Neutralized chimeric DNA probe for detection of single nucleotide polymorphism on surface plasmon resonance biosensor

Specific and efficient knockdown of intracellular miRNA using partially neutralized phosphate-methylated DNA oligonucleic acid-loaded mesoporous silica nanoparticles

Antisense oligonucleotides (ASOs) are molecules used to regulate RNA expression by targeting specific RNA sequences. One specific type of ASO, known as neutralized DNA (nDNA), contains site-specific methyl phosphotriester (MPTE) linkages on the phosphate backbone, changing the negatively charged DNA phosphodiester into a neutralized MPTE with designed locations. While nDNA has previously been employed as a sensitive nucleotide sequencing probe for the PCR, the potential of nDNA in intracellular RNA regulation and gene therapy remains underexplored. Our study aims to evaluate the regulatory capacity of nDNA as an ASO probe in cellular gene expression. We demonstrated that by tuning MPTE locations, partially and intermediately methylated nDNA loaded onto mesoporous silica nanoparticles (MSNs) can effectively knock down the intracellular miRNA, subsequently resulting in downstream mRNA regulation in colorectal cancer cell HCT116. Additionally, the nDNA ASO-loaded MSNs exhibit superior efficacy in reducing miR-21 levels over 72 hours compared to the efficacy of canonical DNA ASO-loaded MSNs. The reduction in the miR-21 level subsequently resulted in the enhanced mRNA levels of tumour-suppressing genes PTEN and PDCD4. Our findings underscore the potential of nDNA in gene therapies, especially in cancer treatment via a fine-tuned methylation location.

Recent Progress in Single-Nucleotide Polymorphism Biosensors

Single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in the human genome, are the main cause of individual differences. Furthermore, such attractive genetic markers are emerging as important hallmarks in clinical diagnosis and treatment. A variety of destructive abnormalities, such as malignancy, cardiovascular disease, inherited metabolic disease, and autoimmune disease, are associated with single-nucleotide variants. Therefore, identification of SNPs is necessary for better understanding of the gene function and health of an individual. SNP detection with simple preparation and operational procedures, high affinity and specificity, and cost-effectiveness have been the key challenge for years. Although biosensing methods offer high specificity and sensitivity, as well, they suffer drawbacks, such as complicated designs, complicated optimization procedures, and the use of complicated chemistry designs and expensive reagents, as well as toxic chemical compounds, for signal detection and amplifications. This review aims to provide an overview on improvements for SNP biosensing based on fluorescent and electrochemical methods. Very recently, novel designs in each category have been presented in detail. Furthermore, detection limitations, advantages and disadvantages, and challenges have also been presented for each type.

Molecular effects of site-specific phosphate-methylated primer on the structure and motions of Taq DNA polymerase

Polymerase chain reaction (PCR) is a powerful molecular biology assay for gene detection and quantification. Conventional DNA primers for PCR often suffer from poor sensitivity in specific gene detection. Recently, oligonucleotides containing methyl phosphotriester (MPTE-DNA) have been developed with enhanced DNA hybridization and improved gene detection sensitivity. Yet, site-specific MPTE-modifications on DNA primers have been reported to affect PCR amplification efficiencies while the detailed mechanism remains elusive. Here, we utilized molecular dynamics (MD) simulation to examine the effects of site-specific MPTE-modified primers on the structure and motions of DNA/Taq polymerase complexes. All tested MPTE-DNA/Taq complexes exhibited RMSD values below 2 Å, indicating insignificant effects of all methylation sites on the complex stability. The energetic and hydrogen-bonding analyses suggest minor effects of methylation at t-3, t-4, t-6, and t-7 positions on the DNA-Taq interaction. Principal component analyses further reveal that only t-3, and t-7 methylations preserve the motions of the Taq thumb domain. The site-specific methylation affects the interaction between DNA and the surrounding protein residues, resulting in allosteric-like effects on the DNA/Taq complex. The MD data complement the best experimentally observed PCR efficacies for the t-3 and t-7 positions among all tested MPTE-primers. The unveiled molecular insights can benefit the design of novel PCR primers for improving genetic testing platforms.

