A label-free, electrochemical SERS-based assay for detection of DNA hybridization and discrimination of mutations

Targeted synthesis of gold nanorods and characterization of their tailored surface properties using optical and X-ray spectroscopy

In recent years, nanophotonics have had a transformative impact on harnessing energy, directing chemical reactions, and enabling novel molecular dynamics for thermodynamically intensive applications. Plasmonic nanoparticles have emerged as a tool for confining light on nanometer-length scales where regions of intense electromagnetic fields can be precisely tuned for controlled surface chemistry. We demonstrate a precision pH-driven synthesis of gold nanorods with optical resonance properties widely tunable across the near-infrared spectrum. Through controlled electrostatic interactions, we can perform selective adsorbate molecule attachment and monitor the surface transitions through spectroscopic techniques that include ground-state absorption spectrophotometry, two-dimensional X-ray absorption near-edge spectroscopy, Fourier-transform infrared spectroscopy, and surface-enhanced Raman spectroscopy. We elucidate the electronic, structural, and chemical factors that contribute to plasmon-molecule dynamics at the nanoscale with broad implications for the fields of energy, photonics, and bio-inspired materials.

Colorimetric detection of single-nucleotide mutations based on rolling circle amplification and G-quadruplex-based DNAzyme

In this work, we proposed a sensitive and selective colorimetric assay for single nucleotide mutation (SNM) detection combining rolling circle amplification (RCA) and G-quadruplex/hemin DNAzyme complex formation. In the detection principle, the first step involves ssDNA hybridization with a padlock probe (PLP) DNA, which can discriminate a single base mismatch. The successful ligation is followed by an RCA event to generate an abundance of G-quadruplexes (GQ-RCA) which are then transformed into a DNAzyme (G-quadruplex/hemin complex) by the addition of hemin. The color change from colorless 3,3',5,5'-tetramethylbenzidine (TMB) into colored oxTMB when hydrogen peroxide (H2O2) is added indicated the presence of a mutation. The assay had a limit of detection (LOD) of 2.14 pM. Mutations in samples from breast cancer patients were successfully detected with an accuracy of 100% when compared to Sanger sequencing results. The method is easily applicable even in resource poor setting regions given that it doesn't require any sophisticated or expensive instruments, and the signal readout is detectable simply by the naked eye. Our assay might be a useful tool for genetic analysis and clinical molecular diagnosis for breast cancer risk assessment and early detection.

A Dual-Function AgNW@COF SERS Membrane for Organic Pollutant Removal and Simultaneous Concentration Determination

Surface enhanced Raman spectroscopy (SERS) is a highly sensitive analytical detection method commonly employed in biochemical and environmental analysis. Nevertheless, the rapid movement of analytes and interfering components in flow systems can impact the real-time, online detection capability of Raman spectroscopy. To address this issue, we developed an innovative approach utilizing covalent organic framework (COF), a robust porous material with excellent water stability, to coat the surface of Ag nanowire (AgNW) for synthesizing AgNW@COF hybrid. The regular pores of the COF serve to effectively eliminate large interfering molecules while facilitating the efficient transport of specific analytes to SERS hot spots. Additionally, the fluid flow-induced scouring effect aids in excluding interfering molecules from the surface of AgNW. By incorporating AgNW@COF into a bifunctional filter membrane with simultaneous filtration and sensing capabilities, we had achieved efficient purification of organic pollutants as well as real-time identification of pollutant species and concentration.

Detection of necrotrophic DNA marker of anthracnose causing Colletotrichum gloeosporioides fungi in harvested produce using surface plasmon resonance

Agriculture and food crops monitoring is extremely important for securing the food supply chain to human society. Here, we developed a highly specific detection method for monitoring pathogenic fungus Colletotrichum gloeosporioides using necrotrophic DNA biomarker as the recognition element and surface plasmon resonance (SPR) as transducing mechanism in the prism coupling configuration. The sensor shows its response for a wide range of concentrations from pM to μM of target DNA sequence using a complementary DNA probe immobilized on the sensor surface, which could detect concentrations as low as 7 pM. The detection limit is found to be comparable with conventional molecular-based detection platforms, achieved due to optimized spectral SPR bimetallic substrate with subpixel resolution obtained by post processing. The response time of the sensor for detection is less than 30 min at room temperature. The quick detection scheme of the sensor may facilitate the screening of a large number of samples acquired for the sorting of harvested produce. This sensor is fast, reliable, cost-effective, and can be miniaturized for portability for the screening of real samples (mRNA) in the field and packaging house.

