A novel K(+)-dependent DNA synthesis arrest site in a commonly occurring sequence motif in eukaryotes

We have found that a strong DNA synthesis arrest site forms in the chicken beta-globin promoter in vitro under physiological conditions. The arrest site is located in a G+C-rich region in which the guanines are located predominately on the top strand and the pyrimidines on the bottom strand. This region is non-palindromic and has no mirror symmetry. Arrest of DNA synthesis is only observed when the G-rich strand of the promoter is used as the template, and shows an absolute requirement for K+. The sequence G16CG(GGT)3 is necessary and sufficient to arrest DNA synthesis. This arrest is template concentration independent and is eliminated by blocking the N7 positions of the last 4 guanine residues in the arrest site. These observations suggest that the basis of the block to chain extension is the formation of an unusual tetraplex-like structure by the template strand. Sequences able to form intrastrand tetraplexes are ubiquitous in eukaryotes. We show that known intrastrand tetraplex-forming sequences arrest DNA synthesis in vitro, suggesting that this may be a general property of DNA tetraplexes. We suggest that the arrest of DNA synthesis by some of these structures may account for some of the high frequency of recombination associated with these loci, perhaps by promoting strand slippage or providing an opportunity for strand exchange.