Nucleotide Interaction with Nanocrystalline Ceria Surface

The adsorption of nucleotides on the surface of nanocrystalline cerium dioxide (pHpzc = 6.3) in NaCl solutions was investigated using multi-batch adsorption experiments over a wide range of pH. The obtained results were interpreted as a formation of outer and inner sphere surface complexes with the participation of phosphate moieties. The Basic Stern surface complexation model was applied to obtain quantitative equilibrium reaction constants.

DNA methylation detection and site analysis by using an electrochemical biosensor constructed based on toehold-mediated strand displacement reaction

DNA methylation has become a novel target for early diagnosis and prognosis of cancer as well as other related diseases. The accurate detection of the methylation sites of specific genes proved to be of great significance. However, the complex biological nature of clinical samples and the detection of low-abundance targets led to higher requirements for the testing technology. It has been found that by virtue of high sensitivity, rapid response, low cost, facile operation and applicability to microanalysis, electrochemical sensors have greatly contributed to the process of clinical diagnosis. In this study, a facile, rapid and highly sensitive electrochemical biosensor based on the peak current change was developed on the basis of high selectivity of toehold and greater efficiency of PNA strand displacement and used for the detection and site analysis of DNA methylation. Moreover, compared with non-methylated DNA sequences, methylated DNA sequences could be readily invaded by PNA probes, thereby resulting in the strand displacement and significant electrical signals. Therefore, methylation of cytosine sites was primarily analyzed based on electrical signals. Strand displacement by the target DNA sequences with different methylated sites can lead to substantial changes of strand displacement efficiency. As a result, the methylation sites can be analyzed on the basis of corresponding peak current response relation. This method has a detection limit of 0.075 pM and does not involve various complicated steps such as bisulfite treatment, enzyme digestion and PCR amplification. Indeed, one detection cycle can be completed in 60 min. The proposed technology might exhibit great potential in early clinical diagnosis and risk assessment of cancers and related diseases.

Research advances on surface plasmon resonance biosensors

The surface plasmon resonance (SPR) phenomenon is of wide interest due to its sensitivity to changes in surface refractive index for the label-free, highly sensitive and rapid detection of biomarkers. This paper reviews research progress on SPR biosensors modified with different substrate structures and surface materials, surface plasmon resonance imaging (SPRI), and SPR-enhanced electrochemiluminescent (ECL) biosensors for applications in biosensing in the last five years. This paper focuses on the research on the application of the SPR phenomenon in the field of bio-detection, reviews the sensing characteristics of SPR biosensors with substrate structures of prisms, gratings, and optical fibers, and summarizes and analyzes the sensitivity and interference resistance of SPR sensors with surface modification of different materials (high-refractive index dielectric films, metallic micro- and nanostructures, and surface antifouling materials). Considering that imaging is an important tool for biomedical detection, this paper reviews the research progress on SPRI technology in the field of biomedical detection. In addition, this paper also reviews the research progress on SPR-enhanced ECL biosensors in the field of biosensing. Finally, this paper provides an outlook on the development trends of biosensing technology in terms of portable high-precision SPR sensors, reduction of self-loss of thin film materials, optimization of image processing techniques and simplification of electrode modification for ECL sensors.

Detection of cholera toxin with surface plasmon field-enhanced fluorescent spectroscopy

In this work, a biosensor based on surface plasmon field-enhanced florescence spectroscopy (SPFS) method was successfully constructed to detect the truncated form of cholera toxin, that is, its beta subunit (CTX-B). CTX-B is a relatively small molecule (12 kDa) and it was chosen as model analyte for the detection of protein toxins originated from waterborne pathogens. Recognition layer was prepared on gold-coated LaSFN9 glasses modified with 11-mercaptoundecanoic acid (11-MUA). Biotin-conjugated anti-CTX-B polyclonal antibody (B-Ab) was immobilized on streptavidin (SA) layer constructed on the 11-MUA-modified surface. CTX-B amount was determined with direct assay using B-Ab in surface plasmon resonance (SPR) mode and with sandwich assay in SPFS mode using Cy5-conjugated anti-CTX-B polyclonal antibody. Minimum detected CTX-B concentrations were 10 and 0.01 μg/ml with SPR and SPFS, respectively, showing the sensitivity of the SPFS system over the conventional one. The detection was done in 2-6 h, which was faster than both culture and polymerase chain reaction (PCR)-based methods. Stability tests were performed with SA-coated sensors (excluding B-Ab). In this form, the layer was stable after 30 days of storage in phosphate-buffered saline (PBS; 0.01 M, pH = 7.4) at +4°C. B-Ab layer was formed immediately on them before each measurement.

