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 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.
Liu
Xiao
X
Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.
Noll
David M
DM
Lieb
Jason D
JD
Clarke
Neil D
ND
D001483:Base Sequence; D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D047468:Immunoprecipitation / Q000379:methods; D066298:In Vitro Techniques; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D011485:Protein Binding
D004247:DNA