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

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Abstract
DNA sequences of 1496 somatic cell illegitimate crossing over regions were compiled and analyzed. Sites for non-homologous recombination on linear DNA5 transfected into mammalian cells (Transfected Linear DNA5; 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 114% of TLD. Adenine-Thymine rich regions of five or more bases were found in 114% 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 14% 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.