Periodically programmed building and collapse of DNA networks enables an ultrahigh signal amplification effect for ultrasensitive nucleic acids analysis

ANALYSIS

of molecular species is needed for applications in diagnosis of infections and genetic diseases. Herein, we demonstrate a target DNA-responsive ultrahigh fluorescence signal-on DNA amplification system via periodically programmed building and collapse of DNA networks. In this system, a pair of oligonucleotides of padlock probe (PP) and palindromic hairpin probe (PHP) are utilized. The presence of target DNA firstly hybridizes with PP, allowing the occurrence of rolling circle amplification (RCA) to produce RCA products with tandem repeats in abundance to bind and unfold numbers of PHPs. The conformational change of PHPs enables the building of DNA networks via the intermolecular palindrome pairing, but then makes the DNA networks collapsed via the palindrome-induced strand displacement polymerization. The displaced RCA products are dynamically reused to undergo periodically programmed multiple rounds of DNA network building and collapse. Depend on the bidirectional DNA assembly and disassembly, a strikingly amplified fluorescence can be collected to ultrasensitive and specific detection of target DNA. The practicability has been demonstrated by evaluating target-spiked human serum, saliva, and urine samples with acceptable recoveries and reproducibility. Therefore, this newly explored method opens a promising avenue for the detection of nucleic acids with low abundance in biochemical analysis and diseases diagnosis.

Nucleic Acid-Based Sensing Techniques for Diagnostics and Surveillance of Influenza

Influenza virus poses a threat to global health by causing seasonal outbreaks as well as three pandemics in the 20th century. In humans, disease is primarily caused by influenza A and B viruses, while influenza C virus causes mild disease mostly in children. Influenza D is an emerging virus found in cattle and pigs. To mitigate the morbidity and mortality associated with influenza, rapid and accurate diagnostic tests need to be deployed. However, the high genetic diversity displayed by influenza viruses presents a challenge to the development of a robust diagnostic test. Nucleic acid-based tests are more accurate than rapid antigen tests for influenza and are therefore better candidates to be used in both diagnostic and surveillance applications. Here, we review various nucleic acid-based techniques that have been applied towards the detection of influenza viruses in order to evaluate their utility as both diagnostic and surveillance tools. We discuss both traditional as well as novel methods to detect influenza viruses by covering techniques that require nucleic acid amplification or direct detection of viral RNA as well as comparing advantages and limitations for each method. There has been substantial progress in the development of nucleic acid-based sensing techniques for the detection of influenza virus. However, there is still an urgent need for a rapid and reliable influenza diagnostic test that can be used at point-of-care in order to enhance responsiveness to both seasonal and pandemic influenza outbreaks.

Novel Homogeneous Anion Exchange Membranes for Reproducible and Sensitive Nucleic Acid Detection via Current-Voltage Characteristic Measurement

One-pot synthesis of novel hydrogel-based anion exchange membranes (AEMs), with only a single-phase monomer mixture, was used to eliminate surface heterogeneity and generate reproducible electroconvective microvortices in the over-limiting region of the current-voltage characteristic (CVC) curves. Diallyldimethylammonium chloride (DDA) was used as the main component to provide the cation charge groups, and 2-hydroxyethyl methacrylate (HEMA) and ethylene glycol dimethyl acrylate (EGDMA) were used as the auxiliary structure monomers. The uniform membrane structure allowed reproducible and sensitive DNA detection and quantification, as probe-target surface complexes can gate the ion flux and produce large voltage shifts in the over-limiting region. Suppressed membrane curvature due to controlled swelling is a crucial part to avoid the reduction of depletion region for maintaining the influence of target gene hybridization. Fourier-transform infrared (FTIR) spectroscopy verified the synthesized membrane structure, with a residual vinyl group that allows easy carboxylation via additional photografting reaction. Consequently, a significantly higher DNA probe functionalization efficiency is obtained on the homogeneous AEMs, evidenced by the increasing nitrogen element content and bonding via X-ray photoelectron spectroscopy (XPS). The DDA content was optimized to provide a sufficient coulomb force between AEM and nucleic acid backbone to promote the specific binding efficiency but without high dimensional swelling which might change the surface geometry and restrict the voltage shifting for sensing in the over-limiting region, and the optimal DDA/HEMA ratio was found to be 4/10. The synthesized AEM sensor for recombinant 35S promoter sequence identification exhibited a reproducible calibration standard curve with dynamic range between 30 fM and 1 μM and high selectivity with only 0.01 V shift for 1 μM nontarget oligo.

