microarray.Nanotechnology, science and applications · 2009Article
- Design and analysis of mismatch probes for long oligonucleotide microarrays.BMC genomics · 2008Article
- "Hook"-calibration of GeneChip-microarrays: chip characteristics and expression measures.Algorithms for molecular biology : AMB · 2008Article
- "Hook"-calibration of GeneChip-microarrays: theory and algorithm.Algorithms for molecular biology : AMB · 2008Article
- Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction.Nucleic acids research · 2008Review
- Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays.BMC genomics · 2007Article
- Temperature effects on DNA chip experiments from surface plasmon resonance imaging: isotherms and melting curves.Biophysical journal · 2007Article
- DNA multiplex hybridization on microarrays and thermodynamic stability in solution: a direct comparison.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression analysis by means of microarrays is based on the sequence-specific binding of RNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving sequences other than the intended target is problematic because it adds a chemical background to the signal, which is not related to the expression degree of the target gene. The article presents a molecular signature of specific and nonspecific hybridization with potential consequences for gene expression analysis. We analyzed the signal intensities of perfect match (PM) and mismatch (MM) probes of GeneChip microarrays to specify the effect of specific and nonspecific hybridization. We found that these events give rise to different relations between the PM and MM intensities as function of the middle base of the PM, namely a triplet-like (C > G approximately T > A > 0) and a duplet-like (C approximately T > 0 > G approximately A) pattern of the PM-MM log-intensity difference upon binding of specific and nonspecific RNA fragments, respectively. The systematic behavior of the intensity difference can be rationalized on the level of basepairings of DNA/RNA oligonucleotide duplexes in the middle of the probe sequence. Nonspecific binding is characterized by the reversal of the central Watson-Crick (WC) pairing for each PM/MM probe pair, whereas specific binding refers to the combination of a WC and a self-complementary (SC) pairing in PM and MM probes, respectively. The Gibbs free energy contribution of WC pairs to duplex stability is asymmetric for purines and pyrimidines of the PM and decreases according to C > G approximately T > A. SC pairings on the average only weakly contribute to duplex stability. The intensity of complementary MM introduces a systematic source of variation which decreases the precision of expression measures based on the MM intensities.
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