DNA Biosensors and Microarrays

Advances in conductive hydrogels for neural recording and stimulation

The brain-computer interface (BCI) allows the human or animal brain to directly interact with the external environment through the neural interfaces, thus playing the role of monitoring, protecting, improving/restoring, enhancing, and replacing. Recording electrophysiological information such as brain neural signals is of great importance in health monitoring and disease diagnosis. According to the electrode position, it can be divided into non-implantable, semi-implantable, and implantable. Among them, implantable neural electrodes can obtain the highest-quality electrophysiological information, so they have the most promising application. However, due to the chemo-mechanical mismatch between devices and tissues, the adverse foreign body response and performance loss over time seriously restrict the development and application of implantable neural electrodes. Given the challenges, conductive hydrogel-based neural electrodes have recently attracted much attention, owing to many advantages such as good mechanical match with the native tissues, negligible foreign body response, and minimal signal attenuation. This review mainly focuses on the current development of conductive hydrogels as a biocompatible framework for neural tissue and conductivity-supporting substrates for the transmission of electrical signals of neural tissue to speed up electrical regeneration and their applications in neural sensing and recording as well as stimulation.

Therapeutic and diagnostic applications of antisense peptide nucleic acids

Peptide nucleic acids (PNAs) are synthetic nucleic acid analogs with a neutral N-(2-aminoethyl) glycine backbone. PNAs possess unique physicochemical characteristics such as increased resistance to enzymatic degradation, ionic strength and stability over a wide range of temperatures and pH, and low intrinsic electrostatic repulsion against complementary target oligonucleotides. PNA has been widely used as an antisense oligonucleotide (ASO). Despite the favorable characteristics of PNA, in comparison with other ASO technologies, the use of antisense PNA for novel therapeutics has lagged. This review provides a brief overview of PNA, its antisense mechanisms of action, delivery strategies, and highlights successful applications of PNA, focusing on anti-pathogenic, anti-neurodegenerative disease, anti-cancer, and diagnostic agents. For each application, several studies are discussed focusing on the different target sites of the PNA, design of different PNAs and the therapeutic outcome in different cell lines and animal models. Thereafter, persisting limitations slowing the successful integration of antisense PNA therapeutics are discussed in order to highlight actionable next steps in the development and optimization of PNA as an ASO.

Double-Stranded DNA Immobilized in Lying-Flat and Upright Orientation on a PNIPAm-Coated Surface: A Theoretical Study

Surface-immobilized double-stranded DNA (dsDNA) in upright orientation plays an important role in optimizing and understanding DNA-based nanosensors and nanodevices. However, it is difficult to regulate the surface density of upright DNA due to the fact that DNA usually stands vertically at a high packing density but may lie down at a low packing density. We herein report dsDNA immobilized in upright orientation on a poly(N-isopropylacrylamide) (PNIPAm)-coated surface in theory. The theoretical results reveal that the angle of upright DNA relative to the surface is larger than that of DNA immobilized on the bare surface caused by the lying-flat DNA under proper PNIPAm surface coverage at 45 °C. The surface density of upright DNA is significantly influenced by DNA concentration and DNA length. It is envisioned that the density-regulated DNA molecules immobilized in upright orientation in the present work are well suited to bottom-up construction of complex DNA-based nanostructures and nanodevices.

Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be precisely controlled to achieve the required accuracy and sensitivity. In particular, achieving high hybridization density at the sensing surface is a prerequisite to reach a low limit of detection. We herein describe a strategy based on peptides as anchoring units to immobilize DNA probes at the surface of borosilicate slides. While the coating pathway involves copper-catalyzed click chemistry, a copper-free variation is also reported. The resulting biochips display a high hybridization density (2.9 pmol per cm2) with their targeted gene sequences.

Peptide Nucleic Acids Containing Cationic/Amino-Alkyl Modified Bases Promote Enhanced Hybridization Kinetics and Thermodynamics with Single-Strand DNA

Peptide nucleic acids (PNAs) are antisense molecules with excellent polynucleotide hybridization properties; they are resistant to nuclease degradation but often have poor cell permeability leading to moderate cellular activity and limited clinical results. The addition of cationic substitutions (positive charges) to PNA molecules greatly increases cell permeability. In this report, we describe the synthesis and polynucleotide hybridization properties of a novel cationic/amino-alkyl nucleotide base-modified PNA (OPNA). This study was designed to quantitate the effect the cationic/amino-alkyl nucleotide base modification had on the kinetic and thermodynamic properties of OPNA-DNA hybridization using surface plasmon resonance and UV thermal melt studies. Kinetic studies reveal a favorable 10-30 fold increase in affinity for a single cationic modification on the base of an adenine, cytosine, or guanidine OPNA sequence compared to the nonmodified PNA strand. The increase in affinity is correlated directly with a favorable decrease in the dissociation rate constant and increase in the association rate constant. Introducing additional amino-alkyl base modifications further favors a decrease in the dissociation rate (3-10-fold per amino-alkyl). The thermodynamics driving the OPNA hybridization is promoted by an additional favorable -80 kJ/mol enthalpy of binding for a single amino-alkyl modification compared to the PNA strand. This increase in enthalpy is consistent with an ion-ion interaction with the DNA strand. These kinetic and thermodynamic hybridization studies reveal for the first time that this type of cationic/amino-alkyl base-modified PNA has favorable hybridization properties suitable for development as an antisense oligomer.

Surface plasmon resonance-based oligonucleotide biosensor for Salmonella Typhi detection

Due to high mortality rates, typhoid fever still is one of the major health problems in the world, particularly in developing countries. The lack of highly specific and sensitive diagnostic tests and the great resemblance of typhoid fever symptoms to other diseases made the false-negative diagnosis a major challenge in typhoid fever management. Hence, we decided to design a Surface Plasmon Resonance (SPR) based biosensor for specific detection of Salmonella typhi through DNA hybridization. The results showed that the 10 nM of the synthetic target sequence, as well as 1 nM of PCR product, were the lowest feasible detected concentrations by the designed biosensor. This genosensor was also found to significantly distinguish the complementary sequence with the accuracy of one base mismatch sequence. The surface of the chip can be regenerated with NaOH solution and used for consecutive diagnosis. Therefore, the function of the designed biosensor indicates its high potential for Salmonella typhi detection practice.