Advanced Evanescent-Wave Optical Biosensors for the Detection of Nucleic Acids: An Analytic Perspective

Evanescent-wave optical biosensors have become an attractive alternative for the screening of nucleic acids in the clinical context. They possess highly sensitive transducers able to perform detection of a wide range of nucleic acid-based biomarkers without the need of any label or marker. These optical biosensor platforms are very versatile, allowing the incorporation of an almost limitless range of biorecognition probes precisely and robustly adhered to the sensor surface by covalent surface chemistry approaches. In addition, their application can be further enhanced by their combination with different processes, thanks to their integration with complex and automated microfluidic systems, facilitating the development of multiplexed and user-friendly platforms. The objective of this work is to provide a comprehensive synopsis of cutting-edge analytical strategies based on these label-free optical biosensors able to deal with the drawbacks related to DNA and RNA detection, from single point mutations assays and epigenetic alterations, to bacterial infections. Several plasmonic and silicon photonic-based biosensors are described together with their most recent applications in this area. We also identify and analyse the main challenges faced when attempting to harness this technology and how several innovative approaches introduced in the last years manage those issues, including the use of new biorecognition probes, surface functionalization approaches, signal amplification and enhancement strategies, as well as, sophisticated microfluidic solutions.

Neutralized chimeric DNA probe for the improvement of GC-rich RNA detection specificity on the nanowire field-effect transistor

Silicon nanowire (SiNW) field-effect transistors (FETs) is a powerful tool in genetic molecule analysis because of their high sensitivity, short detection time, and label-free detection. In nucleic acid detection, GC-rich nucleic acid sequences form self- and cross-dimers and stem-loop structures, which can easily obtain data containing signals from nonspecific DNA binding. The features of GC-rich nucleic acid sequences cause inaccuracies in nucleic acid detection and hinder the development of precision medicine. To improve the inaccurate detection results, we used phosphate-methylated (neutral) nucleotides to synthesize the neutralized chimeric DNA oligomer probe. The probe fragment originated from a primer for the detection of hepatitis C virus (HCV) genotype 3b, and single-mismatched and perfect-matched targets were designed for single nucleotide polymorphisms (SNP) detection on the SiNW FET device. Experimental results revealed that the HCV-3b chimeric neutralized DNA (nDNA) probe exhibited better performance for SNP discrimination in 10 mM bis-tris propane buffer at 25 °C than a regular DNA probe. The SNP discrimination of the nDNA probe could be further improved at 40 °C on the FET device. Consequently, the neutralized chimeric DNA probe could successfully distinguish SNP in the detection of GC-rich target sequences under optimal operating conditions on the SiNW FET device.

Designed phosphate-methylated oligonucleotides as PCR primers for SNP discrimination

Polymerase chain reaction (PCR) is a powerful technique for the detection and quantification of nucleic acids and has enormous applications to research in molecular biology. Certain inherited diseases, caused by single nucleotide mutations, however, are difficult to identify by PCR, using DNA primers and probes, in a situation where a false diagnosis may lead to incorrect or delayed treatment. With the aim of enhancing the specificity of PCR, we used novel chemically synthesized oligonucleotides containing site-specific methyl phosphotriester (MPTE) inter-nucleoside linkage(s) as primers and probes. The methyl phosphotriester linkages carry no charge, so the reduction in the electrostatic repulsion of an MPTE-DNA/DNA duplex shows stronger hybridization affinity compared to a DNA/DNA duplex. However, the electrosteric effects introduced by the methyl group may result in instability of the double-stranded DNA (dsDNA) formed. With the use of specific MPTE modification sites and optimization of the number of MPTE modifications, greater delta melting temperature (ΔT_m) may be obtained, in concert with adjustment of PCR operating conditions, especially with respect to the annealing temperature, to achieve more discriminatory results between the target template and the perfectly matched primer and the mismatched primer. In single nucleotide polymorphism (SNP) genotyping, the results demonstrated that MPTE-modified probes can improve specificity. In summary, MPTE-modified oligonucleotides are a promising DNA analog applied to PCR primers and probes to enhance the specificity and to provide more precise detection results for various applications, such as for genetic diagnosis. In summary, two common DNA polymerases we tested could successfully recognize the MPTE-modified primers and probes. Under the optimal operating conditions, MPTE modification has the ability to improve the discrimination of single nucleotide polymorphism by increasing the ΔT_m of the perfect match and mismatch sequences and to provide more precise detection results for various applications, such as genetic diagnosis.

