Detection of DNA sequences refractory to PCR amplification using a biophysical SERRS assay (Surface Enhanced Resonant Raman Spectroscopy)

PLoS One. 2014 Dec 12;9(12):e114148. doi: 10.1371/journal.pone.0114148. eCollection 2014.

Abstract

The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction - based amplification is impeded by DNA damage. Blocking lesions such as abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Artifacts
  • Base Sequence
  • DNA / chemistry
  • DNA / genetics*
  • DNA / metabolism
  • DNA Damage
  • DNA-Directed DNA Polymerase / metabolism
  • Molecular Sequence Data
  • Nucleic Acid Hybridization
  • Polymerase Chain Reaction*
  • Spectrum Analysis, Raman / methods*

Substances

  • DNA
  • DNA-Directed DNA Polymerase

Grants and funding

The project was supported by the Interdisciplinary Program of CNRS “Interface physique, biologie et chimie: soutien à la prise de risque”, the Interdisciplinary program of Ecole Normale Supérieure de Lyon and by the Région Rhone-Alpes CIBLE 2011. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.