Urine protein quantification in human urine on boron-doped diamond electrodes based on the electrochemical reaction of Coomassie brilliant blue

Urinalysis is attracting interest in personal healthcare management as part of a general move to improve quality of life. Urine contains various metabolites and the protein level in urine is an indicator of kidney function. In this study, a novel electrochemical sensing system based on boron-doped diamond (BDD) electrodes was developed for the detection of protein concentrations in human urine. BDD electrodes have the advantages of a wide electrochemical potential window and low non-specific adsorption, making them ideal for simple, rapid, and compact devices for home detection of bio-relevant substances. Coomassie brilliant blue (CBB), a dye that selectively and strongly binds to urine proteins, was found to be a redox-active indicator to show a decrease in its redox currents in relation to the concentration of protein in urine samples. Our detailed studies of BDD electrodes showed their limit of detection to be 2.57 μg mL-1 and that they have a linear response that ranges from 0 to 400 μg mL-1 in urine samples. We also investigated the detection of urine protein in different urine samples. Our results agreed with those obtained using conventional colorimetric analysis. We believe this to be the first study of electrochemical detection of urine protein in urine samples on BDD electrodes, which is of great significance to be able to obtain results with electrical signals rapidly compared to conventional colorimetric analysis. This CBB-BDD technique has the potential to assist healthcare management in the form of a rapid daily diagnostic test to judge whether a more detailed examination is needed.

Silicon Carbide-Based DNA Sensing Technologies

DNA sensing is critical in various applications such as the early diagnosis of diseases and the investigation of forensic evidence, food processing, agriculture, environmental protection, etc. As a wide-bandgap semiconductor with excellent chemical, physical, electrical, and biocompatible properties, silicon carbide (SiC) is a promising material for DNA sensors. In recent years, a variety of SiC-based DNA-sensing technologies have been reported, such as nanoparticles and quantum dots, nanowires, nanopillars, and nanowire-based field-effect-transistors, etc. This article aims to provide a review of SiC-based DNA sensing technologies, their functions, and testing results.

LSPR-Based Biosensing Enables the Detection of Antimicrobial Resistance Genes

The development of rapid, simple, and accurate bioassays for the detection of nucleic acids has received increasing demand in recent years. Here, localized surface plasmon resonance (LSPR) spectroscopy for the detection of an antimicrobial resistance gene, sulfhydryl variable β-lactamase (blaSHV), which confers resistance against a broad spectrum of β-lactam antibiotics is used. By performing limit of detection experiments, a 23 nucleotide (nt) long deoxyribonucleic acid (DNA) sequence down to 25 nm was detected, whereby the signal intensity is inversely correlated with sequence length (23, 43, 63, and 100 nt). In addition to endpoint measurements of hybridization events, the setup also allowed to monitor the hybridization events in real-time, and consequently enabled to extract kinetic parameters of the studied binding reaction. Performing LSPR measurements using single nucleotide polymorphism (SNP) variants of blaSHV revealed that these sequences can be distinguished from the fully complementary sequence. The possibility to distinguish such sequences is of utmost importance in clinical environments, as it allows to identify mutations essential for enzyme function and thus, is crucial for the correct treatment with antibiotics. Taken together, this system provides a robust, label-free, and cost-efficient analytical tool for the detection of nucleic acids and will enable the surveillance of antimicrobial resistance determinants.

Current and emerging trends in techniques for plant pathogen detection

Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.

Phosphate-driven H2O2 decomposition on DNA-bound bio-inspired activated carbon-based sensing platform for biological and food samples

Hydrogen peroxide (H₂O₂) is one of the most important reactive oxygen species (ROS). Increased endogenous H₂O₂ levels indicate oxidative stress and could be a potential marker of many diseases, including Alzheimer's, cardiovascular diseases, and diabetes. However, consuming H₂O_2-incorporated food has adverse effects on humans and is a serious health concern. We used salmon testes DNA with bio-inspired activated carbon (AC) as an electrocatalyst for developing a novel H₂O₂ sensor. The phosphate backbone of DNA contains negatively charged oxygen groups that specifically attract protons from H₂O₂ reduction. We observed a linearity range of 0.01-250.0 μM in the H₂O₂ reduction peak current with a detection limit of 2.5 and 45.7 nM for chronoamperometric and differential pulse voltammetric studies. High biocompatibility of the sensor was achieved by the DNA, facilitating endogenous H₂O₂ detection. Moreover, this non-enzymatic sensor could also help in the rapid screening of H₂O₂-contaminated foods.

A Simplified Amplification-Free Strategy with Lyophilized CRISPR-CcrRNA System for Drug-Resistant Salmonella Detection

Drug resistance in pathogenic bacteria has become a major threat to global health. The misuse of antibiotics has increased the number of resistant bacteria in the absence of rapid, accurate, and cost-effective diagnostic tools. Here, an amplification-free CRISPR-Cas12a time-resolved fluorescence immunochromatographic assay (AFC-TRFIA) is used to detect drug-resistant Salmonella. Multi-locus targeting in combination crRNA (CcrRNA) is 27-fold more sensitive than a standalone crRNA system. The lyophilized CRISPR system further simplifies the operation and enables one-pot detection. Induction of nucleic acid fixation via differentially charged interactions reduced the time and cost required for flowmetric chromatography with enhanced stability. The induction of nucleic acid fixation via differentially charged interactions reduces the time and cost required for flowmetric chromatography with enhanced stability. The platform developed for the detection of drug-resistant Salmonella has an ultra-sensitive detection limit of 84 CFU mL^-1 within 30 min, with good linearity in the range of 10² -10⁶ CFU mL^-1 . In real-world applications, spiked recoveries range from 76.22% to 145.91%, with a coefficient of variation less than 10.59%. AFC-TRFIA offers a cost-effective, sensitive, and virtually equipment-independent platform for preventing foodborne illnesses, screening for drug-resistant Salmonella, and guiding clinical use.

