Recent advancements in optical DNA biosensors: exploiting the plasmonic effects of metal nanoparticles

Discrimination of Genetic Biomarkers of Disease through Machine-Learning-Based Hypothesis Testing of Direct SERS Spectra of DNA and RNA

Cancer is globally a leading cause of death that would benefit from diagnostic approaches detecting it in its early stages. However, despite much research and investment, cancer early diagnosis is still underdeveloped. Owing to its high sensitivity, surface-enhanced Raman spectroscopy (SERS)-based detection of biomarkers has attracted growing interest in this area. Oligonucleotides are an important type of genetic biomarkers as their alterations can be linked to the disease prior to symptom onset. We propose a machine-learning (ML)-enabled framework to analyze complex direct SERS spectra of short, single-stranded DNA and RNA targets to identify relevant mutations occurring in genetic biomarkers, which are key disease indicators. First, by employing ad hoc-synthesized colloidal silver nanoparticles as SERS substrates, we analyze single-base mutations in ssDNA and RNA sequences using a direct SERS-sensing approach. Then, an ML-based hypothesis test is proposed to identify these changes and differentiate the mutated sequences from the corresponding native ones. Rooted in "functional data analysis," this ML approach fully leverages the rich information and dependencies within SERS spectral data for improved modeling and detection capability. Tested on a large set of DNA and RNA SERS data, including from miR-21 (a known cancer miRNA biomarker), our approach is shown to accurately differentiate SERS spectra obtained from different oligonucleotides, outperforming various data-driven methods across several performance metrics, including accuracy, sensitivity, specificity, and F1-scores. Hence, this work represents a step forward in the development of the combined use of SERS and ML as effective methods for disease diagnosis with real applicability in the clinic.

A Target Recycling Amplification Process for the Digital Detection of Exosomal MicroRNAs through Photonic Resonator Absorption Microscopy

Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer development, dis-ease progression, treatment effects and prognosis. Here, we report an efficient target recycling amplification process (TRAP) for the digital detection of miRNAs using photonic resonator absorption microscopy. We achieve multiplex digital detection with sub-attomolar sensitivity in 20 minutes, robust selectivity for single nucleotide variants, and a broad dynamic range from 1 aM to 1 pM. Compared with traditional qRT-PCR, TRAP showed similar accuracy in profiling exosomal miRNAs derived from cancer cells, but also exhibited at least 31-fold and 61-fold enhancement in the limits of miRNA-375 and miRNA-21 detection, respectively. The TRAP approach is ideal for exosomal or circulating miRNA biomarker quantification, where the miRNAs are present in low concentrations or sample volume, with potentials for frequent, low-cost, and minimally invasive point-of-care testing.

Charge transfer effect: a new assignment of the abnormal optical absorption band of gold nanoparticles

As a significant accompanying phenomenon of surface-enhanced Raman scattering (SERS), the addition of foreign molecules to colloidal gold or silver nanoparticles results in a new abnormal optical absorption (AOA) band, which usually appears in the long-wavelength region. The assignment of this AOA band has long been debated as an important issue that is desired to be addressed in the SERS field, which is crucial for a clear understanding of the SERS enhancement mechanism and beneficial to surface plasmonics. In this study, both the calculated and measured optical absorptions of gold nanoparticle monomers and dimers as well as their interactions with adsorbed molecules, showed that the AOA band in the long-wavelength region which was assigned to the characteristic longitudinal localized surface plasmon resonance (LSPR) effect of gold nanoparticle chain aggregates in conventional SERS electromagnetic theory, should be attributed to the charge-transfer resonance absorption from gold nanoparticles to adsorbed molecules. This was further confirmed by the corresponding SERS effects. As the excitation wavelength at 785 nm was resonant with the broad AOA band centered at 750 nm, the SERS peaks of the adsorbed pyridine molecules could be dramatically enhanced due to the charge-transfer resonance effect. In contrast, under an excitation wavelength of 532 nm, the SERS peaks appeared very weak, although the excitation wavelength was resonant with the LSPR absorption band of the individual gold nanoparticles.

