Pentaprobe: a comprehensive sequence for the one-step detection of DNA-binding activities

Nucleic Acids Res. 2003 Oct 15;31(20):e124. doi: 10.1093/nar/gng124.


The rapid increase in the number of novel proteins identified in genome projects necessitates simple and rapid methods for assigning function. We describe a strategy for determining whether novel proteins possess typical sequence-specific DNA-binding activity. Many proteins bind recognition sequences of 5 bp or less. Given that there are 4(5) possible 5 bp sites, one might expect the length of sequence required to cover all possibilities would be 4(5) x 5 or 5120 nt. But by allowing overlaps, utilising both strands and using a computer algorithm to generate the minimum sequence, we find the length required is only 516 base pairs. We generated this sequence as six overlapping double-stranded oligonucleotides, termed pentaprobe, and used it in gel retardation experiments to assess DNA binding by both known and putative DNA-binding proteins from several protein families. We have confirmed binding by the zinc finger proteins BKLF, Eos and Pegasus, the Ets domain protein PU.1 and the treble clef N- and C-terminal fingers of GATA-1. We also showed that the N-terminal zinc finger domain of FOG-1 does not behave as a typical DNA-binding domain. Our results suggest that pentaprobe, and related sequences such as hexaprobe, represent useful tools for probing protein function.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Base Sequence
  • Binding Sites / genetics
  • Binding, Competitive
  • DNA / genetics
  • DNA / metabolism
  • DNA-Binding Proteins / metabolism
  • Electrophoretic Mobility Shift Assay
  • Molecular Sequence Data
  • Oligonucleotide Probes / genetics
  • Oligonucleotide Probes / metabolism*
  • Protein Binding


  • DNA-Binding Proteins
  • Oligonucleotide Probes
  • DNA