A Short Review on Miniaturized Biosensors for the Detection of Nucleic Acid Biomarkers

Even today, most biomarker testing is executed in centralized, dedicated laboratories using bulky instruments, automated analyzers, and increased analysis time and expenses. The development of miniaturized, faster, low-cost microdevices is immensely anticipated for substituting for these conventional laboratory-oriented assays and transferring diagnostic results directly onto the patient's smartphone using a cloud server. Pioneering biosensor-based approaches might make it possible to test biomarkers with reliability in a decentralized setting, but there are still a number of issues and restrictions that must be resolved before the development and use of several biosensors for the proper understanding of the measured biomarkers of numerous bioanalytes such as DNA, RNA, urine, and blood. One of the most promising processes to address some of the issues relating to the growing demand for susceptible, quick, and affordable analysis techniques in medical diagnostics is the creation of biosensors. This article critically discusses a short review of biosensors used for detecting nucleic acid biomarkers, and their use in biomedical prognostics will be addressed while considering several essential characteristics.

Ionic Strength and Hybridization Position near Gold Electrodes Can Significantly Improve Kinetics in DNA-Based Electrochemical Sensors

A variety of electrochemical (EC) biosensors play critical roles in disease diagnostics. More recently, DNA-based EC sensors have been established as promising for detecting a wide range of analyte classes. Since most of these sensors rely on the high specificity of DNA hybridization for analyte binding or structural control, it is crucial to understand the kinetics of hybridization at the electrode surface. In this work, we have used methylene blue-labeled DNA strands to monitor the kinetics of DNA hybridization at the electrode surface with square-wave voltammetry. By varying the position of the double-stranded DNA segment relative to the electrode surface as well as the bulk solution's ionic strength (0.125-1.00 M), we observed significant interferences with DNA hybridization closer to the surface, with more substantial interference at lower ionic strength. As a demonstration of the effect, toehold-mediated strand displacement reactions were slowed and diminished close to the surface, while strategic placement of the DNA binding site improved reaction rates and yields. This work manifests that both the salt concentration and DNA hybridization site relative to the electrode are important factors to consider when designing DNA-based EC sensors that measure hybridization directly at the electrode surface.

Optimization of Functional Group Concentration of N, N-Dimethylacrylamide-based Polymeric Coatings and Probe Immobilization for DNA and Protein Microarray Applications

We report here a deep investigation into the effect of the concentration of a polymeric coating's functional groups on probe density immobilization with the aim of establishing the optimal formulation to be implemented in specific microarray applications. It is widely known that the ideal performance of a microarray strictly depends on the way probes are tethered to the surface since it influences the way they interact with the complementary target. The N, N-dimethylacrylamide-based polymeric coating introduced by our research group in 2004 has already proven to offer great flexibility for the customization of surface properties; here, we demonstrate that it also represents the perfect scaffold for the modulation of probe grafting. With this aim in mind, polymers with increasing concentrations of N-acryloyloxysuccinimide (NAS) were synthesized and the coating procedure optimized accordingly. These were then tested not only in DNA microarray assays, but also using protein probes (with different MWs) to establish which formulation improves the assay performance in specific applications. The flexibility of this polymeric platform allowed us also to investigate a different immobilization chemistry-specifically, click chemistry reactions, thanks to the insertion of azide groups into the polymer chains-and to evaluate possible differences generated by this modification.

Ultrasensitive electrochemical biosensors based on zinc sulfide/graphene hybrid for rapid detection of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) is a highly contagious and fatal disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In general, the diagnostic tests for COVID-19 are based on the detection of nucleic acid, antibodies, and protein. Among different analytes, the gold standard of the COVID-19 test is the viral nucleic acid detection performed by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) method. However, the gold standard test is time-consuming and requires expensive instrumentation, as well as trained personnel. Herein, we report an ultrasensitive electrochemical biosensor based on zinc sulfide/graphene (ZnS/graphene) nanocomposite for rapid and direct nucleic acid detection of SARS-CoV-2. We demonstrated a simple one-step route for manufacturing ZnS/graphene by employing an ultrafast (90 s) microwave-based non-equilibrium heating approach. The biosensor assay involves the hybridization of target DNA or RNA samples with probes that are immersed into a redox active electrolyte, which are detectable by electrochemical measurements. In this study, we have performed the tests for synthetic DNA samples and, SARS-CoV-2 standard samples. Experimental results revealed that the proposed biosensor could detect low concentrations of all different SARS-CoV-2 samples, using such as S, ORF 1a, and ORF 1b gene sequences as targets. This microwave-synthesized ZnS/graphene-based biosensor could be reliably used as an on-site, real-time, and rapid diagnostic test for COVID-19.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s42114-023-00630-7.

Biofunctionalization of Multiplexed Silicon Photonic Biosensors

Silicon photonic (SiP) sensors offer a promising platform for robust and low-cost decentralized diagnostics due to their high scalability, low limit of detection, and ability to integrate multiple sensors for multiplexed analyte detection. Their CMOS-compatible fabrication enables chip-scale miniaturization, high scalability, and low-cost mass production. Sensitive, specific detection with silicon photonic sensors is afforded through biofunctionalization of the sensor surface; consequently, this functionalization chemistry is inextricably linked to sensor performance. In this review, we first highlight the biofunctionalization needs for SiP biosensors, including sensitivity, specificity, cost, shelf-stability, and replicability and establish a set of performance criteria. We then benchmark biofunctionalization strategies for SiP biosensors against these criteria, organizing the review around three key aspects: bioreceptor selection, immobilization strategies, and patterning techniques. First, we evaluate bioreceptors, including antibodies, aptamers, nucleic acid probes, molecularly imprinted polymers, peptides, glycans, and lectins. We then compare adsorption, bioaffinity, and covalent chemistries for immobilizing bioreceptors on SiP surfaces. Finally, we compare biopatterning techniques for spatially controlling and multiplexing the biofunctionalization of SiP sensors, including microcontact printing, pin- and pipette-based spotting, microfluidic patterning in channels, inkjet printing, and microfluidic probes.