Biopolymer Composites with Sensors for Environmental and Medical Applications

One of the biggest economic and environmental sustainability problems is the over-reliance on petroleum chemicals in polymer production. This paper presents an overview of the current state of knowledge on biopolymers combined with biosensors in terms of properties, compounding methods and applications, with a focus on medical and environmental aspects. Therefore, this article is devoted to environmentally friendly polymer materials. The paper presents an overview of the current state of knowledge on biopolymers combined with biosensors in terms of properties, compounding methods and applications, with a special focus on medical and environmental aspects. The paper presents the current state of knowledge, as well as prospects. The article shows that biopolymers made from renewable raw materials are of great interest in various fields of science and industry. These materials not only replace existing polymers in many applications, but also provide new combinations of properties for new applications. Composite materials based on biopolymers are considered superior to traditional non-biodegradable materials due to their ability to degrade when exposed to environmental factors. The paper highlights the combination of polymers with nanomaterials which allows the preparation of chemical sensors, thus enabling their use in environmental or medical applications due to their biocompatibility and sensitivity. This review focuses on analyzing the state of research in the field of biopolymer-sensor composites.

Hyperspectral dark field optical microscopy for orientational imaging of a single plasmonic nanocube using a physics-based learning method

Rotational dynamics at the molecular level could provide additional data regarding protein diffusion and cytoskeleton formation at the cellular level. Due to the isotropic emission pattern of fluorescence molecules, it is challenging to extract rotational information from them during imaging. Metal nanoparticles show a polarization-dependent response and could be used for sensing rotational motion. Nanoparticles as an orientation sensing probe offer bio-compatibility and robustness against photo-blinking and photo-bleaching compared to conventional fluorescent molecules. Previously, asymmetric geometrical structures such as nanorods have been used for orientational imaging. Here, we show orientational imaging of symmetric geometrical structures such as 100 nm isolated silver nanocubes by coupling a hyperspectral detector and a focused ion beam (FIB)-fabricated correlating substrate. More than 100 nanocubes are analyzed to confirm spectral shifts in the scattering spectra due to variations in the orientation of the nanocubes with respect to the incoming light. Results are further validated using finite-difference time-domain simulations. Our observations suggest a novel strategy for high-throughput orientation imaging of nanoparticles.

Non-Coding RNA-Based Biosensors for Early Detection of Liver Cancer

Primary liver cancer is an aggressive, lethal malignancy that ranks as the fourth leading cause of cancer-related death worldwide. Its 5-year mortality rate is estimated to be more than 95%. This significant low survival rate is due to poor diagnosis, which can be referred to as the lack of sufficient and early-stage detection methods. Many liver cancer-associated non-coding RNAs (ncRNAs) have been extensively examined to serve as promising biomarkers for precise diagnostics, prognostics, and the evaluation of the therapeutic progress. For the simple, rapid, and selective ncRNA detection, various nanomaterial-enhanced biosensors have been developed based on electrochemical, optical, and electromechanical detection methods. This review presents ncRNAs as the potential biomarkers for the early-stage diagnosis of liver cancer. Moreover, a comprehensive overview of recent developments in nanobiosensors for liver cancer-related ncRNA detection is provided.

An electrochemical biosensor based on a graphene oxide modified pencil graphite electrode for direct detection and discrimination of double-stranded DNA sequences

The ability to directly recognize double-stranded DNA (ds-DNA) is a major challenge in disease diagnosis and gene therapy because DNA is naturally double-stranded. Herein, a novel electrochemical biosensor for the sequence-specific recognition of ds-DNA using a peptide nucleic acid (PNA) probe and graphene oxide (GO) modified pencil graphite electrode is reported and applied for the direct detection of the desired sequence in plasmid samples. For this purpose, GO was assembled onto the pencil graphite electrode surface (GO/PGE) by a simple casting method and applied for PNA probe immobilization (PNA-GO/PGE). Upon addition of ds-DNA, the interaction of the PNA probe with ds-DNA induces probe detachment from the electrode surface which results in a guanine oxidation signal decrease. Under optimized conditions, the guanine oxidation signal decreased linearly with the ds-DNA concentration increasing in the range from 30 pM to 10 nM, with a detection limit of 1.3 pM. Moreover, the proposed biosensor was applied for the sensitive and selective detection of double-stranded target DNA in plasmid samples. This proposed method could be used as a platform for direct detection of various sequences in double-stranded genomic DNA.

