Sensitive detection of point mutation using exponential strand displacement amplification-based surface enhanced Raman spectroscopy

SERS-based methods for the detection of genomic biomarkers of cancer

Genomic biomarkers of cancer are based on changes in nucleic acids, which include abnormal expression levels of some miRNAs, point mutations in DNA sequences, and altered levels of DNA methylation. The presence of tumor-related nucleic acids in body fluids (blood, saliva, or urine) makes it possible to achieve a non-invasive early-stage cancer diagnosis. Currently existing techniques for the discovery of nucleic acids require complex, time-consuming, costly assays and have limited multiplexing abilities. Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that is able to provide molecular specificity combined with trace sensitivity. SERS has gained research attention as a tool for the detection of nucleic acids because of its promising potential: label-free SERS can decrease the complexity of assays currently used with fluorescence-based detection due to the absence of the label, while labeled SERS may outperform the gold standard in terms of the multiplexing ability. The first papers about SERS-based methods for the measurement of genomic biomarkers were written in 2008, and since then, more than 150 papers have been published. The aim of this paper is to review and evaluate the proposed SERS-based methods in terms of their level of development and their potential for liquid biopsy application, as well as to contribute to their further evolution by attracting research attention to the field. This goal will be reached by grouping, on the basis of their experimental protocol, all the published manuscripts on the topic and evaluating each group in terms of its limit of detection and applicability to real body fluids. Thus, the methods are classified according to their working principles into five main groups, including capture-based, displacement-based, sandwich-based, enzyme-assisted, and specialized protocols.

Deep Learning Assisted Surface-Enhanced Raman Spectroscopy (SERS) for Rapid and Direct Nucleic Acid Amplification and Detection: Toward Enhanced Molecular Diagnostics

Surface-enhanced Raman scattering (SERS) has evolved into a robust analytical technique capable of detecting a variety of biomolecules despite challenges in securing a reliable Raman signal. Conventional SERS-based nucleic acid detection relies on hybridization assays, but reproducibility and signal strength issues have hindered research on directly amplifying nucleic acids on SERS surfaces. This study introduces a deep learning assisted ZnO-Au-SERS-based direct amplification (ZADA) system for rapid, sensitive molecular diagnostics. The system employs a SERS substrate fabricated by depositing gold on uniformly grown ZnO nanorods. These nanorods create hot spots for the amplification of the target nucleic acids directly on the SERS surface, eliminating the need for postamplification hybridization and Raman reporters. The limit of detection of the ZADA system was superior to those of the conventional amplification methods. Clinical validation of the ZADA system with coronavirus disease 2019 (COVID-19) samples from human patients yielded a sensitivity and specificity of 92.31% and 81.25%, respectively. The integration of a deep learning program further enhanced sensitivity and specificity to 100% and reduced SERS analysis time, showcasing the potential of the ZADA system for rapid, label-free disease diagnosis via direct nucleic acid amplification and detection within 20 min.

A review of surface-enhanced Raman spectroscopy in pathological processes

With the continuous growth of the human population and new challenges in the quality of life, it is more important than ever to diagnose diseases and pathologies with high accuracy, sensitivity and in different scenarios from medical implants to the operation room. Although conventional methods of diagnosis revolutionized healthcare, alternative analytical methods are making their way out of academic labs into clinics. In this regard, surface-enhanced Raman spectroscopy (SERS) developed immensely with its capability to achieve single-molecule sensitivity and high-specificity in the last two decades, and now it is well on its way to join the arsenal of physicians. This review discusses how SERS is becoming an essential tool for the clinical investigation of pathologies including inflammation, infections, necrosis/apoptosis, hypoxia, and tumors. We critically discuss the strategies reported so far in nanoparticle assembly, functionalization, non-metallic substrates, colloidal solutions and how these techniques improve SERS characteristics during pathology diagnoses like sensitivity, selectivity, and detection limit. Moreover, it is crucial to introduce the most recent developments and future perspectives of SERS as a biomedical analytical method. We finally discuss the challenges that remain as bottlenecks for a routine SERS implementation in the medical room from in vitro to in vivo applications. The review showcases the adaptability and versatility of SERS to resolve pathological processes by covering various experimental and analytical methods and the specific spectral features and analysis results achieved by these methods.

