Expanded genetic codes in next generation sequencing enable decontamination and mitochondrial enrichment

PLoS One. 2014 May 2;9(5):e96492. doi: 10.1371/journal.pone.0096492. eCollection 2014.

Abstract

We have developed a PCR method, coined Déjà vu PCR, that utilizes six nucleotides in PCR with two methyl specific restriction enzymes that respectively digest these additional nucleotides. Use of this enzyme-and-nucleotide combination enables what we term a "DNA diode", where DNA can advance in a laboratory in only one direction and cannot feedback into upstream assays. Here we describe aspects of this method that enable consecutive amplification with the introduction of a 5th and 6th base while simultaneously providing methylation dependent mitochondrial DNA enrichment. These additional nucleotides enable a novel DNA decontamination technique that generates ephemeral and easy to decontaminate DNA.

MeSH terms

  • Codon / genetics*
  • DNA / genetics*
  • DNA Methylation
  • DNA Restriction Enzymes / metabolism
  • DNA, Mitochondrial / genetics*
  • DNA, Mitochondrial / metabolism
  • Genetic Code
  • High-Throughput Nucleotide Sequencing / methods*
  • Models, Genetic
  • Nucleotides / genetics
  • Nucleotides / metabolism
  • Polymerase Chain Reaction / methods*
  • Reproducibility of Results

Substances

  • Codon
  • DNA, Mitochondrial
  • Nucleotides
  • DNA
  • DNA Restriction Enzymes

Grants and funding

The authors have no support or funding to report.