Demonstration of a Superior Deep-UV Surface-Enhanced Resonance Raman Scattering (SERRS) Substrate and Single-Base Mutation Detection in Oligonucleotides

In life science, rapid mutation detection in oligonucleotides is in a great demand for genomic and medical screening. To satisfy this demand, surface-enhanced resonance Raman spectroscopy (SERRS) in the deep-UV (DUV) regime offers a promising solution due to its merits of label-free nature, strong electromagnetic confinement, and charge transfer effect. Here, we demonstrate an epitaxial aluminum (Al) DUV-SERRS substrate that resonates effectively with the incident Raman laser and the ss-DNA at 266 nm, yielding significant SERRS signals of the detected analytes. For the first time, to the best of our knowledge, we obtaine SERRS spectra for all bases of oligonucleotides, not only revealing maximum characteristic Raman peaks but also recording the highest enhancement factor of up to 10⁶ for a 1 nm thick adenine monomer. Moreover, our epitaxial Al DUV-SERRS substrate is able to enhance the Raman signal of all four bases of 12-mer ss-DNA and to further linearly quantify the single-base mutation in the 12-mer ss-DNA.

In Situ Growth of AuNPs on Glass Nanofibers for SERS Sensors

It is challenging to fabricate plasmonic nanosensors on high-curvature surfaces with high sensitivity and reproducibility at low cost. Here, we report a facile and straightforward strategy, based on an in situ growth technique, for fabricating glass nanofibers covered by asymmetric gold nanoparticles (AuNPs) with tunable morphologies and adjustable spacings, leading to much improved surface-enhanced Raman scattering (SERS) sensitivity because of hotspots generated by the AuNP surface irregularities and adjacent AuNP coupling. First, nanosensors covered with uniform and well-dispersed citrate-capped spherical AuNPs were constructed using a polystyrene-b-poly(4-vinylpyridine) (PS-P4VP, with 33 mol % P4VP content and 61 kg/mol total molecular weight) block copolymer brush-layer templating method, and then, the deposited AuNPs were grown to asymmetric AuNPs. AuNP morphologies and hence the optical characteristics of AuNP-covered glass nanofibers were easily controlled by the choice of experimental parameters, such as the growth time and growth solution composition. In particular, tunable AuNP average diameters between about 40 and 80 nm with AuNP spacings between about 50 and 1 nm were achieved within 15 min of growth. The SERS sensitivity of branched AuNP-covered nanofibers (3 min growth time) was demonstrated to be more than threefold more intense than that of the original spherical AuNP-covered nanofibers using a 633 nm laser. Finite-difference time-domain simulations were performed, showing that the electric field enhancement is highest for intermediate AuNP diameters. Furthermore, SERS applications of these nanosensors for H₂O₂ detection and pH sensing were demonstrated, offering appealing and promising candidates for real-time monitoring of extra/intracellular species in vitro and in vivo.

Electron Transfer in DNA at Electrified Interfaces

The ability of the DNA double helix to transport electrons underlies many life-centered biological processes and bio-electronic applications. However, there is little consensus on how efficiently the base pair π-stacks of DNA mediate electron transport. This minireview scrutinizes the current state-of-the-art knowledge on electron transfer (ET) properties of DNA and its long-range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA-mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA's ET in living systems and to advances in molecular bioelectronics.

Novel Surface-Enhanced Raman Spectroscopy Techniques for DNA, Protein and Drug Detection

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique in which the Raman scattering signal strength of molecules, absorbed by rough metals or the surface of nanoparticles, experiences an exponential growth (10³-10⁶ times and even 10¹⁴-10¹⁵ times) because of electromagnetic or chemical enhancements. Nowadays, SERS has attracted tremendous attention in the field of analytical chemistry due to its specific advantages, including high selectivity, rich informative spectral properties, nondestructive testing, and the prominent multiplexing capabilities of Raman spectroscopy. In this review, we present the applications of state-of-the-art SERS for the detection of DNA, proteins and drugs. Moreover, we focus on highlighting the merits and mechanisms of achieving enhanced SERS signals for food safety and clinical treatment. The machine learning techniques, combined with SERS detection, are also indicated herein. This review concludes with recommendations for future studies on the development of SERS.

