Nucleic Acids Research, 2003, Vol. 31, No. 20 e124
© 2003 Oxford University Press
Pentaprobe: a comprehensive sequence for the one-step detection of DNA-binding activities
School of Molecular and Microbial Biosciences, G08, University of Sydney, NSW 2006, Australia
*To whom correspondence should be addressed. Tel: +61 2 9351 2233; Fax: +61 2 9351 4726; Email: m.crossley{at}mmb.usyd.edu.au
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 45 possible 5 bp sites, one might expect the length of sequence required to cover all possibilities would be 45 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.
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