DIP-chip: rapid and accurate determination of DNA-binding specificity

We have developed a new method for determining the DNA-binding specificity of proteins. In DIP-chip (DNA immunoprecipitation with microarray detection), protein.DNA complexes are isolated from an in vitro mixture of purified protein and naked genomic DNA. Whole-genome DNA microarrays are used to ide...

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Bibliographic Details
Published inGenome research Vol. 15; no. 3; pp. 421 - 427
Main Authors Liu, Xiao, Noll, David M, Lieb, Jason D, Clarke, Neil D
Format Journal Article
LanguageEnglish
Published United States Cold Spring Harbor Laboratory Press 01.03.2005
Subjects
Base Sequence
DNA - genetics
DNA - metabolism
Electrophoretic Mobility Shift Assay
Immunoprecipitation - methods
In Vitro Techniques
Methods
Oligonucleotide Array Sequence Analysis - methods
Oligonucleotide Array Sequence Analysis - statistics & numerical data
Protein Binding
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Summary:We have developed a new method for determining the DNA-binding specificity of proteins. In DIP-chip (DNA immunoprecipitation with microarray detection), protein.DNA complexes are isolated from an in vitro mixture of purified protein and naked genomic DNA. Whole-genome DNA microarrays are used to identify the protein-bound DNA fragments, and the sequence of the identified fragments is used to derive binding-site descriptions. Using objective criteria for assessing the accuracy of DNA-binding motifs, and using yeast Leu3p as a model, we demonstrate that motifs determined by DIP-chip are as effective at predicting the location of bound proteins in vivo as are motifs determined by conventional low-throughput in vitro methods.
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Corresponding author. E-mail nclarke@jhmi.edu ; fax (410) 614-0338.
ISSN:1088-9051
1549-5469
DOI:10.1101/gr.3256505