Plasmonic Nanoassemblies: Tentacles Beat Satellites for Boosting Broadband NIR Plasmon Coupling Providing a Novel Candidate for SERS and Photothermal Therapy

Optical theranostic applications demand near-infrared (NIR) localized surface plasmon resonance (LSPR) and maximized electric field at nanosurfaces and nanojunctions, aiding diagnosis via Raman or optoacoustic imaging, and photothermal-based therapies. To this end, multiple permutations and combinations of plasmonic nanostructures and molecular "glues" or linkers are employed to obtain nanoassemblies, such as nanobranches and core-satellite morphologies. An advanced nanoassembly morphology comprising multiple linear tentacles anchored onto a spherical core is reported here. Importantly, this core-multi-tentacle-nanoassembly (CMT) benefits from numerous plasmonic interactions between multiple 5 nm gold nanoparticles (NPs) forming each tentacle as well as tentacle to core (15 nm) coupling. This results in an intense LSPR across the "biological optical window" of 650-1100 nm. It is shown that the combined interactions are responsible for the broadband LSPR and the intense electric field, otherwise not achievable with core-satellite morphologies. Further the sub 80 nm CMTs boosted NIR-surface-enhanced Raman scattering (SERS), with detection of SERS labels at 47 × 10^-9 m, as well as lower toxicity to noncancerous cell lines (human fibroblast Wi38) than observed for cancerous cell lines (human breast cancer MCF7), presents itself as an attractive candidate for use as biomedical theranostics agents.

Enzyme Responsive Inverse Opal Hydrogels

Structured color in nature is controlled by nano- and micro-structured interfaces giving rise to a photonic bandgap. This study presents a biomimetic optical material based on polymeric inverse opals that respond to enzyme activity. Polymer colloids provide a template in which acryloyl-functionalized poly(ethylene glycol) is integrated; dissolution of the colloids leads to a hydrogel inverse opal that can be lithographically patterned using transfer printing. Incorporating enzyme substrates within the voids provides a material that responds to the presence of proteases through a shift in the optical properties.

Comparative study of serum sample preparation methods in aggregation-based plasmonic sensing

The use of nanoparticle-based colorimetric methods has received considerable attention for clinical analysis in biofluids. Sample preparation methods are surveyed here to minimize the impact of the sample matrix on the performance of a nanoparticle aggregation assay.

Polymerase chain reaction - surface-enhanced Raman spectroscopy (PCR-SERS) method for gene methylation level detection in plasma

Gene promoter hypermethylation is a vital step in tumorigenesis. This paper set out to explore the use of polymerase chain reaction - surface-enhanced Raman spectroscopy (PCR-SERS) for the detection of gene methylation levels, with a focus on cancer diagnosis. Methods: PCR with methylation independent primers were used on DNA samples to amplify target genes regardless of their methylation states. SERS was used on the obtained PCR products to generate spectra that contained peak changes belonging to CG and AT base pairs. Multiple linear regression (MLR) was then used to deconvolute the SERS spectra so that the CG/AT ratios of the sample could be obtained. These MLR results were used to calculate methylation levels of the target genes. For protocol verification, three sets of seven reference DNA solutions with known methylation levels (0%, 1%, 5%, 25%, 50%, 75%, and 100%) were analysed. Clinically, blood plasma samples were taken from 48 non-small-cell lung cancer (NSCLC) patients and 51 healthy controls. The methylation levels of the genes p16, MGMT, and RASSF1 were determined for each patient using this method. Results: Verification experiment on the mixtures with known methylation levels resulted in an error of less than 6% from the actual levels. When applied to our clinical samples, the frequency of methylation in at least one of the three target genes among the NSCLC patients was 87.5%, but this percentage decreased to 11.8% for the control group. The methylation levels of p16 were found to be significantly higher in NSCLC patients with more pack-years smoked (p=0.04), later cancer stages (p=0.03), and cancer types of squamous cell and large cell versus adenocarcinoma (p=0.03). Prediction accuracy of 88% was achieved from classification and regression trees (CART) based on methylation levels and states, respectively. Conclusion: This research showed that the PCR-SERS protocol could quantitatively measure the methylation levels of genes in plasma. The methylation levels of the genes p16, MGMT, and RASSF1 were higher in NSCLC patients than in controls.