Fluid nanoporous microinterface enables multiscale-enhanced affinity interaction for tumor-derived extracellular vesicle detection

Tumor-derived extracellular vesicles (T-EVs) represent valuable markers for tumor diagnosis and treatment guidance. However, nanoscale sizes and the low abundance of marker proteins of T-EVs restrict interfacial affinity reaction, leading to low isolation efficiency and detection sensitivity. Here, we engineer a fluid nanoporous microinterface (FluidporeFace) in a microfluidic chip by decorating supported lipid bilayers (SLBs) on nanoporous herringbone microstructures with a multiscale-enhanced affinity reaction for efficient isolation of T-EVs. At the microscale level, the herringbone micropattern promotes the mass transfer of T-EVs to the surface. At the nanoscale level, nanoporousity can overcome boundary effects for close contact between T-EVs and the interface. At the molecular level, fluid SLBs afford clustering of recognition molecules at the binding site, enabling multivalent binding with an ∼83-fold increase of affinity compared with the nonfluid interface. With the synergetic enhanced mass transfer, interface contact, and binding affinity, FluidporeFace affords ultrasensitive detection of T-EVs with a limit of detection of 10 T-EVs μL −1 , whose PD-L1 expression levels successfully distinguish cancer patients from healthy donors. We expect this multiscale enhanced interfacial reaction strategy will inspire the biosensor design and expand liquid biopsy applications, especially for low-abundant targets in clinical samples.

Capture, detection and purification of dsDNA amplicons using a DNA binding protein on magnetic beads

Magnetic separation has been widely exploited for capture and detection of nucleic acids, including amplicons. Streptavidin-magnetic beads (SA-MB) are typically employed for this purpose, as well as in biosensing applications. However, remaining biotinylated primer in the amplification reaction can compete with labeled amplicon for binding to the beads. Also, the harsh conditions needed for elution of bound amplicons restrict their use for purification purposes. Herein we show that a sequence-specific DNA binding protein immobilized on magnetic beads can serve as an alternative to SA-MB for these applications. This is enabled by the high binding affinity of scCro DNA binding protein for its specific sequence and its ability to bind dsDNA but not ssDNA. This specific sequence is easily incorporated in the amplicon during amplification with an extended primer. The scCro-MB exhibited higher amplicon binding capacity and detection sensitivity compared to SA-MB when both synthetic and genomic DNA were used as templates for PCR. This resulted not only from increased protein load on the beads but also from minimized interference of excess labeled primer remaining in the unpurified amplification reactions. Finally, a proof-of-concept was provided for the use of the scCro-MB for PCR amplicon purification under mild elution conditions using salt.

State-of-the-Art Development in Liquid Crystal Biochemical Sensors

As an emerging stimuli-responsive material, liquid crystal (LC) has attracted great attentions beyond display applications, especially in the area of biochemical sensors. Its high sensitivity and fast response to various biological or chemical analytes make it possible to fabricate a simple, real-time, label-free, and cost-effective LC-based detection platform. Advancements have been achieved in the development of LC-based sensors, both in fundamental research and practical applications. This paper briefly reviews the state-of-the-art research on LC sensors in the biochemical field, from basic properties of LC material to the detection mechanisms of LC sensors that are categorized into LC-solid, LC–aqueous, and LC droplet platforms. In addition, various analytes detected by LCs are presented as a proof of the application value, including metal ions, nucleic acids, proteins, glucose, and some toxic chemical substances. Furthermore, a machine-learning-assisted LC sensing platform is realized to provide a foundation for device intelligence and automatization. It is believed that a portable, convenient, and user-friendly LC-based biochemical sensing device will be achieved in the future.

A comprehensive review on advancements in tissue engineering and microfluidics toward kidney-on-chip

This review provides a detailed literature survey on microfluidics and its road map toward kidney-on-chip technology. The whole review has been tailored with a clear description of crucial milestones in regenerative medicine, such as bioengineering, tissue engineering, microfluidics, microfluidic applications in biomedical engineering, capabilities of microfluidics in biomimetics, organ-on-chip, kidney-on-chip for disease modeling, drug toxicity, and implantable devices. This paper also presents future scope for research in the bio-microfluidics domain and biomimetics domain.

Attomolar Sensitivity in Single Biomarker Counting upon Aqueous Two-Phase Surface Enrichment

From longstanding techniques like enzyme-linked immunosorbent assay (ELISA) to modern next-generation sequencing, many of the most sensitive and specific biomarker detection assays require capture of the analyte at a surface. While surface-based assays provide advantages, including the ability to reduce background by washing away excess reagents and/or increase specificity through analyte-specific capture probes, the limited efficiency of capture from dilute solution often restricts assay sensitivity to the femtomolar-to-nanomolar range. Although assays for many nucleic acid analytes can decrease limits of detection (LODs) to the subfemtomolar range using polymerase chain reaction, such amplification may introduce biases, errors, and an increased risk of sample cross-contamination. Furthermore, many analytes cannot be amplified easily, including short nucleic acid fragments, epigenetic modifications, and proteins. To address the challenge of achieving subfemtomolar LODs in surface-based assays without amplification, we exploit an aqueous two-phase system (ATPS) to concentrate target molecules in a smaller-volume phase near the assay surface, thus increasing capture efficiency compared to passive diffusion from the original solution. We demonstrate the utility of ATPS-enhanced capture via single molecule recognition through equilibrium Poisson sampling (SiMREPS), a microscopy technique previously shown to possess >99.9999% detection specificity for DNA mutations but an LOD of only ∼1-5 fM. By combining ATPS-enhanced capture with a Förster resonance energy transfer (FRET)-based probe design for rapid data acquisition over many fields of view, we improve the LOD ∼ 300-fold to <10 aM for an EGFR exon 19 deletion mutation. We further validate this ATPS-assisted FRET-SiMREPS assay by detecting endogenous exon 19 deletion molecules in cancer patient blood plasma.

