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.
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Acknowledgments
This work was supported by the Crop Functional Genomics Center of the Frontier Research Program, funded by the Ministry of Science and Technology (B.H.N., grant no, CG1122) and by the BioGreen21 Program (Y.-K.K., grant no. 20070401034008; B.H.N., grant no. 20090101060028), funded by RDA of the Republic of Korea. Also, B.H.N. was supported by BK21.
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Kim, MJ., Chung, P.J., Lee, TH., Kim, TH., Nahm, B.H., Kim, YK. (2012). Convenient Determination of Protein-Binding DNA Sequences Using Quadruple 9-Mer-Based Microarray and DsRed-Monomer Fusion Protein. In: Deplancke, B., Gheldof, N. (eds) Gene Regulatory Networks. Methods in Molecular Biology, vol 786. Humana Press. https://doi.org/10.1007/978-1-61779-292-2_4
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DOI: https://doi.org/10.1007/978-1-61779-292-2_4
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