Tagged Core-Satellite Nanoassemblies: Role of Assembling Sequence on Surface-Enhanced Raman Scattering (SERS) Performance

Plasmonic nanoassemblies with amplified optical responses are attractive as chemo/bio sensors and diagnostic tracking agents. For real-life implementation, such nanostructures require a well-designed and controlled formation for maximizing the optical amplification. Forming these nanoassemblies typically requires numerous steps; however, the importance of the sequence of the steps is typically not discussed. Thus, here we have investigated the role of the sequence of tagging (or labeling, barcoding) of such plasmonic nanoassemblies with Raman active molecules in a quest to maximize the surface-enhanced Raman scattering (SERS) enhancement that could be achieved from the nanoassemblies. We have chosen the core-satellite nanoassembly arrangement to study the role of tagging sequence because it allows us to keep structural parameters constant that would otherwise influence the SERS amplification. We demonstrate that incorporating the tag molecule at an assembly point before formation of the nanojunctions leads to more tag molecules being positioned at the core-satellite nanojunctions, thereby resulting in higher SERS signal enhancement. This will thus prove to be a useful tool in fully utilizing the nanoassembly morphology generated hot-spot and maximizing its SERS performance.

Graphene and Graphene-Based Nanomaterials for DNA Detection: A Review

DNA detection with high sensitivity and specificity has tremendous potential as molecular diagnostic agents. Graphene and graphene-based nanomaterials, such as graphene nanopore, graphene nanoribbon, graphene oxide, and reduced graphene oxide, graphene-nanoparticle composites, were demonstrated to have unique properties, which have attracted increasing interest towards the application of DNA detection with improved performance. This article comprehensively reviews the most recent trends in DNA detection based on graphene and graphene-related nanomaterials. Based on the current understanding, this review attempts to identify the future directions in which the field is likely to thrive, and stimulate more significant research in this subject.

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.

Optimizations needed for lateral flow assay for rapid detection of pathogenic E. coli

Lateral flow assay (LFA), or the immunochromatographic strip test, is popular to use for rapid and sensitive immunoassays. Gold nanoparticles (GNPs), due to tunable optical characteristics and easy manipulation of size or shape, represent an attractive approach for LFA technology. Since most enterohemorrhagic infections result from water and food contaminations of Escherichia coli O157:H7, selective and rapid detection of this organism in environmental and biological complexes is necessary. In this study, optimized parameters of antibody (Ab)-based LFA for rapid detection of pathogenic E. coli O157:H7 are described. GNPs were used as visualizing agents. The measuring parameters include the Ab concentration on the capture lines, the concentration of gold conjugate, and flow rate. M180 and 36 nm were the ideal membrane and GNP size, respectively, for bacterial detection of LFA. The target, E. coli O157:H7, could be detected with a visual limit of detection of 105 cfu/mL in 3-5 min. Selectivity of the system was very high and the target was recognized by developed strips, regardless of its presence singly or in mixed bacterial samples.

Liquid-to-gel transition for visual and tactile detection of biological analytes

So far all visual and instrument-free methods have been based on a color change. However, colorimetric assays cannot be used by blind or color-blind people. Here we introduce a liquid-to-gel transition as a general output platform. The signal output (a piece of gel) can be unambiguously distinguished from liquid both visually and by touch. This approach promises to contribute to the development of an accessible environment for visually impaired persons.

