Recombinational resolution in primate cells of two homologous human DNA segments with a gradient of sequence divergence

Human α-thalassemia-2 genotype -α4.2 is the result of meiotic recombination between two 1.3 kb long, homologous DNA segments, X(α2) and X(α1), located in the adult α globin locus. The two segments can also undergo intramolecular recombination on extrachromosomal vectors transfected into mitoically dividing primate cells (COS 7). The existence of a gradient of sequence divergence between X(α2) and X(α1) makes them an interesting system to study the relationship between efficiencies of homologous DNA recombinaiion and the extent of dispersed and localized base mismatches. By partial restriction mapping and DNA sequencing of plasmids recombined in COS 7 cells and rescued from bacteria HB 101, we have determined the distribution of recombinational resolution sites along the two X blocks. Most, if not all, of the homologous recombination events between the two X blocks appear to be single crossing-over without efficient gene correction or repair of base mismatches. The distribution of the sites of recombinational resolution is inversely correlated with that of the gradient of sequence divergence, with only approximately 7% of the X recombinants resolved within the 3′ third of the X blocks where two diverged Alu family repeats reside. The Alu sequence within which one of the X recombinants resolved is homologous to a previously characterized α thalassemia deletion point.