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1: Genome Res. 2005 Mar;15(3):421-7. Epub 2005 Feb 14.
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DIP-chip: rapid and accurate determination of DNA-binding specificity.

Liu X, Noll DM, Lieb JD, Clarke ND.

Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.

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.

Publication Types:
PMID: 15710749 [PubMed - indexed for MEDLINE]

PMCID: PMC551568