Naturally occurring DNA repeat sequences can form non-canonical DNA structures such as H-DNA and Z-DNA, which are abundant in mammalian genomes and have the potential to regulate gene expression and genetic stability. Here we show that both H-DNA and Z-DNA structures are intrinsically mutagenic in mammalian cells. We found that the endogenous H-DNA-forming sequence of the human c-myc promoter, when placed in the context of a reporter gene, induced mutation frequencies ∼20-fold over background. We also found that the c-myc H-DNA-forming sequence induced double-strand breaks (DSBs) near the H-DNA locus and the structures of the mutants revealed microhomologies at the breakpoints, consistent with a non-homologous end-joining repair of the DSBs. These findings suggest that DNA is a causative factor in mutagenesis and not just the end product, and implicate H-DNA-induced DSBs in c-myc gene translocations in diseases such as Burkitt’s lymphoma, where most breakpoints are found near the H-DNA-forming site. Z-DNA-forming sequences have also been reported to correlate with chromosomal breakpoints in human tumors. However, very little is known about the mechanisms that contribute to the breakages near Z-DNA loci. We found in mammalian cells, that the Z-DNA-forming CG(14) repeats lead to DSBs surrounding the Z-DNA structure, resulting in large-scale deletions. Moreover, we found that CG(14)-induced small deletions within the repeats are replication-dependent likely due to misalignment. Surprisingly, the more common large-scale deletions found in mammalian cells are replication-independent, and are likely initiated by repair processing cleavages surrounding the Z-DNA structure. Our findings suggest that both H-DNA and Z-DNA are sources of genetic instability resulting from DSBs, and demonstrate that naturally occurring DNA sequences are mutagenic in mammalian cells and may contribute to genetic evolution and disease.

[Proc Amer Assoc Cancer Res, Volume 47, 2006]