Functional Biointerfaces Based on Mixed Zwitterionic Self-Assembled Monolayers for Biosensing Applications

Surface modification for biosensors has focused attention for improvement of their sensitivity and specificity, particularly for the detection in complex medium. In this work, we have synthesized zwitterionic carboxybetaine-thiols (CB-thiols) and sulfobetaine-thiols (SB-thiols) for modification of gold substrates to form a functional self-assembled monolayer (SAM) for the immunoassay in a surface plasmon resonance (SPR) biosensor. X-ray photoelectron spectroscopy (XPS), contact angle goniometer, and cyclic voltammetry were applied for characterizations of elemental composition, surface wettability, and packing density, respectively. The antifouling properties of the SAMs were accessed by quantitative analysis of protein and bacterial adsorption. The results from the SAMs with a single component indicated that the SB-thiol SAM provides better surface hydrophilicity, fouling resistance, and packing density as compared to the CB-thiol SAM, likely due to the ionic association of CB moieties. However, the CB-thiol with the functional carboxylate group plays a critical role in postmodification of biomolecules via commercially available amine coupling chemistry. Thus, the mixed SAMs were prepared to integrate the unique characteristics from CB- and SB-thiols to control compositions and surface properties. The immunoassay was performed in the SPR biosensor, showing that the zwitterionic mixed SAM enables immobilization of biorecognition elements (BREs), and improved sensitivity and specificity. Consequently, the work reveals excellent and attractive versatility, antifouling, and functionalizable properties of zwitterionic mixed SAMs comprising CB- and SB-thiols for biosensing applications. This surface chemistry is expected to be applicable to monitor specific molecular recognition events.

Dual-Channel Surface Plasmon Resonance for Quantification of ApoE Gene and Genotype Discrimination in Unamplified Genomic DNA Extracts

Identification of gene variation is of great importance for attaining information related to disease susceptibility. A highly sensitive and specific surface plasmon resonance (SPR) method for quantification of the apoE gene and genotype discrimination was demonstrated. The complementary sequences with the specific recognition sites of GCGC bases upon hybridization to the preimmobilized biotinylated probes could be cleaved by the restriction enzyme HhaI, while the existence of the single-base mismatch (GTGC) prevented the cleavage reaction. In both cases, the incorporation of streptavidin increased the sensitivity of the SPR assay, and the detection levels of 10 fM and 50 fM for the complementary and single-base mismatched sequences were attained, respectively. The sensing protocol is simple, label-free, and quantitative, thus avoiding the complicated polymerase chain reaction (PCR) amplification procedures. The proposed method serves as a viable means for facile and sensitive analyses of apoE genes in four unamplified genomic DNA extracts.

Pressure-Modulated Selective Electrokinetic Trapping for Direct Enrichment, Purification, and Detection of Nucleic Acids in Human Serum

Micro total-analysis systems (μTAS) have been extensively developed for the detection of nucleic acids (NAs) in resource-limited settings in recent years, yet the sample-preparation steps that interface real-world samples with on-chip analytics remain as the technical bottleneck. We report pressure-modulated selective electrokinetic trapping (PM-SET) for the direct enrichment, purification, and detection of NAs in human serum in one step without involving tedious solid-phase extraction, chemical amplification, and surface-hybridization-based assays. Under appropriately modulated hydrostatic pressures, NAs in human serum were selectively enriched in an electrokinetic concentrator with the majority of background proteins removed, achieving an enrichment factor of >4800 in 15 min. A sequence-specific NA was detected simultaneously during the enrichment process using a complementary morpholino (MO) probe, realizing a limit of detection of 3 pM in 15 min. PM-SET greatly reduces the cost, time, and complexity of sample preparation for NA detection and could be easily interfaced with existing NA-detection devices to achieve true sample-to-answer biomolecular analytics.

