Specific detection of DNA through coupling of a TaqMan assay with surface enhanced Raman scattering (SERS)

Harper, Mhairi M.; Robertson, Barry; Ricketts, Alastair; Faulds, Karen

doi:10.1039/c2cc34859d

Cited by 17 publications

(13 citation statements)

References 18 publications

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“…82 Harper et al developed a new detection assay based upon the commonly used TaqMan assay, where SERS detection was used to improve sensitivity over the commonly employed fluorescence detection. 83 TaqMan assays involve enzymatic probe cleavage where the TaqMan probe contains both a fluorophore and a quencher, connected by a DNA sequence, allowing quenching of the fluorescence due to the close proximity of the fluorophore and the quencher. 84,85 The TaqMan probe hybridises to the target sequence at a site adjacent to the primer binding site and, during PCR, the Thermus aquaticus (Taq) polymerase enzyme will both amplify the target DNA and, in the process, digest the TaqMan probe.…”

Section: Sers Detection Of Dye-labelled Dnamentioning

confidence: 99%

“…The 10A base region attached to the TAMRA acts as a tail and facilitates adsorption of the DNA onto the colloidal surface since dye-labelled DNA gives a stronger SERS response than dye alone, this results in an increase in SERS signal. 83,86 Following amplification of the template and digestion of the probe to separate the biotin and the TAMRA dye, any undigested probe was removed from the mixture using streptavidin-coated magnetic beads so that SERS signal was only obtained from the TAMRA from the digested probe ( Figure 3). As well as the target sequence coding for the methilin resistant mecA gene from MRSA, the authors analysed a nonsense sequence, which did not contain a region complementary to the mecA probe region so that no hybridisation or digestion should occur.…”

Section: Sers Detection Of Dye-labelled Dnamentioning

confidence: 99%

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Multiplex in vitro detection using SERS

2016

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The ability to detect multiple disease-related targets from a single biological sample in a quick and reliable manner is of high importance in diagnosing and monitoring disease. The technique known as surface enhanced Raman scattering (SERS) has been developed for the simultaneous detection of multiple targets present in biological samples. Advances in the SERS method have allowed for the sensitive and specific detection of biologically relevant targets, such as DNA and proteins, which could be useful for the detection and control of disease. This review focuses on the strengths of SERS for the detection of target molecules from complex mixtures and the clinical relevance of recent work combining SERS with multiplexed detection of biological targets.

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Section: Sers Detection Of Dye-labelled Dnamentioning

confidence: 99%

Section: Sers Detection Of Dye-labelled Dnamentioning

confidence: 99%

Multiplex in vitro detection using SERS

2016

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“…The combination of SERS and biological amplification methods can further increase detection sensitivity. For example, a Taqman assay-based SERS detection method reached a detection limit of 7×10 -15 mol/m 3 for DNA sequences 35 , an ion-mediated cascade amplification SERS method had a detection limit of 30 fM for target DNA 36 , and a single base extension-based SERS method detected methylation down to 3 pM 37 . These combinations either utilize dyes to probe target sequences, Ag nano-particles tagged by complementary sequences with target mutations, or they use dye-labeled single bases in the amplification process.…”

Section: Discussionmentioning

confidence: 99%

Surface Enhanced Raman Spectroscopy (SERS) for the Multiplex Detection of Braf, Kras, and Pik3ca Mutations in Plasma of Colorectal Cancer Patients

