Jan 30, 2015

Exploring possible DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data

BMC Bioinformatics
Sterling SawayaNeil J Gemmell

Abstract

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. 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. We discuss the implications of ...Continue Reading

  • References64
  • Citations3

References

  • References64
  • Citations3

Mentioned in this Paper

Real-Time Polymerase Chain Reaction
Patterns
Polymerase
Molecular Helix
Tandem Repeat Sequences
Helix (Snails)
Carrageenan
G-Quadruplexes
Sequence Determinations, DNA
Nucleotides

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