Thioflavin T specifically brightening “Guanine Island” in duplex-DNA: a novel fluorescent probe for single-nucleotide mutation

Here, we found that Thioflavin T (ThT) could specifically bind with a G-GGG unit (named as “Guanine Island”) in double stranded DNA (ds-DNA).

Ultraspecific and Amplification-Free Quantification of Mutant DNA by Single-Molecule Kinetic Fingerprinting

Conventional techniques for detecting rare DNA sequences require many cycles of PCR amplification for high sensitivity and specificity, potentially introducing significant biases and errors. While amplification-free methods exist, they rarely achieve the ability to detect single molecules, and their ability to discriminate between single-nucleotide variants is often dictated by the specificity limits of hybridization thermodynamics. Here we show that a direct detection approach using single-molecule kinetic fingerprinting can surpass the thermodynamic discrimination limit by 3 orders of magnitude, with a dynamic range of up to 5 orders of magnitude with optional super-resolution analysis. This approach detects mutations as subtle as the drug-resistance-conferring cancer mutation EGFR T790M (a single C → T substitution) with an estimated specificity of 99.99999%, surpassing even the leading PCR-based methods and enabling detection of 1 mutant molecule in a background of at least 1 million wild-type molecules. This level of specificity revealed rare, heat-induced cytosine deamination events that introduce false positives in PCR-based detection, but which can be overcome in our approach through milder thermal denaturation and enzymatic removal of damaged nucleobases.

Enzymatically activated reduction-caged SERS reporters for versatile bioassays

Here we report a facile strategy for activating reduction caged Raman reporters for surface-enhanced Raman scattering (SERS) with peroxidases. After selecting suitable caged reporters, versatile bioassays were developed. First, the bioassays for bioactive small molecules were developed. Then, the immunoassay was developed for C reactive protein (CRP), a biomarker for cardiovascular diseases.

Exploring the margins of SERS in practical domain: An emerging diagnostic modality for modern biomedical applications

Excellent multiplexing capability, molecular specificity, high sensitivity and the potential of resolving complex molecular level biological compositions augmented the diagnostic modality of surface-enhanced Raman scattering (SERS) in biology and medicine. While maintaining all the merits of classical Raman spectroscopy, SERS provides a more sensitive and selective detection and quantification platform. Non-invasive, chemically specific and spatially resolved analysis facilitates the exploration of SERS-based nano probes in diagnostic and theranostic applications with improved clinical outcomes compared to the currently available so called state-of-art technologies. Adequate knowledge on the mechanism and properties of SERS based nano probes are inevitable in utilizing the full potential of this modality for biomedical applications. The safety and efficiency of metal nanoparticles and Raman reporters have to be critically evaluated for the successful translation of SERS in to clinics. In this context, the present review attempts to give a comprehensive overview about the selected medical, biomedical and allied applications of SERS while highlighting recent and relevant outcomes ranging from simple detection platforms to complicated clinical applications.

Electron Transfer in Spacer-Free DNA Duplexes Tethered to Gold via dA10 Tags

Electrical properties of DNA critically depend on the way DNA molecules are integrated within the electronics, particularly on DNA-electrode immobilization strategies. Here, we show that the rate of electron transport in DNA duplexes spacer-free tethered to gold via the adenosine terminal region (a dA₁₀ tag) is enhanced compared to the hitherto reported DNA-metal electrode tethering chemistries. The rate of DNA-mediated electron transfer (ET) between the electrode and methylene blue intercalated into the dA₁₀-tagged DNA duplex approached 361 s^-1 at a ca. half-monolayer DNA surface coverage Γ_DNA (with a linear regression limit of 670 s^-1 at Γ_DNA → 0), being 2.7-fold enhanced compared to phosphorothioated dA₅* tethering (6-fold for the C₆-alkanethiol linker representing an additional ET barrier). X-ray photoelectron spectroscopy evidenced dA₁₀ binding to the Au surface via the purine N, whereas dA₅* predominantly coordinated to the surface via sulfur atoms of phosphothioates. The latter apparently induces the DNA strand twist in the point of surface attachment affecting the local DNA conformation and, as a result, decreasing the ET rates through the duplex. Thus, a spacer-free DNA coupling to electrodes via dA₁₀ tags thus allows a perspective design of DNA electronic circuits and sensors with advanced electronic properties and no implication from more expensive, synthetic linkers.

