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Nucleic Acids Research, 1988, Vol. 16, No. 5 1739-1758
© 1988

Articles

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

Andrzej K. Konopka

National Institutes of Health, National Cancer Institute, Laboratory of Mathematical Biology FCRF, Building 469, Room 151, Frederick, MD 21701, USA

Received September 12, 1987. Revised December 19, 1987. Accepted December 19, 1987.

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.


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