Covalently Attaching Hollow Silica Nanoparticles on a COC Surface for the Fabrication of a Three-Dimensional Protein Microarray

Compared to traditional two-dimensional (2D) biochips, three-dimensional (3D) biochips exhibit the advantages of higher probe density and detection sensitivity due to their designable surface microstructure as well as enlarged surface area. In the study, we proposed an approach to prepare a 3D protein chip by deposition of a monolayer of functionalized hollow silica nanoparticles (HSNs) on an activated cyclic olefin copolymer (COC) substrate. First, the COC substrate was chemically modified through the photografting technique to tether poly[3-(trimethoxysilyl) propyl methacrylate] (PTMSPMA) brushes on it. Then, a monolayer of HSNs was deposited on the modified COC and covalently attached via a condensation reaction between the hydrolyzed pendant siloxane groups of PTMSPMA and the Si-OH groups of HSNs. The roughness of the COC substrate significantly increased to 50.3 nm after depositing a monolayer of HSNs (ranging from 100 to 700 nm), while it only caused a negligible reduction in the light transmittance of COC. The HSN-modified COC was further functionalized with epoxide groups by a silane coupling agent for binding proteins. Immunoglobulin G could be effectively immobilized on this substrate with the highest immobilization efficiency of 75.2% and a maximum immobilization density of 1.236 μg/cm², while the highest immobilization efficiency on a 2D epoxide group-modified glass slide was only 57.4%. Moreover, immunoassay results confirmed a competitive limit of detection (LOD) (1.06 ng/mL) and a linear detection range (1-100 ng/mL) of the 3D protein chip. This facile and effective approach for fabricating nanoparticle-based 3D protein microarrays has great potential in the field of biorelated detection.

XNAs: A Troubleshooter for Nucleic Acid Sensing

The strategies for nucleic acid sensing based on nucleic acid hybridization between the target sequence and the capture probe sequence are considered to be largely successful as far as detection of a specific target of known sequence is concerned. However, when compared with other complementary methods, like direct sequencing, a number of results are still found to be either "false positives" or "false negatives". This suggests that modifications in these strategies are necessary to make them more accurate. In this minireview, we propose that one way toward improvement could be replacement of the DNA capture probes with the xeno nucleic acid or XNA capture probes. This is because the XNAs, especially the locked nucleic acid, the peptide nucleic acid, and the morpholino, have shown better single nucleobase mismatch discrimination capacity than the DNA capture probes, indicating their capacity for more precise detection of nucleic acid sequences, which is beneficial for detection of gene stretches having point mutations. Keeping the current trend in mind, this minireview will include the recent developments in nanoscale, fluorescent label-free applications, and present the cases where the XNA probes show clear advantages over the DNA probes.

Space-Confinment-Enhanced Fluorescence Detection of DNA on Hydrogel Particles Array

Fluorescent biosensors have been widely applied in DNA detection because of their reliability and reproducibility. However, low kinetics in DNA hybridization often brings out long test terms, thus restricting their practical use. Here, we demonstrate unexpected fast DNA fluorescence detection on the confined surface of hydrogel particles. When the pore size and surface charge of hydrogel particles are tailored, DNA molecules can be confined in the outer water layer of hydrogel particles. We fabricated a fluorescence-on DNA sensor based on the hydrogel particle array by utilizing the fluorescence quenching property of graphene oxide and its different adsorption behaviors toward single-strand DNA or double-strand DNA. Benefiting from the confinement effect of hydrogel particle surface and the enrichment effect of water evaporation, the DNA-recognition time was descreased significantly from 3000 s to less than 10 s under the target concentration of 400 nM. Moreover, rapid detection can be achieved at concentrations between 50 and 400 nM. The study provides another insight to fabricate fast biosensors and shows great potential in DNA diagnostics, gene analysis, and liquid biopsy.

Electrochemical genosensor based on gold nanostars for the detection of Escherichia coli O157:H7 DNA

Escherichia coli O157:H7 (E. coli O157:H7) is an enterohemorrhagic E. coli (EHEC), which has been issued as a major threat to public health worldwide due to fatal contamination of water and food. Thus, its rapid and accurate detection has tremendous importance in environmental monitoring and human health. In this regard, we report a simple and sensitive electrochemical DNA biosensor by targeting Z3276 as a genetic marker in river water. The surface of the designed gold electrode was functionalized with gold nanostars and an aminated specific sensing probe of E. coli O157:H7 to fabricate the genosensor. Cyclic voltammetry (CV) and square wave voltammetry (SWV) techniques were applied for electrochemical characterization and detection. The synthesized gold nanostars were characterized using different characterization techniques. The fabricated DNA-based sensor exhibited a high selective ability for one, two, and three-base mismatched sequences. Regeneration, stability, selectivity, and kinetics of the bioassay were investigated. Under optimal conditions, the fabricated genosensor exhibited a linear response range of 10^-5 to 10^-17 μM in the standard sample and 7.3 to 1 × 10^-17 μM in water samples with a low limit of quantification of 0.01 zM in water samples. The detection strategy based on silver plated gold nanostars and DNA hybridization improved the sensitivity and specificity of the assay for E. coli O157:H7 detection in real water samples without filtration. The detection assay has the advantages of high selectivity, sensitivity, low amounts of reagents, short analysis time, commercialization, and potential application for the determination of other pathogenic bacteria.

Superwettable Biosensor for Disease Biomarker Detection

Bioinspired superwettable materials have aroused wide interests in recent years for their promising application fields from service life to industry. As one kind of emerging application, the superwettable surfaces used to fabricate biosensors for the detection of disease biomarkers, especially tumor biomarkers, have been extensively studied. In this mini review, we briefly summarized the sensing strategy for disease biomarker detection based on superwettable biosensors, including fluorescence, electrochemistry, surface-enhanced Raman scattering, and visual assays. Finally, the challenges and direction for future development of superwettable biosensors are also discussed.

