Label‐Free Detection of Single‐Base Mismatches in DNA by Surface‐Enhanced Raman Spectroscopy

Papadopoulou, Evanthia; Bell, Steven E. J.

doi:10.1002/anie.201102776

Cited by 171 publications

(166 citation statements)

References 13 publications

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“…SNP discrimination using SERS has been previously reported (Cao et al, 2002; Jiang et al, 2012; Johnson et al, 2012; Li et al, 2013b; Mahajan et al, 2008; Papadopoulou and Bell, 2011; Wei et al, 2013). To demonstrate the SNP discrimination capability of the nanorattle-based method, we used as models wild type and mutant DNA sequences of the malaria parasite P. falciparum gene PF3D7_1343700 (“K13”).…”

Section: Resultsmentioning

confidence: 99%

Sensitive DNA detection and SNP discrimination using ultrabright SERS nanorattles and magnetic beads for malaria diagnostics

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Gandra

Fales

et al. 2016

Biosensors and Bioelectronics

117

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One of the major obstacles to implement nucleic acid-based molecular diagnostics at the point-of-care (POC) and in resource-limited settings is the lack of sensitive and practical DNA detection methods that can be seamlessly integrated into portable platforms. Herein we present a sensitive yet simple DNA detection method using a surface-enhanced Raman scattering (SERS) nanoplatform: the ultrabright SERS nanorattle. The method, referred to as the nanorattle-based method, involves sandwich hybridization of magnetic beads that are loaded with capture probes, target sequences, and ultrabright SERS nanorattles that are loaded with reporter probes. Upon hybridization, a magnet was applied to concentrate the hybridization sandwiches at a detection spot for SERS measurements. The ultrabright SERS nanorattles, composed of a core and a shell with resonance Raman reporters loaded in the gap space between the core and the shell, serve as SERS tags for signal detection. Using this method, a specific DNA sequence of the malaria parasite Plasmodium falciparum could be detected with a detection limit of approximately 100 attomoles. Single nucleotide polymorphism (SNP) discrimination of wild type malaria DNA and mutant malaria DNA, which confers resistance to artemisinin drugs, was also demonstrated. These test models demonstrate the molecular diagnostic potential of the nanorattle-based method to both detect and genotype infectious pathogens. Furthermore, the method’s simplicity makes it a suitable candidate for integration into portable platforms for POC and in resource-limited settings applications.

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Section: Resultsmentioning

confidence: 99%

Sensitive DNA detection and SNP discrimination using ultrabright SERS nanorattles and magnetic beads for malaria diagnostics

Ngo

Gandra

Fales

et al. 2016

Biosensors and Bioelectronics

117

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“…The observed SERS spectra of unthiolated DNA arose from each constituent base, which identified nucleotide components in the DNA sequence. 57–58 Digital subtraction produced difference spectrum that contained positive and negative features attributed to changes in the DNA sequence, and even detecting single base mismatches in short DNA strands. 57 Recently, Guerrini et al introduced the used of spermine bound to AgNPs for label free and direct analysis of DNA duplexes.…”

Section: Nucleic Acids and Nucleotidesmentioning

confidence: 99%

“…57–58 Digital subtraction produced difference spectrum that contained positive and negative features attributed to changes in the DNA sequence, and even detecting single base mismatches in short DNA strands. 57 Recently, Guerrini et al introduced the used of spermine bound to AgNPs for label free and direct analysis of DNA duplexes. 59 Spermine acts as a stabilizer to promote controlled aggregation between positively charge AgNPs and negatively charged DNAs into small clusters without the need of external aggregation agents.…”

Section: Nucleic Acids and Nucleotidesmentioning

confidence: 99%

Bioanalytical applications of surface-enhanced Raman spectroscopy: de novo molecular identification

Nguyen

Peters

Schultz

2017

Reviews in Analytical Chemistry

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Surface enhanced Raman scattering (SERS) has become a powerful technique for trace analysis of biomolecules. The use of SERS-tags has evolved into clinical diagnostics, the enhancement of the intrinsic signal of biomolecules on SERS active materials shows tremendous promise for the analysis of biomolecules and potential biomedical assays. The detection of the de novo signal from a wide range of biomolecules has been reported to date. In this review, we examine different classes of biomolecules for the signals observed and experimental details that enable their detection. In particular, we survey nucleic acids, amino acids, peptides, proteins, metabolites, and pathogens. The signals observed show that the interaction of the biomolecule with the enhancing nanostructure has a significant influence on the observed spectrum. Additional experiments demonstrate that internal standards can correct for intensity fluctuations and provide quantitative analysis. Experimental methods that control the interaction at the surface are providing for reproducible SERS signals. Results suggest that combining advances in methodology with the development of libraries for SERS spectra may enable the characterization of biomolecules complementary to other existing methods.

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“…Label free approaches that directly detect the distinctive SERS spectra from DNA bases have been reported [14][15][16][17], in particular the discrimination of single basemismatches within short single stranded oligonucleotides has been shown [14]. Although these approaches do not require a hybridization event to discriminate DNA sequences, they have currently been restricted to studies of short (b 25 base pairs (bp)) synthetic DNA samples and no data have been published that show discrimination of long (N 100 bp) DNA strands generated from biological samples.…”

Section: Introductionmentioning

confidence: 99%

The effect of temperature on electrochemically driven denaturation monitored by SERS

Papadopoulou

Meneghello

Marafini

et al. 2015

Bioelectrochemistry

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Label‐Free Detection of Single‐Base Mismatches in DNA by Surface‐Enhanced Raman Spectroscopy

Cited by 171 publications

References 13 publications

Sensitive DNA detection and SNP discrimination using ultrabright SERS nanorattles and magnetic beads for malaria diagnostics

Sensitive DNA detection and SNP discrimination using ultrabright SERS nanorattles and magnetic beads for malaria diagnostics

Bioanalytical applications of surface-enhanced Raman spectroscopy: de novo molecular identification

The effect of temperature on electrochemically driven denaturation monitored by SERS

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