RT Journal
A1 Liu, Xiao
A1 Noll, David M.
A1 Lieb, Jason D.
A1 Clarke, Neil D.
T1 DIP-chip: Rapid and accurate determination of DNA-binding specificity
JF Genome Research 
JO Genome Research 
YR 2005 
FD March 01 
VO 15 
IS 3 
SP 421 
OP 427 
DO 10.1101/gr.3256505 
UL http://genome.cshlp.org/content/15/3/421.abstract 
AB 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.