BACKGROUND: Meiotic recombination ensures proper segregation of homologous 
chromosomes and creates genetic variation. In many organisms, recombination 
occurs at limited sites, termed 'hotspots', whose positions in mammals are 
determined by PR domain member 9 (PRDM9), a long-array zinc-finger and 
chromatin-modifier protein. Determining the rules governing the DNA binding of 
PRDM9 is a major issue in understanding how it functions.
RESULTS: Mouse PRDM9 protein variants bind to hotspot DNA sequences in a manner 
that is specific for both PRDM9 and DNA haplotypes, and that in vitro binding 
parallels its in vivo biological activity. Examining four hotspots, three 
activated by Prdm9Cst and one activated by Prdm9Dom2, we found that all binding 
sites required the full array of 11 or 12 contiguous fingers, depending on the 
allele, and that there was little sequence similarity between the binding sites 
of the three Prdm9Cst activated hotspots. The binding specificity of each 
position in the Hlx1 binding site, activated by Prdm9Cst, was tested by mutating 
each nucleotide to its three alternatives. The 31 positions along the binding 
site varied considerably in the ability of alternative bases to support binding, 
which also implicates a role for additional binding to the DNA phosphate 
backbone.
CONCLUSIONS: These results, which provide the first detailed mapping of PRDM9 
binding to DNA and, to our knowledge, the most detailed analysis yet of DNA 
binding by a long zinc-finger array, make clear that the binding specificities 
of PRDM9, and possibly other long-array zinc-finger proteins, are unusually 
complex.