dorsal/arxiv
View SchemaSpecific and non specific hybridization of oligonucleotide probes on microarrays
| Authors | Hans Binder, Stephan Preibisch |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0410028 |
| URL | https://arxiv.org/abs/q-bio/0410028 |
| DOI | 10.1529/biophysj.104.055343 |
Abstract
Gene expression analysis by means of microarrays is based on the sequence specific binding of mRNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving other sequences 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 paper presents a molecular signature of specific and non specific 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 non specific 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 PMs, namely a triplet- (C>G=T>A>0) and a duplet-like (C=T>0>G=A) pattern of the PM-MM log-intensity difference upon binding of specific and non specific RNA fragments, respectively. The systematic behaviour of the intensity difference can be rationalized on the level of base pairings of DNA/RNA oligonucleotide duplexes in the middle of the probe sequence. Non-specific 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 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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"abstract": "Gene expression analysis by means of microarrays is based on the sequence\nspecific binding of mRNA to DNA oligonucleotide probes and its measurement\nusing fluorescent labels. The binding of RNA fragments involving other\nsequences than the intended target is problematic because it adds a \"chemical\nbackground\" to the signal, which is not related to the expression degree of the\ntarget gene. The paper presents a molecular signature of specific and non\nspecific hybridization with potential consequences for gene expression\nanalysis. We analyzed the signal intensities of perfect match (PM) and mismatch\n(MM) probes of GeneChip microarrays to specify the effect of specific and non\nspecific hybridization. We found that these events give rise to different\nrelations between the PM and MM intensities as function of the middle base of\nthe PMs, namely a triplet- (C\u003eG=T\u003eA\u003e0) and a duplet-like (C=T\u003e0\u003eG=A) pattern of\nthe PM-MM log-intensity difference upon binding of specific and non specific\nRNA fragments, respectively. The systematic behaviour of the intensity\ndifference can be rationalized on the level of base pairings of DNA/RNA\noligonucleotide duplexes in the middle of the probe sequence. Non-specific\nbinding is characterized by the reversal of the central Watson Crick (WC)\npairing for each PM/MM probe pair, whereas specific binding refers to the\ncombination of a WC and a self complementary (SC) pairing in PM and MM probes,\nrespectively. The intensity of complementary MM introduces a systematic source\nof variation which decreases the precision of expression measures based on the\nMM intensities.",
"arxiv_id": "q-bio/0410028",
"authors": [
"Hans Binder",
"Stephan Preibisch"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1529/biophysj.104.055343",
"title": "Specific and non specific hybridization of oligonucleotide probes on microarrays",
"url": "https://arxiv.org/abs/q-bio/0410028"
},
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