The Bloom's and Werner's syndrome proteins are DNA structure-specific helicases

BLM and WRN, the products of the Bloom's and Werner's syndrome genes, are m embers of the RecQ family of DNA helicases, Although both have been shown p reviously to unwind simple, partial duplex DNA substrates with 3 ' -->5 ' p olarity, little is known about the structural features of DNA that determin e the substrate specificities of these enzymes. We have compared the substr ate specificities of the BLM and WRN proteins using a variety of partial du plex DNA molecules, which are based upon a common core nucleotide sequence. We show that neither BLM nor WRN is capable of unwinding duplex DNA from a blunt-ended terminus or from an internal nick, However, both enzymes effic iently unwind the same blunt-ended duplex containing a centrally located 12 nt single-stranded 'bubble', as well as a synthetic X-structure (a model f or the Holiday junction recombination intermediate) in which each 'arm' of the 4-way junction is blunt-ended. Surprisingly, a 3 ' -tailed duplex, a st andard substrate for 3 ' -->5 ' helicases, is unwound much less efficiently by BLM and WRN than are the bubble and X-structure substrates, These data show conclusively that a single-stranded 3 ' -tail is not a structural requ irement for unwinding of standard B-form DNA by these helicases, BLM and WR N also both unwind a variety of different forms of G-quadruplex DNA, a stru cture that can form at guanine-rich sequences present at several genomic lo ci. Our data indicate that BLM and WRN are atypical helicases that are high ly DNA structure specific and have similar substrate specificities, We inte rpret these data in the light of the genomic instability and hyper-recombin ation characteristics of cells from individuals with Bloom's or Werner's sy ndrome.