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Feuillie C. Raman spectroscopy in biomedicine: new advances in SERRS cancer imaging. ANNALS OF TRANSLATIONAL MEDICINE 2015; 3:347. [PMID: 26807402 DOI: 10.3978/j.issn.2305-5839.2015.09.34] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Cécile Feuillie
- Geophysical laboratory, Carnegie Institution of Washington, Washington, DC 20015, USA
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Papadopoulou E, Goodchild SA, Cleary DW, Weller SA, Gale N, Stubberfield MR, Brown T, Bartlett PN. Using surface-enhanced Raman spectroscopy and electrochemically driven melting to discriminate Yersinia pestis from Y. pseudotuberculosis based on single nucleotide polymorphisms within unpurified polymerase chain reaction amplicons. Anal Chem 2015; 87:1605-12. [PMID: 25551670 DOI: 10.1021/ac503063c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of sensors for the detection of pathogen-specific DNA, including relevant species/strain level discrimination, is critical in molecular diagnostics with major impacts in areas such as bioterrorism and food safety. Herein, we use electrochemically driven denaturation assays monitored by surface-enhanced Raman spectroscopy (SERS) to target single nucleotide polymorphisms (SNPs) that distinguish DNA amplicons generated from Yersinia pestis, the causative agent of plague, from the closely related species Y. pseudotuberculosis. Two assays targeting SNPs within the groEL and metH genes of these two species have been successfully designed. Polymerase chain reaction (PCR) was used to produce Texas Red labeled single-stranded DNA (ssDNA) amplicons of 262 and 251 bases for the groEL and metH targets, respectively. These amplicons were used in an unpurified form to hybridize to immobilized probes then subjected to electrochemically driven melting. In all cases electrochemically driven melting was able to discriminate between fully homologous DNA and that containing SNPs. The metH assay was particularly challenging due to the presence of only a single base mismatch in the middle of the 251 base long PCR amplicon. However, manipulation of assay conditions (conducting the electrochemical experiments at 10 °C) resulted in greater discrimination between the complementary and mismatched DNA. Replicate data were collected and analyzed for each duplex on different days, using different batches of PCR product and different sphere segment void (SSV) substrates. Despite the variability introduced by these differences, the assays are shown to be reliable and robust providing a new platform for strain discrimination using unpurified PCR samples.
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Affiliation(s)
- Evanthia Papadopoulou
- Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, United Kingdom
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Feuillie C, Merheb MM, Gillet B, Montagnac G, Daniel I, Hänni C. Detection of DNA sequences refractory to PCR amplification using a biophysical SERRS assay (Surface Enhanced Resonant Raman Spectroscopy). PLoS One 2014; 9:e114148. [PMID: 25502338 PMCID: PMC4264738 DOI: 10.1371/journal.pone.0114148] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 11/04/2014] [Indexed: 11/18/2022] Open
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.
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Affiliation(s)
- Cécile Feuillie
- 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
- * E-mail:
| | - Maxime M. Merheb
- 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
| | - Benjamin Gillet
- 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
| | - Gilles Montagnac
- 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
| | - Isabelle Daniel
- 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
| | - Catherine Hänni
- 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
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