title: Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data.
abstract: BACKGROUND
  Pausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA sequences. The Pacific Biosciences sequencer uses optics to view a polymerase and its interaction with a single DNA molecule in real-time, offering a unique way to detect potential alternative DNA structures.
  
  
  RESULTS
  We have developed a new way to examine polymerase kinetics data and relate it to the DNA sequence by using a wavelet transform of read information from the sequencer. We use this method to examine how polymerase kinetics are related to nucleotide base composition. We then examine tandem repeat sequences known for their ability to form different DNA structures: (CGG)n and (CG)n repeats which can, respectively, form G-quadruplex DNA and Z-DNA. We find pausing around the (CGG)n repeat that may indicate the presence of G-quadruplexes in some of the sequencer reads. The (CG)n repeat does not appear to cause polymerase pausing, but its kinetics signature nevertheless suggests the possibility that alternative nucleotide conformations may sometimes be present.
  
  
  CONCLUSIONS
  We discuss the implications of using our method to discover DNA sequences capable of forming alternative structures. The analyses presented here can be reproduced on any Pacific Biosciences kinetics data for any DNA pattern of interest using an R package that we have made publicly available.
authors: Institute for Behavioral Genetics, University of Colorado, Boulder, USA. sterlingsawaya@gmail.com.|Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand. sterlingsawaya@gmail.com.
authors: Sterling
authors: S
authors: Sawaya
authors: Department of Biochemistry, University of Otago, Dunedin, New Zealand. james.boocock@otago.ac.nz.
authors: James
authors: J
authors: Boocock
authors: Department of Biochemistry, University of Otago, Dunedin, New Zealand. mik.black@otago.ac.nz.
authors: Michael A
authors: MA
authors: Black
authors: Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand. neil.gemmell@otago.ac.nz.
authors: Neil J
authors: NJ
authors: Gemmell
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D043542:DNA, Z-Form / Q000737:chemistry*; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry* / Q000378:metabolism; D054856:G-Quadruplexes; D006801:Humans; D007700:Kinetics; D008958:Models, Molecular; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D043542:DNA, Z-Form; D004247:DNA; D004259:DNA-Directed DNA Polymerase
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