Abstract

   Background: Mitochondrial DNA (mtDNA)  deletions  cause disease and
   accumulate during aging,  yet  our  understanding  of the molecular
   mechanisms   underlying   their   formation  remains   rudimentary.
   Guanine-quadruplex (GQ) DNA structures are  associated with nuclear
   DNA instability in cancer; recent evidence indicates  they can also
   form in mitochondrial nucleic  acids,  suggesting  that these non-B
   DNA  structures   could   be   associated   with  mtDNA  deletions.
   Currently, the multiple types of GQ sequences and their association
   with human mtDNA stability are unknown.

   Results: Here, we show an association between  human mtDNA deletion
   breakpoint locations (sites where DNA ends rejoin after deletion of
   a section) and sequences with G-quadruplex forming potential (QFP),
   and establish the  ability  of  selected  sequences  to  form GQ in
   vitro.  QFP contain four runs of  either  two  or three consecutive
   guanines (2G and 3G, respectively), and we identified four types of
   QFP for subsequent analysis: intrastrand 2G, intrastrand 3G, duplex
   derived  interstrand  (ddi)  2G,  and  ddi  3G  QFP sequences.   We
   analyzed the position of each motif set relative to either 5' or 3'
   unique mtDNA deletion breakpoints, and  found  that intrastrand QFP
   sequences,  but   not   ddi   QFP   sequences,  showed  significant
   association with mtDNA deletion breakpoint  locations.  Moreover, a
   large proportion of these QFP sequences occur  at smaller distances
   to  breakpoints  relative  to  distribution-matched controls.   The
   positive association of 2G QFP sequences persisted when breakpoints
   were  divided  into  clinical  subgroups.   We  tested  in vitro GQ
   formation of representative mtDNA sequences containing these 2G QFP
   sequences  and  detected  robust  GQ  structures  by  UVVIS and  CD
   spectroscopy.   Notably,  the  most  frequent deletion breakpoints,
   including those of the "common  deletion",  are  bounded  by 2G QFP
   sequence motifs.

   Conclusions: The potential for GQ to influence mitochondrial genome
   stability   supports   a   high-priority   investigation  of  these
   structures  and  their  regulation   in   normal  and  pathological
   mitochondrial  biology.   These  findings  emphasize the  potential
   importance of helicases that  subsequently  resolve  GQ to maintain
   the stability of the mitochondrial genome.

   (BMC Genomics, Vol~15(1), 677, doi:10.1186/1471-2164-15-677, 2014)