Sensing of circulating cancer biomarkers with metal nanoparticles

The analysis of circulating cancer biomarkers, including cell-free and circulating tumor DNA, circulating tumor cells, microRNA and exosomes, holds promise in revolutionizing cancer diagnosis and prognosis using body fluid analysis, also known as liquid biopsy. To enable clinical application of these biomarkers, new analytical tools capable of detecting them in very low concentrations in complex sample matrixes are needed. Metal nanoparticles have emerged as extraordinary analytical scaffolds because of their unique optoelectronic properties and ease of functionalization. Hence, multiple analytical techniques have been developed based on these nanoparticles and their plasmonic properties. The aim of this review is to summarize and discuss the present development on the use of metal nanoparticles for the analysis of circulating cancer biomarkers. We examine how metal nanoparticles can be used as (1) analytical transducers in various sensing principles, such as aggregation induced colorimetric assays, plasmon resonance energy transfer, surface enhanced Raman spectroscopy, and refractive index sensing, and (2) signal amplification elements in surface plasmon resonance spectroscopy and electrochemical detection. We critically discuss the clinical relevance of each category of circulating biomarkers, followed by a thorough analysis of how these nanoparticle-based designs have overcome some of the main challenges that gold standard analytical techniques currently face, and what new directions the field may take in the future.

Sensitive detection of antibiotics using aptamer conformation cooperated enzyme-assisted SERS technology

Serious healthcare concerns have been raised on the issue of antibiotic residues after overuse, especially by accumulation in the human body through food webs. Here, we report a methodological development for sensitive detection of antibiotics with aptamer conformation cooperated enzyme-assisted SERS (ACCESS) technology. We design and integrate a set of nucleic acid oligos, realizing specific recognition of chloramphenicol (CAP) and efficient exonuclease III-assisted DNA amplification. It features a "signal-on" analysis of CAP with the limit of detection (15 fM), the lowest concentration detectable in the literature. Our method exhibits a high selectivity on the target analyte, free of interference of other potential antibiotic contaminants. The ACCESS assay promises an ultrasensitive and specific detection tool for trace amounts of antibiotic residues in samples of our daily life.

Robust and highly specific fluorescence sensing of Salmonella typhimurium based on dual-functional phi29 DNA polymerase-mediated isothermal circular strand displacement polymerization

A simple and robust fluorescence sensing strategy has been developed for the detection of pathogenic bacteria by the combination of the dual functionality of phi29 DNA polymerase with isothermal circular strand displacement polymerization (ICSDP).

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

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).

A simple and ultrasensitive fluorescence assay for single-nucleotide polymorphism

In this report, a simple, label-free and highly efficient nucleic acid amplification technique is developed for ultrasensitive detection of single-nucleotide polymorphism (SNP). Briefly, a designed padlock probe is first circularized by a DNA ligase when it perfectly complements to a mutant gene. Then, the mutant gene functions as a primer to initiate branched rolling circle amplification reaction (BRCA), generating a large number of branched DNA strands and a lot of pyrophosphate molecules which is equivalent to the number of nucleotides consumed. With the addition of a terpyridine-Zn(II) complex, pyrophosphate molecules can be sensitively detected owing to the formation of a fluorescent terpyridine-Zn(II)-pyrophosphate complex. The fluorescence intensity is directly associated with the content of the mutant gene in a sample solution. On the other hand, the circulation of the padlock probe is prohibited when it hybridizes with the wild-type gene. In this assay, the accumulative nature of the BRCA process produces a detection limit of 0.1 pM and an excellent selectivity factor of 1000 toward SNP. As little as 0.1% mutant in the wild-type gene can be successfully detected. The simple procedure, high sensitivity, and high selectivity of this assay offer a potentially viable alternative for routine SNP analysis. Graphical abstract A simple and label-free fluorescence assay for SNP detection by coupling BRCA with selective fluorescence detection of pyrophosphate using the terpyridine-Zn(II) complex.