Molecularly resolved, label-free nucleic acid sensing at solid-liquid interface using non-ionic DNA analogues

Nucleic acid-based biosensors, where the capture probe is a nucleic acid, e.g., DNA or its synthetic analogue xeno nucleic acid (XNA), offer interesting ways of eliciting clinically relevant information from hybridization/dehybridization signals. In this respect, the application of XNA probes is attractive since the drawbacks of DNA probes might be overcome. Within the XNA probe repertoire, peptide nucleic acid (PNA) and morpholino (MO) are promising since their backbones are non-ionic. Therefore, in the absence of electrostatic charge repulsion between the capture probe and the target nucleic acid, a stable duplex can be formed. In addition, these are nuclease-resistant probes. Herein, we have tested the molecularly resolved nucleic acid sensing capacity of PNA and MO capture probes using a fluorescent label-free single molecule force spectroscopy approach. As far as single nucleobase mismatch discrimination is concerned, both PNA and MO performed better than DNA, while the performance of the MO probe was the best. We propose that the conformationally more rigid backbone of MO, compared to the conformationally flexible PNA, is an advantage for MO, since the probe orientation can be made more upright on the surface and therefore MO can be more effectively accessed by the target sequences. The performance of the XNA probes has been compared to that of the DNA probe, using fixed nucleobase sequences, so that the effect of backbone variation could be investigated. To our knowledge, this is the first report on molecularly resolved nucleic acid sensing by non-ionic capture probes, here, MO and PNA.

Improved nucleic acid sensing in terms of single nucleobase mismatch discrimination, as achieved by the surface-confined non-ionic PNA and MO capture probes, is exemplified by single molecule force spectroscopy.

A Review on Electrochemical Sensors and Biosensors Used in Assessing Antioxidant Activity

Currently, there is growing interest in screening and quantifying antioxidants from biological samples in the quest for natural and effective antioxidants to combat free radical-related pathological complications. Antioxidants play an important role in human health and provide a defense against many diseases. Due to the valuable dietary role of these compounds, the analysis and determination of their amount in food is of particular importance. In recent years, many attempts have been made to provide simple, fast, and economical analytical approaches for the on-site detection and determination of antioxidant activity in food antioxidants. In this regard, electrochemical sensors and biosensors are considered promising tools for antioxidant research due to their high sensitivity, fast response time, and ease of miniaturization; thus, they are used in a variety of fields, including food analysis, drug screening, and toxicity research. Herein, we review the recent advances in sensors and biosensors for the detection of antioxidants, underlying principles, and emphasizing advantages, along with limitations regarding the ability to discriminate between the specific antioxidant or quantifying total antioxidant content. In this work, both direct and indirect methods for antioxidants detecting with electrochemical sensors and biosensors are analyzed in detail. This review aims to prove how electrochemical sensors and biosensors represent reliable alternatives to conventional methods for antioxidant analysis.

Metal organic frameworks for electrochemical sensor applications: A review

Metal-organic frameworks (MOFs) are broadly known as porous coordination polymers, synthesized by metal-based nodes and organic linkers. MOFs are used in various fields like catalysis, energy storage, sensors, drug delivery etc., due to their versatile properties (tailorable pore size, high surface area, and exposed active sites). This review presents a detailed discussion of MOFs as an electrochemical sensor and their enhancement in the selectivity and sensitivity of the sensor. These sensors are used for the detection of heavy metal ions like Cd²⁺, Pb²⁺, Hg²⁺, and Cu²⁺ from groundwater. Various types of organic pollutants are also detected from the water bodies using MOFs. Furthermore, electrochemical sensing of antibiotics, phenolic compounds, and pesticides has been explored. In addition to this, there is also a detailed discussion of metal nano-particles and metal-oxide based composites which can sense various compounds like glucose, amino acids, uric acid etc. The review will be helpful for young researchers, and an inspiration to future research as challenges and future opportunities of MOF-based electrochemical sensors are also reported.

Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects

Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.

Functional Chirality: From Small Molecules to Supramolecular Assemblies

Many structures in nature look symmetric, but this is not completely accurate, because absolute symmetry is close to death. Chirality (handedness) is one form of living asymmetry. Chirality has been extensively investigated at different levels. Many rules were coined in attempts made for many decades to have control over the selection of handedness that seems to easily occur in nature. It is certain that if good control is realized on chirality, the roads will be ultimately open towards numerous developments in pharmaceutical, technological, and industrial applications. This tutorial review presents a report on chirality from single molecules to supramolecular assemblies. The realized functions are still in their infancy and have been scarcely converted into actual applications. This review provides an overview for starters in the chirality field of research on concepts, common methodologies, and outstanding accomplishments. It starts with an introductory section on the definitions and classifications of chirality at the different levels of molecular complexity, followed by highlighting the importance of chirality in biological systems and the different means of realizing chirality and its inversion in solid and solution-based systems at molecular and supramolecular levels. Chirality-relevant important findings and (bio-)technological applications are also reported accordingly.

A Photosensitized Singlet Oxygen (1O2) Toolbox for Bio-Organic Applications: Tailoring 1O2 Generation for DNA and Protein Labelling, Targeting and Biosensing

Singlet oxygen (¹O₂) is the excited state of ground, triplet state, molecular oxygen (O₂). Photosensitized ¹O₂ has been extensively studied as one of the reactive oxygen species (ROS), responsible for damage of cellular components (protein, DNA, lipids). On the other hand, its generation has been exploited in organic synthesis, as well as in photodynamic therapy for the treatment of various forms of cancer. The aim of this review is to highlight the versatility of ¹O_2, discussing the main bioorganic applications reported over the past decades, which rely on its production. After a brief introduction on the photosensitized production of ¹O₂, we will describe the main aspects involving the biologically relevant damage that can accompany an uncontrolled, aspecific generation of this ROS. We then discuss in more detail a series of biological applications featuring ¹O₂ generation, including protein and DNA labelling, cross-linking and biosensing. Finally, we will highlight the methodologies available to tailor ¹O₂ generation, in order to accomplish the proposed bioorganic transformations while avoiding, at the same time, collateral damage related to an untamed production of this reactive species.

