DIP-chip: Rapid and accurate determination of DNA-binding specificity (original) (raw)

  1. Xiao Liu1,
  2. David M. Noll1,
  3. Jason D. Lieb2, and
  4. Neil D. Clarke1,3
  5. 1 Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
  6. 2 Department of Biology and the Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 USA

Abstract

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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