title: Convenient determination of protein-binding DNA sequences using quadruple 9-mer-based microarray and DsRed-monomer fusion protein.
abstract: 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.
authors.affiliation: Genomics Genetics Institute, GreenGene Bio Tech Inc., Yongin, Kyonggi-Do, South Korea.
authors.forename: Min-Jeong
authors.initials: MJ
authors.lastname: Kim
authors.forename: Pil Joong
authors.initials: PJ
authors.lastname: Chung
authors.forename: Tae-Ho
authors.initials: TH
authors.lastname: Lee
authors.forename: Tae-Hoon
authors.initials: TH
authors.lastname: Kim
authors.forename: Baek Hie
authors.initials: BH
authors.lastname: Nahm
authors.forename: Yeon-Ki
authors.initials: YK
authors.lastname: Kim
mesh_terms: D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011993:Recombinant Fusion Proteins / Q000378:metabolism*; D020218:Response Elements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D011993:Recombinant Fusion Proteins; D014157:Transcription Factors