Au Nanoparticle-Based Amplified DNA Detection on Poly-l-lysine Monolayer-Functionalized Electrodes

Affinity sensing of nucleic acids is among the most investigated areas in biosensing due to the growing importance of DNA diagnostics in healthcare research and clinical applications. Here, we report a simple electrochemical DNA detection layer, based on poly-l-lysine (PLL), in combination with gold nanoparticles (AuNPs) as a signal amplifier. The layer shows excellent reduction of non-specific binding and thereby high contrast between amplified and non-amplified signals with functionalized AuNPs; the relative change in current was 10-fold compared to the non-amplified signal. The present work may provide a general method for the detection of tumor markers based on electrochemical DNA sensing.

Biomedical IoT: Enabling Technologies, Architectural Elements, Challenges, and Future Directions

This paper provides a comprehensive literature review of various technologies and protocols used for medical Internet of Things (IoT) with a thorough examination of current enabling technologies, use cases, applications, and challenges. Despite recent advances, medical IoT is still not considered a routine practice. Due to regulation, ethical, and technological challenges of biomedical hardware, the growth of medical IoT is inhibited. Medical IoT continues to advance in terms of biomedical hardware, and monitoring figures like vital signs, temperature, electrical signals, oxygen levels, cancer indicators, glucose levels, and other bodily levels. In the upcoming years, medical IoT is expected replace old healthcare systems. In comparison to other survey papers on this topic, our paper provides a thorough summary of the most relevant protocols and technologies specifically for medical IoT as well as the challenges. Our paper also contains several proposed frameworks and use cases of medical IoT in hospital settings as well as a comprehensive overview of previous architectures of IoT regarding the strengths and weaknesses. We hope to enable researchers of multiple disciplines, developers, and biomedical engineers to quickly become knowledgeable on how various technologies cooperate and how current frameworks can be modified for new use cases, thus inspiring more growth in medical IoT.

Synthesis and structure–activity relationship of peptide nucleic acid probes with improved interstrand-crosslinking abilities: application to biotin-mediated RNA-pulldown

After optimization of interstrand crosslink reaction between furan-containing peptide nucleic acids and target oligonucleotides, the reversibility of the formed product is exploited for the pull-down of a sequence of interest from cell lysates.

Functional nucleic acid biosensors utilizing rolling circle amplification

Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.

Multiplexed sensing of biomolecules with optically detected magnetic resonance of nitrogen-vacancy centers in diamond

In the past decade, a great effort has been devoted to develop new biosensor platforms for the detection of a wide range of analytes. Among the various approaches, magneto-DNA assay platforms have received extended interest for high sensitive and specific detection of targets with a simultaneous manipulation capacity. Here, using nitrogen-vacancy quantum centers in diamond as transducers for magnetic nanotags (MNTs), a hydrogel-based, multiplexed magneto-DNA assay is presented. Near-background-free sensing with diamond-based imaging combined with noninvasive control of chemically robust nanotags renders it a promising platform for applications in medical diagnostics, life science, and pharmaceutical drug research. To demonstrate its potential for practical applications, we employed the sensor platform in the sandwich DNA hybridization process and achieved a limit of detection in the attomolar range with single-base mismatch differentiation.

Copolymer Coatings for DNA Biosensors: Effect of Charges and Immobilization Chemistries on Yield, Strength and Kinetics of Hybridization

The physical–chemical properties of the surface of DNA microarrays and biosensors play a fundamental role in their performance, affecting the signal’s amplitude and the strength and kinetics of binding. We studied how the interaction parameters vary for hybridization of complementary 23-mer DNA, when the probe strands are immobilized on different copolymers, which coat the surface of an optical, label-free biosensor. Copolymers of N, N-dimethylacrylamide bringing either a different type or density of sites for covalent immobilization of DNA probes, or different backbone charges, were used to functionalize the surface of a Reflective Phantom Interface multispot biosensor made of a glass prism with a silicon dioxide antireflective layer. By analyzing the kinetic hybridization curves at different probe surface densities and target concentrations in solution, we found that all the tested coatings displayed a common association kinetics of about 9 × 10⁴ M⁻¹·s⁻¹ at small probe density, decreasing by one order of magnitude close to the surface saturation of probes. In contrast, both the yield of hybridization and the dissociation kinetics, and hence the equilibrium constant, depend on the type of copolymer coating. Nearly doubled signal amplitudes, although equilibrium dissociation constant was as large as 4 nM, were obtained by immobilizing the probe via click chemistry, whereas amine-based immobilization combined with passivation with diamine carrying positive charges granted much slower dissociation kinetics, yielding an equilibrium dissociation constant as low as 0.5 nM. These results offer quantitative criteria for an optimal selection of surface copolymer coatings, depending on the application.

Terrestrial insects as a promising source of chitosan and recent developments in its application for various industries

Chitosan is a deacetylated form of chitin and increasingly important amino-polysaccharide used in many various sectors including agriculture, food, and biomedicine. However, chitosan from marine sources has several adverse effects, including allergenic components harmful to human health. Furthermore, marine resources are seasonal, and availability is limited due to dependency on environmental conditions and climate change. In addition, shell infection in crustaceans and environmental contamination make the harvesting of chitin and chitosan problematic. In recent years, chitosan from terrestrial insects has attracted considerable interest. The discoveries show insect chitosan is more advantageous compared to crustacean chitosan. In addition, we were unable to find any literature about the adverse effects of insect chitosan thus far. This review aims to reveal information regarding crustacean and terrestrial insect chitosan and recent advances in chitosan sources. Applications from specific insect orders and perspectives for further study will also be highlighted, including medical and sensing applications.