Folding- and Dynamics-Based Electrochemical DNA Sensors

A number of electrochemical DNA sensors based on the target-induced change in the conformation and/or flexibility of surface-bound oligonucleotides have been developed in recent years. These sensors, which are often termed E-DNA sensors, are comprised of an oligonucleotide probe modified with a redox label (e.g., methylene blue) at one terminus and attached to a gold electrode via a thiol-gold bond at the other. Binding of the target to the DNA probe changes its structure and dynamics, which, in turn, influences the efficiency of electron transfer to the interrogating electrode. Since electrochemically active contaminants are less common, these sensors are resistant to false-positive signals arising from the nonspecific adsorption of contaminants and perform well even when employed directly in serum, whole blood, and other realistically complex sample matrices. Moreover, because all of the sensor components are chemisorbed to the electrode, the E-DNA sensors are essentially label-free and readily reusable. To date, these sensors have achieved state-of-the-art sensitivity, while offering the unprecedented selectivity, reusability, and the operational convenience of direct electrochemical detection. This chapter reviews the recent advances in the development of both "signal-off" and "signal-on" E-DNA sensors. Critical aspects that dictate the stability and performance of these sensors are also addressed so as to provide a realistic overview of this oligonucleotide detection platform.

Computational Sensing Using Low-Cost and Mobile Plasmonic Readers Designed by Machine Learning

Plasmonic sensors have been used for a wide range of biological and chemical sensing applications. Emerging nanofabrication techniques have enabled these sensors to be cost-effectively mass manufactured onto various types of substrates. To accompany these advances, major improvements in sensor read-out devices must also be achieved to fully realize the broad impact of plasmonic nanosensors. Here, we propose a machine learning framework which can be used to design low-cost and mobile multispectral plasmonic readers that do not use traditionally employed bulky and expensive stabilized light sources or high-resolution spectrometers. By training a feature selection model over a large set of fabricated plasmonic nanosensors, we select the optimal set of illumination light-emitting diodes needed to create a minimum-error refractive index prediction model, which statistically takes into account the varied spectral responses and fabrication-induced variability of a given sensor design. This computational sensing approach was experimentally validated using a modular mobile plasmonic reader. We tested different plasmonic sensors with hexagonal and square periodicity nanohole arrays and revealed that the optimal illumination bands differ from those that are "intuitively" selected based on the spectral features of the sensor, e.g., transmission peaks or valleys. This framework provides a universal tool for the plasmonics community to design low-cost and mobile multispectral readers, helping the translation of nanosensing technologies to various emerging applications such as wearable sensing, personalized medicine, and point-of-care diagnostics. Beyond plasmonics, other types of sensors that operate based on spectral changes can broadly benefit from this approach, including e.g., aptamer-enabled nanoparticle assays and graphene-based sensors, among others.

The Role of Reactive Oxygen Species (ROS) in the Biological Activities of Metallic Nanoparticles

Nanoparticles (NPs) possess unique physical and chemical properties that make them appropriate for various applications. The structural alteration of metallic NPs leads to different biological functions, specifically resulting in different potentials for the generation of reactive oxygen species (ROS). The amount of ROS produced by metallic NPs correlates with particle size, shape, surface area, and chemistry. ROS possess multiple functions in cellular biology, with ROS generation a key factor in metallic NP-induced toxicity, as well as modulation of cellular signaling involved in cell death, proliferation, and differentiation. In this review, we briefly explained NP classes and their biomedical applications and describe the sources and roles of ROS in NP-related biological functions in vitro and in vivo. Furthermore, we also described the roles of metal NP-induced ROS generation in stem cell biology. Although the roles of ROS in metallic NP-related biological functions requires further investigation, modulation and characterization of metallic NP-induced ROS production are promising in the application of metallic NPs in the areas of regenerative medicine and medical devices.

Direct Quantification of DNA Base Composition by Surface-Enhanced Raman Scattering Spectroscopy

Design of ultrasensitive DNA sensors based on the unique physical properties of plasmonic nanostructures has become one of the most exciting areas in nanomedicine. However, despite the vast number of proposed applications, the determination of the base composition in nucleic acids, a fundamental parameter in genomic analyses and taxonomic classification, is still restricted to time-consuming and poorly sensitive conventional methods. Herein, we demonstrate the possibility of determining the base composition in single- and double-stranded DNA by using a simple, low-cost, high-throughput, and label-free surface-enhanced Raman scattering (SERS) method in combination with cationic nanoparticles.