DNA Electrochemistry and Electrochemical Sensors for Nucleic Acids

Sensitive, specific, and fast analysis of nucleic acids (NAs) is strongly needed in medicine, environmental science, biodefence, and agriculture for the study of bacterial contamination of food and beverages and genetically modified organisms. Electrochemistry offers accurate, simple, inexpensive, and robust tools for the development of such analytical platforms that can successfully compete with other approaches for NA detection. Here, electrode reactions of DNA, basic principles of electrochemical NA analysis, and their relevance for practical applications are reviewed and critically discussed.

Electrochemical Monitoring of the Reversible Folding of Surface-Immobilized DNA i-Motifs

Two cytosine (C) rich DNA sequences folding in i-motif upon protonation of C at low pH have been immobilized at gold electrodes to study the impact of the electrode|electrolyte interface on the stability of the noncanonical DNA secondary structure. The effects of the molecular composition and environment on the melting and folding of the structures immobilized at the gold surface have been compared to the properties of the DNA strands in solution. The DNA folding into i-motif upon protonation, both at the surface and in solution, results in a significant variation of the charge density which is monitored electrochemically through the electrostatic interactions between the DNA strand and the electroactive hexaammineruthenium(III). This method is shown to be sufficiently sensitive to distinguish hemiprotonated folded state and single strand unfolded state of i-motif. The pH of melting has been determined for both sequences in the bulk and at the gold|electrolyte interface. The results evidence a stabilizing effect of the interface on i-motif structure, whereby the pH of melting is higher for the sequences immobilized at the surface. The reversibility and precision of the electrochemical model described here allows a clear and simple characterization of DNA structures and does not require any labeling of the sequence.

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.

Electrostatic Cycling of Hybridization Using Nonionic DNA Mimics

This study demonstrates efficient electrostatic control of surface hybridization through use of morpholinos, a charge-neutral DNA mimic, as the immobilized "probes". In addition to being compatible with low ionic strengths, use of uncharged probes renders the field interaction specific to the nucleic acid analyte. In contrast to DNA probes, morpholino probes enable facile cycling between hybridized and dehybridized states within minutes. Impact of ionic strength and temperature on the effectiveness of electrostatics to direct progress of hybridization is evaluated. Optimal electrostatic control is found when stability of probe-analyte duplexes is set so that electrostatics can efficiently switch between the forward (hybridization) and reverse (dehybridization) directions.

Influence of the Thiol Anchor on the Orientation of Surface-Grafted dsDNA Assemblies

The orientation of surface-grafted dsDNA assemblies relative to the surface depends strongly on the nature of the employed thiol anchor. This was shown by ssDNA capture probe strands of 20 bases grafted to a gold surface by three dithiane rings or a single mercaptohexyl group. The capture probe strands were hybridized to one end of complementary ssDNA strands (target) comprising 40, 60, or 80 bases (T₄₀ , T₆₀ , and T₈₀ ). At the other end of the targets a fluorophore-labeled reporter probe ssDNA strand of 20 bases was hybridized. To stiffen the DNA assemblies, the targets T₆₀ and T₈₀ were further hybridized to ssDNA patches of 20 or 40 bases. Whether the fluorescence intensity, and thus the distance between surface and fluorophore, increases or decreases with increasing target length depends on the thiol anchor. Attempts were made to heal the nicks that are present in the formed dsDNA assemblies by ligation. For enzymatic ligation, the presence of a phosphate at the 5'-end of the reporter probe and a patch is required, which may also influence the fluorescence intensity.

