title: Detection of DNA sequences refractory to PCR amplification using a biophysical SERRS assay (Surface Enhanced Resonant Raman Spectroscopy).
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.
authors.affiliation: Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement, UMR 5276, ENS de Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Feuillie
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
authors.forename: Maxime M
authors.initials: MM
authors.lastname: Merheb
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France; Plateforme nationale de Paléogénétique PALGENE, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Gillet
authors.affiliation: Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement, UMR 5276, ENS de Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
authors.forename: Gilles
authors.initials: G
authors.lastname: Montagnac
authors.affiliation: Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement, UMR 5276, ENS de Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Daniel
authors.affiliation: Institut de Génomique Fonctionnelle de Lyon, UMR 5242, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France; Plateforme nationale de Paléogénétique PALGENE, CNRS, Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Hänni
mesh_terms: D016477:Artifacts; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D004249:DNA Damage; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D016133:Polymerase Chain Reaction; D013059:Spectrum Analysis, Raman / Q000379:methods*
chemical_list: D004247:DNA; D004259:DNA-Directed DNA Polymerase