Nanoparticles and DNA - a powerful and growing functional combination in bionanotechnology

Functionally integrating DNA and other nucleic acids with nanoparticles in all their different physicochemical forms has produced a rich variety of composite nanomaterials which, in many cases, display unique or augmented properties due to the synergistic activity of both components. These capabilities, in turn, are attracting greater attention from various research communities in search of new nanoscale tools for diverse applications that include (bio)sensing, labeling, targeted imaging, cellular delivery, diagnostics, therapeutics, theranostics, bioelectronics, and biocomputing to name just a few amongst many others. Here, we review this vibrant and growing research area from the perspective of the materials themselves and their unique capabilities. Inorganic nanocrystals such as quantum dots or those made from gold or other (noble) metals along with metal oxides and carbon allotropes are desired as participants in these hybrid materials since they can provide distinctive optical, physical, magnetic, and electrochemical properties. Beyond this, synthetic polymer-based and proteinaceous or viral nanoparticulate materials are also useful in the same role since they can provide a predefined and biocompatible cargo-carrying and targeting capability. The DNA component typically provides sequence-based addressability for probes along with, more recently, unique architectural properties that directly originate from the burgeoning structural DNA field. Additionally, DNA aptamers can also provide specific recognition capabilities against many diverse non-nucleic acid targets across a range of size scales from ions to full protein and cells. In addition to appending DNA to inorganic or polymeric nanoparticles, purely DNA-based nanoparticles have recently surfaced as an excellent assembly platform and have started finding application in areas like sensing, imaging and immunotherapy. We focus on selected and representative nanoparticle-DNA materials and highlight their myriad applications using examples from the literature. Overall, it is clear that this unique functional combination of nanomaterials has far more to offer than what we have seen to date and as new capabilities for each of these materials are developed, so, too, will new applications emerge.

Fast Optical Chemical and Structural Classification of RNA

As more biological activities of ribonucleic acids continue to emerge, the development of efficient analytical tools for RNA identification and characterization is necessary to acquire an in-depth understanding of their functions and chemical properties. Herein, we demonstrate the capacity of label-free direct surface-enhanced Raman scattering (SERS) analysis to access highly specific structural information on RNAs at the ultrasensitive level. This includes the recognition of distinctive vibrational features of RNAs organized into a variety of conformations (micro-, fully complementary duplex-, small interfering- and short hairpin-RNAs) or characterized by subtle chemical differences (single-base variances, nucleobase modifications and backbone composition). This method represents a key advance in the ribonucleic acid analysis and will have a direct impact in a wide range of different fields, including medical diagnosis, drug design, and biotechnology, by enabling the rapid, high-throughput, simple, and low-cost identification and classification of structurally similar RNAs.

Silver colloids as plasmonic substrates for direct label-free surface-enhanced Raman scattering analysis of DNA

Unraveling the role played by the surface chemistry of silver colloids in the direct SERS analysis of DNA.

Surface Enzyme Chemistries for Ultrasensitive Microarray Biosensing with SPR Imaging

The sensitivity and selectivity of surface plasmon resonance imaging (SPRI) biosensing with nucleic acid microarrays can be greatly enhanced by exploiting various nucleic acid ligases, nucleases, and polymerases that manipulate the surface-bound DNA and RNA. We describe here various examples from each of these different classes of surface enzyme chemistries that have been incorporated into novel detection strategies that either drastically enhance the sensitivity of or create uniquely selective methods for the SPRI biosensing of proteins and nucleic acids. A dual-element generator-detector microarray approach that couples a bioaffinity adsorption event on one microarray element to nanoparticle-enhanced SPRI measurements of nucleic acid hybridization adsorption on a different microarray element is used to quantitatively detect DNA, RNA, and proteins at femtomolar concentrations. Additionally, this dual-element format can be combined with the transcription and translation of RNA from surface-bound double-stranded DNA (dsDNA) templates for the on-chip multiplexed biosynthesis of aptamer and protein microarrays in a microfluidic format; these microarrays can be immediately used for real-time SPRI bioaffinity sensing measurements.

Investigating nanoparticle properties in plasmonic nanoarchitectures with DNA by surface plasmon resonance imaging

The optimal optical coupling conditions between SPWs and nanoparticle LSPs can be achieved by overlapping the source wavelength with the wavelength of excitation of LSPs.

