Compilation of DNA strand exchange sites for non-homologous recombination in somatic cells.

DNA sequences of 496 somatic cell illegitimate crossing over regions were compiled and analyzed. Sites for non-homologous recombination on linear DNAs transfected into mammalian cells (Transfected Linear DNAs; TLD) were analyzed separately from the remaining illegitimate recombination regions (IRR). Trinucleotides that are preferentially cleaved by rat liver topoisomerase I in vitro (CAT, CTY, GTY, RAT where R = purine, Y = pyrimidine) were present in the 10 base pair (bp) vicinity of the cross-over sites in 92% of IRR and 93% of TLD. Multiple repeats of these trinucleotides have been observed in 39% of IRR and 38% of TLD. Runs of five or more contiguous purines (or pyrimidines on the complementary strand) were found in 26% of IRR and 14% of TLD. Adenine-Thymine rich regions of five or more bases were found in 14% of IRR and 21% of TLD. Alternating purine-pyrimidine tracks longer than four nucleotides in length were found in 11% of IRR, though only in 4% of TLD. I discuss the possible biological significance of these findings and present an appendix containing the sequences in the 10 bp vicinity of the non-homologous recombination sites analyzed.