Naked-eye detection of site-specific ssRNA and ssDNA using PAMmer-assisted CRISPR/Cas9 coupling with exponential amplification reaction

Accurate and effective detection of single-stranded nucleic acids is vital in both disease diagnosis and pathological studies. Hence, we develop a PAMmer-assisted CRISPR/Cas9 system mediated G4-EXPAR (Cas-G4EX) strategy for site-specific detection of ssRNA and ssDNA. PAMmer-assisted CRISPR/Cas9 executes the site-specific cleavage of target ssRNA or ssDNA and released product fragment with the desired sequence at the 3'-terminal. This fragment serves as a primer to activate subsequent sequence-dependent exponential amplification reaction (EXPAR). The G-rich EXPAR products assembles with hemin to form a G-Quadruplex (G4/hemin). G4/hemin catalyzes ABTS-H₂O₂ system with the appearance of vivid green color, realizing naked-eye analysis. Cas-G4EX integrates the superiority of CRISPR/Cas9 and EXPAR, presenting outstanding site-specific recognition and high-performance amplification efficiency. Meanwhile, the programmability of CRISPR/Cas9 system makes the proposed method become a universal detection paradigm for any ssRNA or ssDNA. Cas-G4EX assay shows the linear relationship from 250 aM to 2.5 nM for ssRNA detection with the actual LOD of 250 aM, and that ranges from 100 aM to 1 nM for ssDNA detection with the actual LOD of 100 aM. Additionally, the acceptable recoveries of 101.48%-109.61% for ssRNA and 93.25%-111.98% for ssDNA in real detection of human serum are obtained for detection of single-strand nucleic acid in real samples. Cas-G4EX also exhibits the excellent discrimination for single-base mutation of single-stranded nucleic acids. Therefore, Cas-G4EX assay provides a promising platform in the applications of molecular diagnosis and pathological analysis.

Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors

Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensors due to their higher stability and increased sensitivity than common DNA probes. The neutral pseudopeptide backbone of PNAs not only makes the PNA/DNA duplexes more stable but also provides many opportunities to construct ultrasensitive nucleic acid sensors. This review presents the details of various protocols for the construction of PNA-based electrochemical nucleic acid sensors. The crucial factors, origin, and development of PNA, immobilization methods of PNA probes and signal generation mechanisms, are discussed. This review aims to provide a reference for ultrasensitive PNA electrochemical biosensor preparation.

Light-Regulated Natural Fluorescence of the PCC 6803@ZIF-8 Composite as an Encoded Microsphere for the Detection of Multiple Biomarkers

The use of color-encoded microspheres for a bead-based assay has attracted increasing attention for high-throughput multiplexed bioassays. A fluorescent PCC 6803@ZIF-8 composite was prepared as a bead-based assay platform by a self-assembled zeolitic imidazolate framework (ZIF-8) on the surface of inactivated PCC 6803 cells. The composite fluorescence owing to the presence of pigment proteins in PCC 6803 could be gradually bleached with the prolongation of the ultraviolet light irradiation time. The composites with different fluorescence intensities were therefore obtained as encoded microspheres for the multiplexed assay. ZIF-8 provides a stable, rigid shell and a large specific surface area for composites, which prevent the composites from breakage during use and storage, simplify the protein immobilization procedure, reduce non-specific adsorption, and enhance the detection sensitivity. The encoded composites were successfully used to detect multiple DNA insertion sequences of Mycobacterium tuberculosis. The presented strategy offers an innovative color-encoding method for high-throughput multiplexed bioassays without the need of using chemically synthesized fluorescent materials.

Application of peptide nucleic acid in electrochemical nucleic acid biosensors

The early diagnosis of major diseases, such as malignant tumors, has always been an important field of research. Through screening, early detection of such diseases, and timely and effective treatment can significantly improve the survival rate of patients and reduce medical costs. Therefore, the development of a simple detection method with high sensitivity and strong specificity, and that is low cost is of great significance for the diagnosis and prognosis of the disease. Electrochemical DNA biosensing analysis is a technology based on Watson Crick base complementary pairing, which uses the capture probe of a known sequence to specifically recognize the target DNA and detect its concentration. Because of its advantages of low cost, simple operation, portability, and easy miniaturization, it has been widely researched and has become a cutting-edge topic in the field of biochemical analysis and precision medicine. However, the existing methods for electrochemical DNA biosensing analysis have some shortcomings, such as poor stability and specificity of capture probes, insufficient detection sensitivity, and long detection cycles. In this review, we focus on improving the sensitivity and practicability of electrochemical DNA biosensing analysis methods and summarize a series of research work carried out by using electrically neutral peptide nucleic acid as an immobilized capture probe.

Confocal Raman Microscopy Enables Label-Free, Quantitative, and Structurally Informative Detection of DNA Hybridization at Porous Silica Surfaces

Characterization of DNA at solid/liquid interfaces remains a challenge because most surface-sensitive techniques are unable to provide quantitative insight into the base content, length, or structure. Surface-enhanced Raman scattering measurements of DNA hybridization on plasmonic-metal substrates have been used to overcome small Raman-scattering cross-sections; however, surface-enhanced Raman spectroscopy measurements are not generally quantitative due to the fall-off in the scattering signal with the decay of the electric field enhancement from the surface, which also limits the length of oligonucleotides that can be investigated. In this work, we introduce an experimental methodology in which confocal Raman microscopy is used to characterize hybridization reactions of ssDNA immobilized at the solid/liquid interface of porous silica particles. By focusing the femtoliter confocal probe volume within a single porous particle, signal enhancement arises from the ∼1500-times greater surface area detected compared to a planar substrate. Because the porous support is a purely dielectric material, the scattering signal is independent of the proximity of the oligonucleotide to the silica surface. With this technique, we characterize a 19-mer capture strand and determine its hybridization efficiency with 9-mer and 16-mer target sequences from the scattering of a structurally insensitive phosphate-stretching mode. Changes in polarizability and frequency of scattering from DNA bases were observed, which are consistent with Watson-Crick base pairing. Quantification of base content from their duplex scattering intensities allows us to discriminate between hybridization of two target strands of equivalent length but with different recognition sequences. A duplex having a single-nucleotide polymorphism could be distinguished from hybridization of a fully complementary strand based on differences in base content and duplex conformation.