Li¹,

Yang²,

Li³

et al. 2018

Theranostics

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In this paper, we discuss the use of a procedure based on polymerase chain reaction (PCR) and surface enhanced Raman spectroscopy (SERS) (PCR-SERS) to detect DNA mutations.Methods: This method was implemented by first amplifying DNA-containing target mutations, then by annealing probes, and finally by applying SERS detection. The obtained SERS spectra were from a mixture of fluorescence tags labeled to complementary sequences on the mutant DNA. Then, the SERS spectra of multiple tags were decomposed to component tag spectra by multiple linear regression (MLR).Results: The detection limit was 10-11 M with a coefficient of determination (R2) of 0.88. To demonstrate the applicability of this process on real samples, the PCR-SERS method was applied on blood plasma taken from 49 colorectal cancer patients to detect six mutations located at the BRAF, KRAS, and PIK3CA genes. The mutation rates obtained by the PCR-SERS method were in concordance with previous research. Fisher's exact test showed that only two detected mutations at BRAF (V600E) and PIK3CA (E542K) were significantly positively correlated with right-sided colon cancer. No other clinical feature such as gender, age, cancer stage, or differentiation was correlated with mutation (V600E at BRAF, G12C, G12D, G12V, G13D at KRAS, and E542K at PIK3CA). Visually, a dendrogram drawn through hierarchical clustering analysis (HCA) supported the results of Fisher's exact test. The clusters drawn by all six mutations did not conform to the distributions of cancer stages, differentiation or cancer positions. However, the cluster drawn by the two mutations of V600E and E542K showed that all samples with those mutations belonged to the right-sided colon cancer group.Conclusion: The suggested PCR-SERS method is multiplexed, flexible in probe design, easy to incorporate into existing PCR conditions, and was sensitive enough to detect mutations in blood plasma.

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“…The development and inclusion of other PCR or SERS technologies can also further increase the prediction accuracy. For example, multiplex detection of mutations techniques such as TaqMan [24] can be incorporated at the PCR step, and magnetic nanoparticles (MNPs) [15] can be used to aggregate target sequences at the SERS step.…”

Section: Discussionmentioning

confidence: 99%

Prenatal detection of thalassemia by cell-free fetal DNA (cffDNA) in maternal plasma using surface enhanced Raman spectroscopy combined with PCR

Yang

et al. 2018

Biomed. Opt. Express

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Thalassemias are widely occurring genetic hemoglobin disorders; patients with severe thalassemia often require regular blood transfusions for survival. Prenatal detection of thalassemia is currently invasive and carries the risk of miscarriage and infection. A polymerase chain reaction (PCR)-based surface enhanced Raman spectroscopy (SERS) technique was investigated in this paper for the purpose of detecting prenatal α-thalassemia Southeast Asian (SEA) type deletion using maternal plasma. Couples with the same SEA thalassemia (-SEA/αα) were selected, and the quantification of SEA and wild type (WT) alleles in the maternal plasma sample predicted the fetal genotype. PCR was performed using two pairs of fluorescence tag-labeled primers to produce tag-labeled PCR products for both the SEA (labeled with R6G) and WT (labeled with Cy3) alleles. Then, the labeled PCR products containing the two fluorescence tags were measured by SERS. The ratios between the R6G and Cy3 tags were obtained using multiple linear regressions (MLR), and these ratios corresponded with the physical ratio of WT and SEA concentrations in maternal plasma. After verifying this technique on DNA mixtures with known SEA and WT ratios, the plasma from 24 pregnant women was screened. An accuracy of 91.7% was achieved for detecting the fetal genotypes of Hb Bart's, alpha-trait, and normal trait. The results indicated that the simple PCR-SERS method may be sensitive enough for use on cell free fetal DNA (cffDNA) in maternal plasma for non-invasive prenatal detection (NIPD).

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Specific detection of DNA through coupling of a TaqMan assay with surface enhanced Raman scattering (SERS)

Cited by 17 publications

References 18 publications

Multiplex in vitro detection using SERS

Multiplex in vitro detection using SERS

Surface Enhanced Raman Spectroscopy (SERS) for the Multiplex Detection of Braf, Kras, and Pik3ca Mutations in Plasma of Colorectal Cancer Patients

Prenatal detection of thalassemia by cell-free fetal DNA (cffDNA) in maternal plasma using surface enhanced Raman spectroscopy combined with PCR

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