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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
4
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pubmed:dateCreated |
2004-3-1
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pubmed:abstractText |
We present a general high-throughput approach to accurately quantify DNA-protein interactions, which can facilitate the identification of functional genetic polymorphisms. The method tested here on two structurally distinct transcription factors (TFs), NF-kappaB and OCT-1, comprises three steps: (i) optimized selection of DNA variants to be tested experimentally, which we show is superior to selecting variants at random; (ii) a quantitative protein-DNA binding assay using microarray and surface plasmon resonance technologies; (iii) prediction of binding affinity for all DNA variants in the consensus space using a statistical model based on principal coordinates analysis. For the protein-DNA binding assay, we identified a polyacrylamide/ester glass activation chemistry which formed exclusive covalent bonds with 5'-amino-modified DNA duplexes and hindered non-specific electrostatic attachment of DNA. Full accessibility of the DNA duplexes attached to polyacrylamide-modified slides was confirmed by the high degree of data correlation with the electromobility shift assay (correlation coefficient 93%). This approach offers the potential for high-throughput determination of TF binding profiles and predicting the effects of single nucleotide polymorphisms on TF binding affinity. New DNA binding data for OCT-1 are presented.
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-10385322,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-10497276,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-10825175,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-11404456,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-11410653,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-11410675,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-11861919,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-12001270,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-12048232,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-12421560,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-12495153,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-12595558,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-12711340,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-1330326,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-1361172,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-14500844,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-1577272,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-1804254,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-2125960,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-6330567,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-6425835,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-7530332,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-7830764,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-7891704,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-8156594,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-8532532,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-8594589,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-9155030,
http://linkedlifedata.com/resource/pubmed/commentcorrection/14990752-9694874
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
http://linkedlifedata.com/resource/pubmed/chemical/Acrylic Resins,
http://linkedlifedata.com/resource/pubmed/chemical/DNA,
http://linkedlifedata.com/resource/pubmed/chemical/DNA-Binding Proteins,
http://linkedlifedata.com/resource/pubmed/chemical/Esters,
http://linkedlifedata.com/resource/pubmed/chemical/HCFC1 protein, human,
http://linkedlifedata.com/resource/pubmed/chemical/Host Cell Factor C1,
http://linkedlifedata.com/resource/pubmed/chemical/NF-kappa B,
http://linkedlifedata.com/resource/pubmed/chemical/Octamer Transcription Factor-1,
http://linkedlifedata.com/resource/pubmed/chemical/POU2F1 protein, human,
http://linkedlifedata.com/resource/pubmed/chemical/Transcription Factors,
http://linkedlifedata.com/resource/pubmed/chemical/polyacrylamide
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pubmed:status |
MEDLINE
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pubmed:issn |
1362-4962
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:volume |
32
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
e44
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pubmed:dateRevised |
2010-9-20
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pubmed:meshHeading |
pubmed-meshheading:14990752-Acrylic Resins,
pubmed-meshheading:14990752-Base Sequence,
pubmed-meshheading:14990752-DNA,
pubmed-meshheading:14990752-DNA-Binding Proteins,
pubmed-meshheading:14990752-Electrophoretic Mobility Shift Assay,
pubmed-meshheading:14990752-Esters,
pubmed-meshheading:14990752-Fluorescent Antibody Technique,
pubmed-meshheading:14990752-Glass,
pubmed-meshheading:14990752-Host Cell Factor C1,
pubmed-meshheading:14990752-Humans,
pubmed-meshheading:14990752-NF-kappa B,
pubmed-meshheading:14990752-Octamer Transcription Factor-1,
pubmed-meshheading:14990752-Oligonucleotide Array Sequence Analysis,
pubmed-meshheading:14990752-Polymorphism, Single Nucleotide,
pubmed-meshheading:14990752-Protein Binding,
pubmed-meshheading:14990752-Reproducibility of Results,
pubmed-meshheading:14990752-Response Elements,
pubmed-meshheading:14990752-Sensitivity and Specificity,
pubmed-meshheading:14990752-Substrate Specificity,
pubmed-meshheading:14990752-Surface Plasmon Resonance,
pubmed-meshheading:14990752-Transcription Factors
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pubmed:year |
2004
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pubmed:articleTitle |
Quantitative high-throughput analysis of transcription factor binding specificities.
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pubmed:affiliation |
Wellcome Trust Centre for Human Genetics, University of Oxford, 7 Roosevelt Drive, Oxford OX3 7BN, UK.
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pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't
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