Sensitive and Direct DNA Mutation Detection by Surface-Enhanced Raman Spectroscopy Using Rational Designed and Tunable Plasmonic Nanostructures

Liu, Yuan; Lyu, Nana; Rajendran, Vinoth Kumar; Piper, James A.; Rodger, Alison; Wang, Yuling

doi:10.1021/acs.analchem.9b04183

Cited by 60 publications

(49 citation statements)

References 47 publications

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“…AuNS were produced through a seedless, surfactant-free synthesis in aqueous solution at ambient temperature. In a variation on the AuNP synthesis, tetrachloroauric acid was used as the precursor, while ascorbic acid (C 6 H 8 O 6 ) acted as the reducing agent and silver nitrate (AgNO 3 ) as the shaping agent in the preparation of AuNS [45]. In a glass beaker, 10 mM AgNO 3 was mixed with 10 mM HAuCl 4 in 1:18 volume ratio for 30 s. The solution color was slightly yellow, due to the presence of yellow gold salt ions.…”

Section: Preparation Of Nanoparticlesmentioning

confidence: 99%

Gold Nanostars with Reduced Fouling Facilitate Small Molecule Detection in the Presence of Protein

et al. 2021

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Gold nanoparticles have the potential to be used in biomedical applications from diagnostics to drug delivery. However, interactions of gold nanoparticles with different biomolecules in the cellular environment result in the formation of a “protein corona”—a layer of protein formed around a nanoparticle, which induces changes in the properties of nanoparticles. In this work we developed methods to reproducibly synthesize spheroidal and star-shaped gold nanoparticles, and carried out a physico-chemical characterization of synthesized anionic gold nanospheroids and gold nanostars through transmission electron microscopy (TEM), dynamic light scattering (DLS), zeta potential (ZP), nanoparticles tracking analysis (NTA), ultraviolet-visible (UV–Vis) spectroscopy and estimates of surface-enhanced Raman spectroscopy (SERS) signal enhancement ability. We analyzed how they interact with proteins after pre-incubation with bovine serum albumin (BSA) via UV–Vis, DLS, ZP, NTA, SERS, cryogenic TEM (cryo-TEM) and circular dichroism (CD) spectroscopy. The tests demonstrated that the protein adsorption on the particles’ surfaces was different for spheroidal and star shaped particles. In our experiments, star shaped particles limited the protein corona formation at SERS “hot spots”. This benefits the small-molecule sensing of nanostars in biological media. This work adds more understanding about protein corona formation on gold nanoparticles of different shapes in biological media, and therefore guides design of particles for studies in vitro and in vivo.

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Section: Preparation Of Nanoparticlesmentioning

confidence: 99%

Gold Nanostars with Reduced Fouling Facilitate Small Molecule Detection in the Presence of Protein

et al. 2021

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“…The same sensitivity was also observed for KRAS G13D and BRAF V600E ( Figure S3 , S4 ). The high sensitivity of this assay could be attributed to the bright SERS nanotags used in our study, the enhancement factor of the AuNPs (60 nm) for Raman reporter TFMBA was estimated to be 5.49×10 6 ( Calculation, Supplementary Material ) 22 , 40 - 42 . The negligible SERS signal from 100% wild-type templates further validate the specificity of primers for PCR amplification.…”

Section: Resultsmentioning

confidence: 82%

“…Successful functionalization of SERS nanotags were confirmed with UV-Vis spectrometry ( Figure S6 ). The enhancement factor of AuNPs to the Raman molecules was estimated to be 10 6 -10 8 22 , 40 - 42 , detailed calculation was described in the Supplementary Material .…”

Section: Methodsmentioning

confidence: 99%

Multiplex detection of ctDNA mutations in plasma of colorectal cancer patients by PCR/SERS assay

Lyu¹,

Rajendran²,

Diefenbach³

et al. 2020

Nanotheranostics

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Molecular diagnostic testing of KRAS and BRAF mutations has become critical in the management of colorectal cancer (CRC) patients. Some progress has been made in liquid biopsy detection of mutations in circulating tumor DNA (ctDNA), which is a fraction of circulating cell-free DNA (cfDNA), but slow analysis for DNA sequencing methods has limited rapid diagnostics. Other methods such as quantitative PCR and more recently, droplet digital PCR (ddPCR), have limitations in multiplexed capacity and the need for expensive specialized equipment. Hence, a robust, rapid and facile strategy is needed for detecting multiple ctDNA mutations to improve the management of CRC patients. To address this significant problem, herein, we propose a new application of multiplex PCR/SERS (surface-enhanced Raman scattering) assay for the detection of ctDNA in CRC, in a fast and non-invasive manner to diagnose and stratify patients for effective treatment. Methods: To discriminate ctDNA mutations from wild-type cfDNA, allele-specific primers were designed for the amplification of three clinically important DNA point mutations in CRC including KRAS G12V, KRAS G13D and BRAF V600E. Surface-enhanced Raman scattering (SERS) nanotags were labelled with a short and specific sequence of oligonucleotide, which can hybridize with the corresponding PCR amplicons. The PCR/SERS assay was implemented by firstly amplifying the multiple mutations, followed by binding with multicolor SERS nanotags specific to each mutation, and subsequent enrichment with magnetic beads. The mutation status was evaluated using a portable Raman spectrometer where the fingerprint spectral peaks of the corresponding SERS nanotags indicate the presence of the mutant targets. The method was then applied to detect ctDNA from CRC patients under a blinded test, the results were further validated by ddPCR. Results: The PCR/SERS strategy showed high specificity and sensitivity for genotyping CRC cell lines and plasma ctDNA, where as few as 0.1% mutant alleles could be detected from a background of abundant wild-type cfDNA. The blinded test using 9 samples from advanced CRC patients by PCR/SERS assay was validated with ddPCR and showed good consistency with pathology testing results. Conclusions: With ddPCR-like sensitivity yet at the convenience of standard PCR, the proposed assay shows great potential in sensitive detection of multiple ctDNA mutations for clinical decision-making.

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“…The significant differences in structural properties of cancerous DNA are due to the pattern of methylations, strongly affecting the DNA adsorption [ 117 ], and resulting in enhanced adenine SERS spectra. Many tunable plasmonic nanostructures sensors as nanowires, nano-stars, nano-shells, nano-spheres, nano-flowers, and three dimensional SERS hotspot matrixes were successfully used for the evaluation of DNA mutation and methylation [ 118 , 119 , 120 , 121 , 122 ]. Recently, the direct SERS detection of nucleic acids was coupled with polymerase chain reaction (PCR) to detect ct-DNA mutations by using spermine-functionalized Ag NP as a plasmonic substrate able reduce noise by minimizing the adsorption of aspecific molecules and interfering signals [ 113 ].…”

Section: Insights Into Double Helix Structure and Analysis: Spectroscopic Approachesmentioning

confidence: 99%

DNA Studies: Latest Spectroscopic and Structural Approaches

et al. 2021

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This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

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Sensitive and Direct DNA Mutation Detection by Surface-Enhanced Raman Spectroscopy Using Rational Designed and Tunable Plasmonic Nanostructures

Cited by 60 publications

References 47 publications

Gold Nanostars with Reduced Fouling Facilitate Small Molecule Detection in the Presence of Protein

Gold Nanostars with Reduced Fouling Facilitate Small Molecule Detection in the Presence of Protein

Multiplex detection of ctDNA mutations in plasma of colorectal cancer patients by PCR/SERS assay

DNA Studies: Latest Spectroscopic and Structural Approaches

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