title: Secondary structure formation and DNA instability at fragile site FRA16B.
abstract: Human chromosomal fragile sites are specific loci that are especially susceptible to DNA breakage following conditions of partial replication stress. They often are found in genes involved in tumorigenesis and map to over half of all known cancer-specific recurrent translocation breakpoints. While their molecular basis remains elusive, most fragile DNAs contain AT-rich flexibility islands predicted to form stable secondary structures. To understand the mechanism of fragile site instability, we examined the contribution of secondary structure formation to breakage at FRA16B. Here, we show that FRA16B forms an alternative DNA structure in vitro. During replication in human cells, FRA16B exhibited reduced replication efficiency and expansions and deletions, depending on replication orientation and distance from the origin. Furthermore, the examination of a FRA16B replication fork template demonstrated that the majority of the constructs contained DNA polymerase paused within the FRA16B sequence, and among the molecules, which completed DNA synthesis, 81% of them underwent fork reversal. These results strongly suggest that the secondary-structure-forming ability of FRA16B contributes to its fragility by stalling DNA replication, and this mechanism may be shared among other fragile DNAs.
authors.affiliation: Department of Biochemistry, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1016, USA.
authors.forename: Allison A
authors.initials: AA
authors.lastname: Burrow
authors.forename: Allison
authors.initials: A
authors.lastname: Marullo
authors.forename: Lindsay R
authors.initials: LR
authors.lastname: Holder
authors.forename: Yuh-Hwa
authors.initials: YH
authors.lastname: Wang
mesh_terms: D002460:Cell Line; D043283:Chromosome Fragile Sites; D004247:DNA / Q000096:biosynthesis / Q000737:chemistry* / Q000648:ultrastructure; D004261:DNA Replication; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D006801:Humans; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA; D004259:DNA-Directed DNA Polymerase