Electrochemical detection of azidothymidine on modified probes based on chitosan stabilised silver nanoparticles hybrid material

Silver nanoparticle stabilized by chitosan is synthesized for modification of sensing probe for AZT estimation in human plasma.

Laser hybrid micro/nano-structuring of Si surfaces in air and its applications for SERS detection

Surface enhanced Raman spectroscopy (SERS) has been widely investigated as an effective technique for low-concentration bio-chemical molecules detection. A rapid two-step approach to fabricate SERS substrates with high controllability in ambient air is developed. Dynamic laser ablation directly creates microgroove on the Si substrate. Meanwhile, nanoparticles are synthesized via the nucleation of laser induced plasma species and the air molecules. It configures the Si surface into four different regions decorated with nanoparticles at different sizes. With Ag film coating, these nanoparticles function as hotspots for SERS. Microsquare arrays are fabricated on the Si surface as large-area SERS substrates by the laser ablation in horizontal and vertical directions. In each microsquare, it exhibits quasi-3D structures with randomly arranged and different shaped nanoparticles aggregated in more than one layer. With Ag film deposition, uniform SERS signals are obtained by detecting the 4-methylbenzenethiol molecules. The SERS signal intensity is determined by the size and shape distributions of the nanoparticles, which depend on the laser processing parameters. With the optimal laser fluence, the SERS signals show a uniform enhancement factor up to 5.5 × 10(6). This provides a high-speed and low-cost method to produce SERS substrates over a large area.

An ion-exchange nanomembrane sensor for detection of nucleic acids using a surface charge inversion phenomenon

We present a novel low-cost biosensor for rapid, sensitive and selective detection of nucleic acids based on an ionic diode feature of an anion exchange nanoporous membrane under DC bias. The ionic diode feature is associated with external surface charge inversion on the positively charged anion exchange nanomembrane upon hybridization of negatively charged nucleic acid molecules to single-stranded oligoprobes functionalized on the membrane surface resulting in the formation of a cation selective monolayer. The resulting bipolar membrane causes a transition from electroconvection-controlled to water-splitting controlled ion conductance, with a large ion current signature that can be used to accurately quantify the hybridized nucleic acids. The platform is capable of distinguishing two base-pair mismatches in a 22-base pairing segment of microRNAs associated with oral cancer, as well as serotype-specific detection of dengue virus. We also show the sensor' capability to selectively capture target nucleic acids from a heterogeneous mixture. The limit of detection is 1 pM for short 27 base target molecules in a 15-min assay. Similar hybridization results are shown for short DNA molecules as well as RNAs from Brucella and Escherichia coli. The versatility and simplicity of this low-cost biosensor should enable point-of-care diagnostics in food, medical and environmental safety markets.

Localized surface plasmon resonance: a unique property of plasmonic nanoparticles for nucleic acid detection

Localized surface plasmon resonance (LSPR) of noble metal nanoparticles (a.k.a. plasmonic nanoparticles) opens up a new horizon for advanced biomolecule sensing. However, an effective and practical sensing system still requires meticulous design to achieve good sensitivity and distinctive selectivity for routine use and high-throughput detection. In particular, the detection of DNA and RNA is crucial in biomedical research and clinical diagnostics. This review describes the fundamental aspects of LSPR and provides an overall account of how it is exploited to assist in nucleic acid sensing. The detection efficiency of each LSPR-based approach is assessed with respect to the assay design, the selection of plasmonic nanoparticles, and the choice of nucleic acid probes which influence the duplex hybridization. Judicious comparison is made among various LSPR-based approaches in terms of the assaying time, the sensitivity or lowest sensing concentration (i.e. limit of detection or LOD), and the single-base mismatch (SBM) selectivity.