Nanoporous Gold Disks Functionalized with Stabilized G-Quadruplex Moieties for Sensing Small Molecules

We report label-free small molecule sensing on nanoporous gold disks functionalized with stabilized Guanine-quadruplex (G4) moieties using surface-enhanced Raman spectroscopy (SERS). By utilizing the unique G4 topological structure, target molecules can be selectively captured onto nanoporous gold (NPG) disk surfaces via π-π stacking and electrostatic attractions. Together with high-density plasmonic "hot spots" of NPG disks, the captured molecules produce a remarkable SERS signal. Our strategy represents the first example of the detection of foreign molecules conjugated to nondouble helical DNA nanostructures using SERS while providing a new technique for studying the formation and evolution of G4 moieties. The molecular specificity of G4 is known to be controlled by its unit sequence. Without losing generality, we have selected d(GGT)₇GG sequence for the sensing of malachite green (MG), a known carcinogen frequently abused illegally in aquaculture. The newly developed technique achieved a lowest detectable concentration at an impressive 50 pM, two orders of magnitude lower than the European Union (EU) regulatory requirement, with high specificity against potential interferents. To demonstrate the translational potential of this technology, we achieved a lowest detectable concentration of 5.0 nM, meeting the EU regulatory requirement, using a portable probe based detection system.

Surface vs. solution hybridization: effects of salt, temperature, and probe type

Hybridization thermodynamics on solid supports are compared with those in solution for two types of hybridization probe, DNA and uncharged morpholino oligonucleotides of identical sequences. Trends in hybridization affinity are discussed with respect to ionic strength, temperature, and surface behavior.

A sandwich-like strategy for the label-free detection of oligonucleotides by surface plasmon fluorescence spectroscopy (SPFS)

Cutting surface-bound optical molecular beacons results in a sandwich-like detection strategy with lower background fluorescence.

For the detection of oligonucleotides a sandwich-like detection strategy has been developed by which the background fluorescence is significantly lowered in comparison with surface-bound molecular beacons. Surface bound optical molecular beacons are DNA hairpin structures comprising a stem and a loop. The end of the stem is modified with a fluorophore and a thiol anchor for chemisorption on gold surfaces. In the closed state the fluorophore is in close proximity to the gold surface, and most of the fluorescence is quenched. After hybridization with a target the hairpin opens, the fluorophore and surface become separated, and the fluorescence drastically increases. Using this detection method the sensitivity is limited by the difference in the fluorescence intensity in the closed and open state. As the background fluorescence is mainly caused by non-quenched fluorophores, a strategy to reduce the background fluorescence is to cut the beacon in two halves. First a thiolated ssDNA capture probe strand (first half) is chemisorbed to a gold surface together with relatively short thiol spacers. Next the target is hybridized by one end to the surface-anchored capture probe and by the other to a fluorophore-labeled reporter probe DNA (second half). The signal readout is done by surface plasmon fluorescence spectroscopy (SPFS). Using this detection strategy the background fluorescence can be significantly lowered, and the detection limit is lowered by more than one order of magnitude. The detection of a target takes only a few minutes and the sensor chips can be used for multiple detection steps without a significant decrease in performance.

Surface-enhanced resonance Raman scattering (SERRS) simulates PCR for sensitive DNA detection

This paper describes a novel double-stranded DNA detection method through resonance between SYBR Green I and DNA with the surface-enhanced resonance Raman scattering (SERRS) assay, which opens an avenue to the quantitative and reliable application of SERRS in DNA detection.

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

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.

Simple, Sensitive and Accurate Multiplex Detection of Clinically Important Melanoma DNA Mutations in Circulating Tumour DNA with SERS Nanotags

Sensitive and accurate identification of specific DNA mutations can influence clinical decisions. However accurate diagnosis from limiting samples such as circulating tumour DNA (ctDNA) is challenging. Current approaches based on fluorescence such as quantitative PCR (qPCR) and more recently, droplet digital PCR (ddPCR) have limitations in multiplex detection, sensitivity and the need for expensive specialized equipment. Herein we describe an assay capitalizing on the multiplexing and sensitivity benefits of surface-enhanced Raman spectroscopy (SERS) with the simplicity of standard PCR to address the limitations of current approaches. This proof-of-concept method could reproducibly detect as few as 0.1% (10 copies, CV < 9%) of target sequences thus demonstrating the high sensitivity of the method. The method was then applied to specifically detect three important melanoma mutations in multiplex. Finally, the PCR/SERS assay was used to genotype cell lines and ctDNA from serum samples where results subsequently validated with ddPCR. With ddPCR-like sensitivity and accuracy yet at the convenience of standard PCR, we believe this multiplex PCR/SERS method could find wide applications in both diagnostics and research.

