Enzyme-free detection and quantification of double-stranded nucleic acids

Feuillie, Cécile; Merheb, Maxime; Gillet, Benjamin; Montagnac, Gilles; Hänni, Catherine; Daniel, Isabelle

doi:10.1007/s00216-012-6133-1

Cited by 5 publications

(16 citation statements)

References 47 publications

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“…Thus, opposite to the 8hydroxy-Guanine, oxidation product of Guanines, Taq will associate an adenine (A) and not cytosine (C) (Lindahl et al, 1993, Feuillie et al, 2012. Once amplifi ed, these molecules will present artifactual substitution type: C to A (Figure. 2).…”

Section: Dna Characteristics In Leather: a Processed Productmentioning

confidence: 99%

Paleogeneticist view of leather: The role of mitochondrial DNA to uncover the mysteries of fake leather and its products

Mata¹,

Merheb²

2016

Biosci. Biotech. Res. Comm

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Currently, Leather-based products are manufactured in abundance, but the fact is; most of these products are manufactured using fake materials which cause a major fraud issue in the market. The extravagance of leather trade led to the extinction of numerous species. Almost 33% of exotic leather comes from endangered species. This trade is shrewdly disguised under the "Fur" industry. With the ability to extract and analyze DNA from ancient substance, molecular species identifi cation methods have been recently developed, including the use of DNA amplifi cation using PCR and derived methods of molecular biology. At a deeper perspective, degraded DNA identifi cation has gained signifi cant advances in the fi eld of criminalistics, forensic science, as well as fraud detection and quality control in food. This study will illustrate the objectives of identifying species origin of leather either for frauds identifi cation and endangered species protection as well. We are presenting also a general assessment of the chemical degradations of DNA that can be extracted from manufactured leather. During tanning process, the rehydration of the skin in warm acid solution promotes the DNA hydrolysis. Rehydration is followed by immersion of the skin in the lime water which induces the DNA oxidation. Finally, adding tannins which are polyphenols known for their inhibitory effect on PCR, will signifi cantly decrease the chance of DNA amplifi cation. In conclusion, one can make an analogy between all these leather processing conditions and the conditions affecting a fossil in its burial environment, therefore, it is essential that the DNA of leather must be considered and analyzed as ancient DNA.

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Section: Dna Characteristics In Leather: a Processed Productmentioning

confidence: 99%

Paleogeneticist view of leather: The role of mitochondrial DNA to uncover the mysteries of fake leather and its products

Mata¹,

Merheb²

2016

Biosci. Biotech. Res. Comm

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“…The method is a valuable tool in detecting and quantifying single-stranded [12], and double-stranded DNA [13]. SERRS consists of an important enhancement event, namely surface enhancement which refers to the adsorption of the analyte onto a SERRS substrate (e.g.…”

Section: Serrs: the Ultimate Redressive Actionmentioning

confidence: 99%

“…With a well demonstrated potential as an alternative to PCR, the method of sandwich-hybridization has been expanded upon to go beyond detecting only singlestranded DNA. Feuillie, Merheb et al [13] applied the SERRS-hybridization assay to the detection of doublestranded DNA. With double-stranded targets, the strands of each duplex ought to be kept apart so that the probes could hybridize with either of them.…”

Section: A Novel Serrs Sandwich-hybridization Assay: a Deep Molecularmentioning

confidence: 99%

“…Absence of blockers drastically downgrade the intensity of the signal as large proportions of the targets will not be secured for SERRS analysis. Moreover, SERRS allows the simultaneous specific detection and quantification of two double-stranded DNA targets [13]. The targets namely, a 92 bp mitochondrial DNA sequence of R. rupicapra (chamois) and an orthologous 91 bp sequence of goat, were studied in varying proportions ranging from 0% to 100% so as to comment on both the qualitative and quantitative aspects of the method.…”

Section: A Novel Serrs Sandwich-hybridization Assay: a Deep Molecularmentioning

confidence: 99%

“…Surface enhanced resonance Raman scattering (SERRS) is a convenient non-enzymatic alternative to the traditional enzymatic methods for the specific detection of DNA. SERRS combines a magnetic amplification of the Raman signal, due to the adsorption of the molecules on a metallic surface, and a resonance effect linked to the use of a chromophore [12,13]. It allows the detection of DNA at very low concentration [14].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Raman Spectroscopy: A Promising Technique for Analyzing Nucleic Acid Refractory to PCR Amplification

Matar¹,

Merheb²

2014

TOSPECJ

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Ancient DNA (aDNA) refers to the genetic material found in dead paleontological and archeological samples. Being subject to various types of stressors, it undergoes different hydrolytic and oxidative post mortem modifications that result in the formation of DNA lesions. These lesions are found to either block the DNA polymerase during replication or induce nucleotide misincorporations. Besides, aDNA samples occur in minimal quantities; which represents an additional obstacle that researchers have to overcome in order to study aDNA. The earliest major efforts included the use of molecular cloning and polymerase chain reaction (PCR) to amplify aDNA sequences. These techniques were later found to be associated with a number of false results and unauthentic findings. There have been numerous attempts to eliminate the shortcomings of PCR and improve the quality of aDNA through avoiding contamination, repairing lesions, using translesion polymerases, etc. However, the majority of these have failed to yield accurate and specific results. Surfaceenhanced resonance Raman scattering (SERRS), on the other hand, starts in the right foot by introducing a sensitive nonenzymatic approach for the specific detection of single-and double-stranded DNA. The ability of this method to evade DNA degradation is particularly important for not only studying aDNA, but also analyzing DNA refractory to PCR amplification in processed products.

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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

et al. 2015

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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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Enzyme-free detection and quantification of double-stranded nucleic acids

Cited by 5 publications

References 47 publications

Paleogeneticist view of leather: The role of mitochondrial DNA to uncover the mysteries of fake leather and its products

Paleogeneticist view of leather: The role of mitochondrial DNA to uncover the mysteries of fake leather and its products

Raman Spectroscopy: A Promising Technique for Analyzing Nucleic Acid Refractory to PCR Amplification

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

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