Convenient Determination of Protein-Binding DNA Sequences Using Quadruple 9-Mer-Based Microarray and DsRed-Monomer Fusion Protein

Protein-binding DNA microarray (PBM) is one of the high-throughput methods to define DNA sequences which potentially bind to a given DNA-binding protein. Quadruple 9-mer-based protein-binding DNA microarray, named Q9-PBM, is designed in such a way that target probes are synthesized as quadruples of all possible 9-mer combinations. Also, recombinant proteins fused with DsRed-monomer fluorescent protein are conveniently constructed. Q9-PBM confirms the well-known DNA-binding sequences of Cbf1 and CBF1/DREB1B transcription factors, and also identifies the adjacent sequences. Moreover, Q9-PBM is applied to elucidate the unidentified cis -acting element of the OsNAC6 rice transcription factor. This technology will facilitate greater understanding of genome-wide interactions between proteins and DNA.