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A novel SERRS sandwich-hybridization assay to detect specific DNA target.

Feuillie C, Merheb MM, Gillet B, Montagnac G, Daniel I, Hänni C - PLoS ONE (2011)

Bottom Line: In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA.In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors.As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Géologie de Lyon-Terre Planètes Environnement, ENS Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon, France.

ABSTRACT
In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR). In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method) with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.

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Related in: MedlinePlus

Specificity and co-contamination assays.All spectra were acquired in 1 acquisition of 30 s. (A) In black, negative control without target DNA. (B) In blue, C. hircus, negative control (5.10−8 M). (C) In green, signal from R. rupicapra (5.10−8 M). (D) In red, signal obtained from an equimolar mix of R. rupicapra and C. hircus DNA (5.10−8 M each).
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pone-0017847-g003: Specificity and co-contamination assays.All spectra were acquired in 1 acquisition of 30 s. (A) In black, negative control without target DNA. (B) In blue, C. hircus, negative control (5.10−8 M). (C) In green, signal from R. rupicapra (5.10−8 M). (D) In red, signal obtained from an equimolar mix of R. rupicapra and C. hircus DNA (5.10−8 M each).

Mentions: We used the SERRS hybridization assay developed in the present study to detect DNA of chamois at concentrations ranging from 10−6 M to 10−8 M, respectively (Figure 2C and Figure 3). Negative controls were performed on solutions without target DNA, but containing both the capture and the detection probes, and then treated as described hereafter in experimental procedures (capture and wash steps). Measurements revealed only the plastic cuvette's signal and no specific Raman peak of R6G in the spectrum (Figure 3A). Figure 3C displays the Raman spectrum of the final elution of the SERRS sandwich-hybridization assay carried out on a 10−8 M DNA sample of R. rupicapra. An intense SERRS signal of the R6G dye is observed with some minor contribution of PMMA from the cuvette. The signal reveals the presence of detection probes that have been, first, hybridized to R. rupicapra, then, bound to the magnetic microbeads and finally, released in the elution supernatant. Thus, the SERRS signal indicates the presence of R. rupicapra DNA target in the sample.


A novel SERRS sandwich-hybridization assay to detect specific DNA target.

Feuillie C, Merheb MM, Gillet B, Montagnac G, Daniel I, Hänni C - PLoS ONE (2011)

Specificity and co-contamination assays.All spectra were acquired in 1 acquisition of 30 s. (A) In black, negative control without target DNA. (B) In blue, C. hircus, negative control (5.10−8 M). (C) In green, signal from R. rupicapra (5.10−8 M). (D) In red, signal obtained from an equimolar mix of R. rupicapra and C. hircus DNA (5.10−8 M each).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3104981&req=5

pone-0017847-g003: Specificity and co-contamination assays.All spectra were acquired in 1 acquisition of 30 s. (A) In black, negative control without target DNA. (B) In blue, C. hircus, negative control (5.10−8 M). (C) In green, signal from R. rupicapra (5.10−8 M). (D) In red, signal obtained from an equimolar mix of R. rupicapra and C. hircus DNA (5.10−8 M each).
Mentions: We used the SERRS hybridization assay developed in the present study to detect DNA of chamois at concentrations ranging from 10−6 M to 10−8 M, respectively (Figure 2C and Figure 3). Negative controls were performed on solutions without target DNA, but containing both the capture and the detection probes, and then treated as described hereafter in experimental procedures (capture and wash steps). Measurements revealed only the plastic cuvette's signal and no specific Raman peak of R6G in the spectrum (Figure 3A). Figure 3C displays the Raman spectrum of the final elution of the SERRS sandwich-hybridization assay carried out on a 10−8 M DNA sample of R. rupicapra. An intense SERRS signal of the R6G dye is observed with some minor contribution of PMMA from the cuvette. The signal reveals the presence of detection probes that have been, first, hybridized to R. rupicapra, then, bound to the magnetic microbeads and finally, released in the elution supernatant. Thus, the SERRS signal indicates the presence of R. rupicapra DNA target in the sample.

Bottom Line: In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA.In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors.As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.

View Article: PubMed Central - PubMed

Affiliation: Laboratoire de Géologie de Lyon-Terre Planètes Environnement, ENS Lyon, Université Lyon 1, CNRS, Ecole Normale Supérieure de Lyon, Lyon, France.

ABSTRACT
In this study, we have applied Surface Enhanced Resonance Raman Scattering (SERRS) technology to the specific detection of DNA. We present an innovative SERRS sandwich-hybridization assay that allows specific DNA detection without any enzymatic amplification, such as is the case with Polymerase Chain Reaction (PCR). In some substrates, such as ancient or processed remains, enzymatic amplification fails due to DNA alteration (degradation, chemical modification) or to the presence of inhibitors. Consequently, the development of a non-enzymatic method, allowing specific DNA detection, could avoid long, expensive and inconclusive amplification trials. Here, we report the proof of concept of a SERRS sandwich-hybridization assay that leads to the detection of a specific chamois DNA. This SERRS assay reveals its potential as a non-enzymatic alternative technology to DNA amplification methods (particularly the PCR method) with several applications for species detection. As the amount and type of damage highly depend on the preservation conditions, the present SERRS assay would enlarge the range of samples suitable for DNA analysis and ultimately would provide exciting new opportunities for the investigation of ancient DNA in the fields of evolutionary biology and molecular ecology, and of altered DNA in food frauds detection and forensics.

Show MeSH
Related in: MedlinePlus