Nucleotide substitution analysis of Hlx1-B6 binding to PRDM9Cst. (A) Competition assay for testing the binding of PRDM9Cst to mutated Hlx1 binding sites. Substitutions of nucleotides 4 to 6; labeled oligos are indicated by asterisk. The compositions of reaction mixtures in the first three lanes are shown above each lane. Lanes 4 to 12 show the competition test with mutated oligos. The position and the nature of each mutation in the oligo are shown. The composition of the reaction mixtures in lanes 4 to 12 is mutated oligo + PRDM9Cst + oligo* (see Materials and methods). The fraction of the shifted band is indicated below each lane. Red arrow, shifted band; black arrow, unbound fragment. (B) Graphic representation of the binding changes at each position produced by the nucleotide substitution analysis. (C) ZF domain of PRDM9Cst. The letters in the boxes show the amino acids at positions -1, 3, and 6 relative to the α-helix of each finger.
Billings et al. Genome Biology 2013 14:R35 doi:10.1186/gb-2013-14-4-r35