Development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) aptasensor for direct detection of DNA hybridization

Rapid detection of disease biomarkers at the patient point-of-care is essential to timely and effective treatment. The research described herein focuses on the development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) DNA aptasensor capable of direct detection of tuberculosis (TB) DNA. Specifically, a plausible DNA biomarker present in TB patient urine was chosen as the model target for detection. Cost-effective screen printed electrodes (SPEs) modified with silver nanoparticles (AgNP) were used as the aptasensor platform, onto which the aptamer specific for the target DNA was immobilized. Direct detection of the target DNA was demonstrated through the appearance of SERS peaks characteristic for adenine, present only in the target strand. Modulation of the applied potential allowed for a sizeable increase in the observed SERS response and the use of thiol back-filling prevented non-specific adsorption of non-target DNA. To our knowledge, this work represents the first EC-SERS study of an aptasensor for the direct, label-free detection of DNA hybridization. Such a technology paves the way for rapid detection of disease biomarkers at the patient point-of-care.

Macrocyclic Metal Complex-DNA Conjugates for Electrochemical Sensing of Single Nucleobase Changes in DNA

The direct incorporation of macrocyclic cyclidene complexes into DNA via automated synthesis results in a new family of metal-functionalized DNA derivatives that readily demonstrate their utility through the ability of one redox-active copper(II)-containing strand to distinguish electrochemically between all four canonical DNA nucleobases at a single site within a target sequence of DNA.

Ultrasensitive surface-enhanced Raman scattering detection in common fluids

Detecting target analytes with high specificity and sensitivity in any fluid is of fundamental importance to analytical science and technology. Surface-enhanced Raman scattering (SERS) has proven to be capable of detecting single molecules with high specificity, but achieving single-molecule sensitivity in any highly diluted solutions remains a challenge. Here we demonstrate a universal platform that allows for the enrichment and delivery of analytes into the SERS-sensitive sites in both aqueous and nonaqueous fluids, and its subsequent quantitative detection of Rhodamine 6G (R6G) down to ∼75 fM level (10(-15) mol⋅L(-1)). Our platform, termed slippery liquid-infused porous surface-enhanced Raman scattering (SLIPSERS), is based on a slippery, omniphobic substrate that enables the complete concentration of analytes and SERS substrates (e.g., Au nanoparticles) within an evaporating liquid droplet. Combining our SLIPSERS platform with a SERS mapping technique, we have systematically quantified the probability, p(c), of detecting R6G molecules at concentrations c ranging from 750 fM (p > 90%) down to 75 aM (10(-18) mol⋅L(-1)) levels (p ≤ 1.4%). The ability to detect analytes down to attomolar level is the lowest limit of detection for any SERS-based detection reported thus far. We have shown that analytes present in liquid, solid, or air phases can be extracted using a suitable liquid solvent and subsequently detected through SLIPSERS. Based on this platform, we have further demonstrated ultrasensitive detection of chemical and biological molecules as well as environmental contaminants within a broad range of common fluids for potential applications related to analytical chemistry, molecular diagnostics, environmental monitoring, and national security.

Potential-Assisted DNA Immobilization as a Prerequisite for Fast and Controlled Formation of DNA Monolayers

Highly reproducible and fast potential-assisted immobilization of single-stranded (ss)DNA on gold surfaces is achieved by applying a pulse-type potential modulation. The desired DNA coverage can be obtained in a highly reproducible way within minutes. Understanding the underlying processes occurring during potential-assisted ssDNA immobilization is crucial. We propose a model that considers the role of ions surrounding the DNA strands, the distance dependence of the applied potentials within the electrolyte solution, and most importantly the shift of the potential of zero charge during the immobilization due to the surface modification with DNA. The control of the surface coverage of ssDNA as well as the achieved speed and high reproducibility are seen as prerequisites for improved DNA-based bioassays.

