Evaluation of DNA-binding preferences of non-metazoan C2H2 zinc finger proteins by PBM. Evaluation of DNA-binding preferences of non-metazoan C2H2 zinc finger proteins by PBM

The largest and most diverse class of eukaryotic transcription factors contain Cys2-His2 zinc fingers (C2H2-ZFs). Here, we have explored the diversity of sequence preferences of C2H2-ZF proteins in non-metazoan organisms using PBM experiments. Overall design: Protein binding microarray (PBM) experiments were performed for a set of 43 full-length non-metazoan C2H2-ZF proteins. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. Details of the PBM protocol are described in Berger et al., Nature Biotechnology 2006.