Electrochemical techniques for characterization of stem-loop probe and linear probe-based DNA sensors

Here we present a summary of the sensor performance of the stem-loop probe (SLP) and linear probe (LP) electrochemical DNA sensors when interrogated using alternating current voltammetry (ACV), cyclic voltammetry (CV), and differential pulse voltammetry (DPV). Specifically, we identified one critical parameter for each voltammetric technique that can be adjusted for optimal sensor performance. Overall, the SLP sensor displayed good sensor performance (i.e., 60+% signal attenuation in the presence of the target) over a wider range of experimental conditions when compared to the LP sensor. When used with ACV, the optimal frequency range was found to be between 5 and 5000 Hz, larger than the 5-100 Hz range observed with the LP sensor. A similar trend was observed for the two sensors in CV; the LP sensor was operational only at scan rates between 30 and 100 V/s, whereas the SLP sensor performed well at scan rates between 1 and 1000 V/s. Unlike ACV and CV, DPV has demonstrated to be a more versatile sensor interrogation technique for this class of sensors. Despite the minor differences in total signal attenuation upon hybridization to the target DNA, both SLP and LP sensors performed optimally under most pulse widths used in this study. More importantly, when used with longer pulse widths, both sensors showed "signal-on" behavior, which is generally more desirable for sensor applications.

Label-free DNA biosensor based on SERS Molecular Sentinel on Nanowave chip

Development of a rapid, cost-effective, label-free biosensor for DNA detection is important for many applications in clinical diagnosis, homeland defense, and environment monitoring. A unique label-free DNA biosensor based on Molecular Sentinel (MS) immobilized on a plasmonic 'Nanowave' chip, which is also referred to as a metal film over nanosphere (MFON), is presented. Its sensing mechanism is based upon the decrease of the surface-enhanced Raman scattering (SERS) intensity when Raman label tagged at one end of MS is physically separated from the MFON's surface upon DNA hybridization. This method is label-free as the target does not have to be labeled. The MFON fabrication is relatively simple and low-cost with high reproducibility based on depositing a thin shell of gold over close-packed arrays of nanospheres. The sensing process involves a single hybridization step between the DNA target sequences and the complementary MS probes on the Nanowave chip without requiring secondary hybridization or posthybridization washing, thus resulting in rapid assay time and low reagent usage. The usefulness and potential application of the biosensor for medical diagnostics is demonstrated by detecting the human radical S-adenosyl methionine domain containing 2 (RSAD2) gene, a common inflammation biomarker.

Tiny grains give huge gains: nanocrystal-based signal amplification for biomolecule detection

Nanocrystals, despite their tiny sizes, contain thousands to millions of atoms. Here we show that the large number of atoms packed in each metallic nanocrystal can provide a huge gain in signal amplification for biomolecule detection. We have devised a highly sensitive, linear amplification scheme by integrating the dissolution of bound nanocrystals and metal-induced stoichiometric chromogenesis, and demonstrated that signal amplification is fully defined by the size and atom density of nanocrystals, which can be optimized through well-controlled nanocrystal synthesis. Further, the rich library of chromogenic reactions allows implementation of this scheme in various assay formats, as demonstrated by the iron oxide nanoparticle linked immunosorbent assay (ILISA) and blotting assay developed in this study. Our results indicate that, owing to the inherent simplicity, high sensitivity and repeatability, the nanocrystal based amplification scheme can significantly improve biomolecule quantification in both laboratory research and clinical diagnostics. This novel method adds a new dimension to current nanoparticle-based bioassays.

Permanent fixing or reversible trapping and release of DNA micropatterns on a gold nanostructure using continuous-wave or femtosecond-pulsed near-infrared laser light

The use of localized surface plasmons (LSPs) for highly sensitive biosensors has already been investigated, and they are currently being applied for the optical manipulation of small nanoparticles. The objective of this work was the optical trapping of λ-DNA on a metallic nanostructure with femtosecond-pulsed (fs) laser irradiation. Continuous-wave laser irradiation, which is generally used for plasmon excitation, not only increased the electromagnetic field intensity but also generated heat around the nanostructure, causing the DNA to become permanently fixed on the plasmonic substrate. Using fs laser irradiation, on the other hand, the reversible trapping and release of the DNA was achieved by switching the fs laser irradiation on and off. This trap-and-release behavior was clearly observed using a fluorescence microscope. This technique can also be used to manipulate other biomolecules such as nucleic acids, proteins, and polysaccharides and will prove to be a useful tool in the fabrication of biosensors.