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Secondary structure formation and DNA instability at fragile site FRA16B

Allison A Burrow1, Allison Marullo, Lindsay R Holder

  • 1Department of Biochemistry, Wake Forest University School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1016, USA.

Nucleic Acids Research
|January 15, 2010
PubMed

Insights

Human chromosomal fragile sites, like FRA16B, form secondary DNA structures that stall replication. This instability contributes to DNA breakage and may be a common mechanism in cancer development.

Area of Science:

  • Genetics
  • Molecular Biology
  • Cancer Research

Background:

  • Human chromosomal fragile sites are DNA regions prone to breakage under replication stress.
  • These sites are frequently located in cancer-associated genes and translocation breakpoints.
  • The molecular basis for fragile site instability is not fully understood, but AT-rich regions are implicated.

Purpose of the Study:

  • To investigate the role of DNA secondary structure formation in the instability of the fragile site FRA16B.
  • To elucidate the mechanism by which FRA16B contributes to DNA breakage.

Main Methods:

  • In vitro analysis of FRA16B's ability to form alternative DNA structures.
  • Replication studies in human cells to assess FRA16B's behavior during DNA synthesis.
  • Examination of replication fork progression and pausing at FRA16B using specific templates.

Main Results:

  • FRA16B was shown to form an alternative DNA structure in vitro.
  • Replication of FRA16B in human cells resulted in reduced efficiency, expansions, and deletions, dependent on orientation and origin distance.
  • DNA polymerase stalling within FRA16B and significant replication fork reversal (81%) were observed.

Conclusions:

  • The secondary-structure-forming potential of FRA16B directly contributes to its fragility by impeding DNA replication.
  • This mechanism of replication stalling due to secondary structures may be a shared characteristic of other human chromosomal fragile sites.

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