The effect of DNA on the oxidase activity of nanoceria with different morphologies

Many nanomaterials have been reported to have enzyme-like activities and are considered as nanozymes. As a multifunctional nanozyme, nanoceria has received much attention due to the dual oxidation states of Ce³⁺/Ce⁴⁺ which facilitate redox reactions at the particle surface. Despite the advantages of nanozymes, their limited activity and lack of enzyme specificity are still problems to be resolved. DNA is used to modulate the oxidase activity of nanoceria because it has recently become an important molecule in bionanotechnology. However, the current research on the effect of DNA on the oxidase mimetic activity of nanoceria is contradictory. It has been discovered that nanoceria used in recent works are different, including in particle size, doping and concentration, and these differences may affect the interaction between DNA and nanoceria, and then affect the oxidase mimetic activity of nanoceria. Hence, it is important to clarify the factors that affect the interaction between DNA with nanoceria. In this work, the interactions between DNA and nanoceria with three different morphologies (nanoparticles, nanocubes, and nanorods) have been investigated. Experimental results show that DNA has different influences on the oxidase mimetic activity of nanoceria with different morphologies. The oxidase mimetic activity of CeO₂ nanoparticles and nanocubes increased, but that of CeO₂ nanorods decreased, after DNA modification. The mechanism of these experimental results has been explored, and it has been found that it is the interaction between cerium and the phosphate backbone of DNA that changes with the different morphologies, resulting in the varying effect of DNA on the oxidase mimetic activity of nanoceria. These results may provide a better understanding of the effect of DNA on the oxidase mimetic activity of nanoceria and promote the applications of nanoceria.

Synergetic improvements of sensitivity and specificity of nanowire field effect transistor gene chip by designing neutralized DNA as probe

Neutral DNA analogs as probes for the detection of target oligomers on the biosensors based on the field-effect transistor (FET) configuration feature advantages in the enhancement of sensitivity and signal-to-noise ratio. Herein, we used phosphate-methylated nucleotides to synthesize two partially neutralized chimeric DNA products and a fully neutralized DNA sequence and adopted a regular DNA oligomer as probes on the polycrystalline silicon nanowire (NW) FET devices. The sequences of two neutralized chimeric DNAs close to the 5′ end were alternately modified with the phosphate-methylated nucleotides, and all probes were immobilized via their 5′ end on the NW surface. The non-specific-to-specific binding ratio indicated that the two 5′-end partially neutralized chimeric DNAs featured better performance than the regular and fully neutralized DNA oligomers. The partially neutralized probe design reduces the ionic strength needed for hybridization and increases the Debye length of detection, thus promoting the detection sensitivity of FET and achieving the limit of detection of 0.1 fM. By using an appropriate probe design, applying DNA oligomers with embedded phosphate-methylated nucleotides in the FET biosensors is a promising way for gene detection with high sensitivity and specificity.

Photonic crystals on copolymer film for label-free detection of DNA hybridization

The presence of a single-nucleotide polymorphism in Apolipoprotein E4 gene is implicated with the increased risk of developing Alzheimer's disease (AD). In this study, detection of AD-related DNA oligonucleotide sequence associated with Apolipoprotein E4 gene sequence was achieved using localized-surface plasmon resonance (LSPR) on 2D-Photonic crystal (2D-PC) and Au-coated 2D-PC surfaces. 2D-PC surfaces were fabricated on a flexible copolymer film using nano-imprint lithography (NIL). The film surface was then coated with a dual-functionalized polymer to react with surface immobilized DNA probe. DNA hybridization was detected by monitoring the optical responses of either a Fresnel decrease in reflectance on 2D-PC surfaces or an increase in LSPR on Au-coated 2D-PC surfaces. The change in response due to DNA hybridization on the modified surfaces was also investigated using mismatched and non-complementary oligonucleotides sequences. The proof-of-concept results are promising towards the development of 2D-PC on copolymer film surfaces as miniaturized and wearable biosensors for various diagnostic and defense applications.