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.
Konopka
A K
AK
National Cancer Institute, Laboratory of Mathematical Biology, Frederick, MD 21701.
D000225:Adenine / Q000378:metabolism; D000818:Animals; D001483:Base Sequence; D003434:Crossing Over, Genetic; D004247:DNA / Q000235:genetics*; D004264:DNA Topoisomerases, Type I / Q000235:genetics; D006822:Hybrid Cells / Q000378:metabolism*; D051379:Mice; D008838:Microcomputers; D008969:Molecular Sequence Data; D011995:Recombination, Genetic; D012689:Sequence Homology, Nucleic Acid; D013941:Thymine / Q000378:metabolism; D014162:Transfection
D004247:DNA; D004264:DNA Topoisomerases, Type I; D000225:Adenine; D013941:Thymine