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Updated: May 29, 2026

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
Published on: February 17, 2023
Convenient determination of protein-binding DNA sequences using quadruple 9-mer-based microarray and DsRed-monomer
Min-Jeong Kim1, Pil Joong Chung, Tae-Ho Lee
1Genomics Genetics Institute, GreenGene Bio Tech Inc., Yongin, Kyonggi-Do, South Korea.
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.