Ultraspecific Multiplexed Detection of Low-Abundance Single-Nucleotide Variants by Combining a Masking Tactic with Fluorescent Nanoparticle Counting

To be able to detect simultaneously multiple single-nucleotide variants (SNVs) with both ultrahigh specificity and low-abundance sensitivity is of pivotal importance for molecular diagnostics and biological research. In this contribution, we for the first time developed a multiplex SNV detection method that combines the masking tactic with fluorescent nanoparticle (FNP) counting based on the sandwich design. The method presents a rivaling performance due to its advantageous features: the masking reagent was designed to hybridize with an extremely large amount of the wild-type sequence to render the assay with high specificity; FNP counting provides a sensitive multiplexed SNV detection; the sandwich design facilitates an easy separation to make the detection free of interferences from the matrix. For single SNV target discrimination, including the 6 most frequently occurring DNA KRAS gene mutations and 2 possible RNA KRAS gene mutations as well as 11 artificial mutations, the discrimination factor ranged from 204 to 1177 with the median being 545. Among the tested 19 SNVs, abundances as low as 0.05% were successfully identified in 14 cases, and an abundance as low as 0.1% was identified for the remaining 5 cases. For multiplexed detection of SNVs in the KRAS gene, abundances as low as 0.05-0.1% were achieved for multiple SNVs occurring at the same and different codons. As low as 0.05% low-abundance detection sensitivity was also achieved for PCR amplicons of human genomic DNA extracted from cell samples. This proposed method presents the potential for ultrahigh specific multiplexed detection of SNVs with low-abundance detection capability, which may be applied to practical applications.

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

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.

Detection of EGFR mutation in plasma using multiplex allele-specific PCR (MAS-PCR) and surface enhanced Raman spectroscopy

In this study, surface enhanced Raman spectroscopy (SERS) in combination with multiplexed polymerase chain reaction (PCR) was utilized to detect mutations of exons 19 and 21 of the epidermal growth factor receptor (EGFR) gene. Through the use of multiplexed PCR, the two mutation types were amplified in a single reaction. SERS was used on the PCR products to detect mutations. DNA mixtures with increasing mutation percentages showed good linear relationship between mutation rates and peak height. Then, this PCR-SERS method was used on the plasma of 48 patients with non-small cell lung cancer (NSCLC) to detect EGFR mutations. Analysis of variance (ANOVA) and receiver operating characteristic (ROC) analysis revealed that the peak height ratios were significant for identifying different mutation types. The specificity, sensitivity and accuracy obtained were all 100%. The proposed method was then validated through comparison with high resolution melting (HRM) and showed high concordance with HRM (Pearson correlation is 0.92). Finally, logistic regression was performed on EGFR mutation status and the clinical features of the 48 patients. Our study indicates that PCR-SERS is an effective, noninvasive, and economical method for the detection and monitoring of EGFR mutations in the plasma of patients with NSCLC.

Visualized detection of single-base difference in multiplexed loop-mediated isothermal amplification amplicons by invasive reaction coupled with oligonucleotide probe-modified gold nanoparticles

Loop-mediated isothermal amplification (LAMP) is a well-developed DNA amplification method with an ultra-high sensitivity, but it is difficult to recognize a single-base difference (like genotyping) in target-specific amplicons by conventional detection ways, such as the intercalation of dyes into dsDNA amplicons or the increase of solution turbidity along with the polymerization process. To allow genotyping based on LAMP suitable for POCT (point-of-care testing) or on-site testing, here we proposed a highly specific and cost-effective method for detecting a single-base difference in LAMP amplicons. The method includes three key steps, sequence amplifier to amplify multiple fragments containing the single nucleotide polymorphisms (SNPs) of interest, allele identifier to recognize a targeted base in the amplicons by invasive reaction, and signal generator to yield signals by hybridization-induced assembly of oligonucleotide probe-modified gold nanoparticles. Because the allele identifier is sensitive to one base difference, it is possible to use multiplexed LAMP (mLAMP) to generate amplicon mixtures for multiple SNP typing. Genotyping of 3 different SNPs (CYP2C19*2, CYP2C19*3 and MDR1-C3435T) for guiding the dosage of clopidogrel is successfully carried out in a 3-plex LAMP on real clinical samples. As our method relies on the naked-eye detection and constant-temperature reaction, no expensive instrument is required for both target amplification and sequence identification, thus much suitable for inexpensive gene-guided personalized medicine in source-limited regions.

A single quantum dot-based biosensor for DNA point mutation assay

We develop a single quantum dot-based biosensor for sensitive and selective detection of DNA point mutation.

A cascade signal amplification strategy for ultrasensitive colorimetric detection of BRCA1 gene

Schematic illustration of a colorimetric biosensor for breast cancer1 gene detection based on DNAzyme assistant DNA recycling and rolling circle amplification.