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

2005; Cold Spring Harbor Laboratory Press; Volume: 15; Issue: 3 Linguagem: Inglês

10.1101/gr.3256505

1549-5469

Xiao Liu, David M. Noll, Jason D. Lieb, Neil D. Clarke,

RNA and protein synthesis mechanisms

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.