DNA sequences that form secondary structures or bind
protein complexes are known barriers to replication and potential inducers of
genome instability. In order to determine which helicases facilitate DNA replication across these barriers, we analyzed fork progression through them in wild-type and mutant yeast cells, using 2-dimensional gel-electrophoretic analysis of the replication intermediates. We show that the Srs2
protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents
chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a
protein-bound repeat. Srs2 helicase activity is required for hairpin unwinding and fork progression. Also, the
PCNA binding domain of Srs2 is required for its in vivo role of replication through hairpins. In contrast, the absence of Sgs1 or Pif1 helicases did not inhibit replication through structural barriers, though Pif1 did facilitate replication of a telomeric
protein barrier. Interestingly, replication through a
protein barrier but not
a DNA structure barrier was modulated by
nucleotide pool levels, illuminating a different mechanism by which cells can regulate fork progression through
protein-mediated stall sites. Our analyses reveal fundamental differences in the replication of
DNA structural versus
protein barriers, with Srs2 helicase activity exclusively required for fork progression through hairpin structures.