SELEX (Systematic Evolution of Ligands by EXponential Enrichment), as a powerful tool for deciphering the protein-DNA interaction space

Methods Mol Biol. 2011;754:249-58. doi: 10.1007/978-1-61779-154-3_14.


DNA-binding proteins, including transcription factors, play essential roles in many biological processes. The identification of the DNA sequences to which these proteins bind is a first, yet still challenging, step for determining their functions. SELEX provides an excellent tool for deciphering protein DNA-binding sequence specificity, and it has been widely adopted for addressing fundamental biological questions. SELEX is an experimental procedure that involves the progressive selection, from a large combinatorial double-stranded oligonucleotide library, of DNA ligands with variable DNA-binding affinities and specificities by repeated rounds of partition and amplification. In this chapter, we describe a SELEX protocol that we have successfully applied to both plant and animal MYB transcription factors.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Aptamers, Nucleotide / genetics
  • Aptamers, Nucleotide / metabolism
  • Arabidopsis Proteins / analysis
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Binding Sites
  • DNA, Plant / metabolism
  • DNA-Binding Proteins / analysis*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Gene Library
  • Ligands
  • Polymerase Chain Reaction
  • Protein Binding / genetics
  • SELEX Aptamer Technique / methods*
  • Transcription Factors / analysis*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism


  • Aptamers, Nucleotide
  • Arabidopsis Proteins
  • DNA, Plant
  • DNA-Binding Proteins
  • Ligands
  • Myb protein, Arabidopsis
  • Transcription Factors