Specifically horizontally tethered DNA probes on Au surfaces allow labelled and label-free DNA detection using SERS and electrochemically driven melting

Controlled covalent attachment of dsDNA horizontally orientated on a gold surface is achieved through the use of a single surface-linker located approximately half way along the attached DNA probe strand.

Controlled covalent attachment of dsDNA horizontally orientated on a gold surface is achieved through the use of a single surface-linker located approximately half way along the attached DNA probe strand. We show that horizontally oriented dsDNA on a gold surface can undergo melting and re-hybridization to target strand in solution and thus can be used for the detection of specific target DNA sequences using surface-enhanced Raman spectroscopy (SERS). We show that a range of lengths of target DNA sequences from ∼30-bases to 78-bases can be specifically hybridized to the short immobilized DNA probe sequence and adopt a horizontal orientation on the gold surface. Following thermal or electrochemically driven melting of the immobilized dsDNA, the target DNA strand diffuses away while the probe strand remains attached to the surface allowing the functionalized surfaces to be reused. The melting of the horizontally orientated immobilized dsDNA can be monitored using SERS either by employing a dye label covalently attached on the DNA target strand or by employing a binding agent selective for dsDNA. This approach of covalently immobilizing the DNA probe strand through a linker located at approximately the middle of the strand has great potential to improve the sensitivity and specificity of molecular assays that employ DNA arrays on solid surfaces.

Structural Characterization of Single-Stranded DNA Monolayers Using Two-Dimensional Sum Frequency Generation Spectroscopy

DNA-covered materials are important in technological applications such as biosensors and microarrays, but obtaining structural information on surface-bound biomolecules is experimentally challenging. In this paper, we structurally characterize single-stranded DNA monolayers of poly(thymine) from 10 to 25 bases in length with an emerging surface technique called two-dimensional sum frequency generation (2D SFG) spectroscopy. These experiments are carried out by adding a mid-IR pulse shaper to a femtosecond broad-band SFG spectrometer. Cross peaks and 2D line shapes in the 2D SFG spectra provide information about structure and dynamics. Because the 2D SFG spectra are heterodyne detected, the monolayer spectra can be directly compared to 2D infrared (2D IR) spectra of poly(thymine) in solution, which aids interpretation. We simulate the 2D SFG spectra using DFT calculations and an excitonic Hamiltonian that relates the molecular geometry to the vibrational coupling. Intrabase cross peaks help define the orientation of the bases and interbase cross peaks, created by coupling between bases, and resolves features not observed in 1D SFG spectra that constrain the relative geometries of stacked bases. We present a structure for the poly(T) oligomer that is consistent with the 2D SFG data. These experiments provide insight into the DNA monolayer structure and set precedent for studying complex biomolecules on surfaces with 2D SFG spectroscopy.

Strain discrimination of Yersinia pestis using a SERS-based electrochemically driven melting curve analysis of variable number tandem repeat sequences

Strain discrimination within genetically highly similar bacteria is critical for epidemiological studies and forensic applications. An electrochemically driven melting curve analysis monitored by SERS has been utilised to reliably discriminate strains of the bacterial pathogen Yersinia pestis, the causative agent of plague. DNA amplicons containing Variable Number Tandem Repeats (VNTRs) were generated from three strains of Y. pestis: CO92, Harbin 35 and Kim. These amplicons contained a 10 base pair VNTR repeated 6, 5, and 4 times in CO92, Harbin 35 and Kim respectively. The assay also included a blocker oligonucleotide comprising 3 repeats of the 10-mer VNTR sequence. The use of the blocker reduced the effective length of the target sequence available to bind to the surface bound probe and significantly improved the sensitivity of the discrimination. The results were consistent during three replicates that were carried out on different days, using different batches of PCR product and different SERS sphere segment void (SSV) substrate. This methodology which combines low cost, speed and sensitivity is a promising alternative to the time consuming current electrophoretic methods.

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

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.

A label-free fluorescent molecular switch for a DNA hybridization assay utilizing a G-quadruplex-selective auramine O

A G-quadruplex molecular switch (G4-MS) assembled using auramine O and the G-rich single stranded DNA is developed for a DNA assay.