Control of metal nanoparticles aggregation and dispersion by PNA and PNA-DNA complexes, and its application for colorimetric DNA detection

A designed DNA/amino acid amphiphile-based supramolecular oxidase-mimetic catalyst for colorimetric DNA detection

DNA is self-assembled with Fmoc-amino acids and Cu2+ to construct a supramolecular catechol oxidase-mimetic catalyst, which exhibits remarkable activity in catalyzing colorimetric reactions. This catalytic system is used for the detection of DNA hybridization with a high selectivity and a low detection limit.

Colorimetric sensing assay based on aptamer-gold nanoparticles for rapid detection of salivary melatonin to monitor circadian rhythm sleep disorders

Salivary melatonin is a clinically used biomarker for diagnosing circadian rhythm sleep disorders. Current melatonin detection assays are complex, expensive, and in many cases do not adequately measure low levels of salivary melatonin. Precisely measuring melatonin levels at multiple time points is crucial for determining dim light melatonin onset to evaluate its circadian fluctuation as well as the extent of circadian disruption and consequently adapt treatment regimens. Moreover, melatonin low levels in saliva challenges the reliability of routine clinical testing. This paper presents the development of a novel, highly sensitive, yet cost-effective, colorimetric assay for the rapid detection of salivary melatonin utilizing aptamer-AuNPs. Among several types of the aptamer tested, the 36-mer MLT-A-2 aptamer-AuNP probe showed the highest sensitivity with a melatonin limit of detection of 0.0011 nM along with a limit of quantification of 0.0021 nM in saliva. Moreover, our assay showed preferential interaction with melatonin when tested in presence of other structurally similar counter-targets. Taken together, this study provides new parameters for a melatonin assay that meets adequate levels of sensitivity and selectivity. The developed colorimetric assay could be adapted in a point-of-care system for profiling salivary melatonin levels at multiple time points during 24 h, crucial for accurately diagnosing and monitoring circadian rhythm sleep disorders and beyond.

Peptide-metal nanohybrids (PMN): Promising entities for combating neurological maladies

Nanotherapeutics are gaining traction in the modern scenario because of their unique and distinct properties which separate them from macro materials. Among the nanoparticles, metal NPs (MNPs) have gained importance due to their distinct physicochemical and biological characteristics. Peptides also exhibit several important functions in humans. Different peptides have received approval as pharmaceuticals, and clinical trials have been commenced for several peptides. Peptides are also used as targeting ligands. Considering all the advantages offered by these two entities, the conjugation of MNPs with peptides has emerged as a potential strategy for achieving successful targeting, diagnosis, and therapy of various neurological pathologies.

Celebrating 25 Years of IMRE: Research Highlights on Nanomaterials and Nanotechnologies

The Institute of Materials Research and Engineering (IMRE) is a research institute of the Science and Engineering Research Council (SERC), Agency for Science, Technology and Research (A*STAR). IMRE was established in September 1997. Over the past 25 years, IMRE has developed core competencies and interdisciplinary teams for material development from fundamental discoveries to industrial translation. Currently, with over 400 researchers and state-of-the-art research facilities, IMRE conducts world class research in important material and material technology fields, including polymer composites, optical materials, electronic materials, soft materials, structural materials, energy materials, biomaterials, quantum technologies, as well as advanced characterization. As a material-centered research institute in Singapore, IMRE has played important roles in pushing science boundaries and developing cutting-edge technologies. One of the key strategies is to partner international organizations, research institutes, and industry to fulfill its vision to be a leading research institute to accelerate materials research, moving from "Made in Singapore" toward "Created in Singapore".

Bio-Receptors Functionalized Nanoparticles: A Resourceful Sensing and Colorimetric Detection Tool for Pathogenic Bacteria and Microbial Biomolecules

Pathogenic bacteria and several biomolecules produced by cells and living organisms are common biological components posing a harmful threat to global health. Several studies have devised methods for the detection of varying pathogenic bacteria and biomolecules in different settings such as food, water, soil, among others. Some of the detection studies highlighting target pathogenic bacteria and biomolecules, mechanisms of detection, colorimetric outputs, and detection limits have been summarized in this review. In the last 2 decades, studies have harnessed various nanotechnology-based methods for the detection of pathogenic bacteria and biomolecules with much attention on functionalization techniques. This review considers the detection mechanisms, colorimetric prowess of bio-receptors and compares the reported detection efficiency for some bio-receptor functionalized nanoparticles. Some studies reported visual, rapid, and high-intensity colorimetric detection of pathogenic bacteria and biomolecules at a very low concentration of the analyte. Other studies reported slight colorimetric detection only with a large concentration of an analyte. The effectiveness of bio-receptor functionalized nanoparticles as detection component varies depending on their selectivity, specificity, and the binding interaction exhibited by nanoparticles, bio-receptor, and analytes to form a bio-sensing complex. It is however important to note that the colorimetric properties of some bio-receptor functionalized nanoparticles have shown strong and brilliant potential for real-time and visual-aided diagnostic results, not only to assess food and water quality but also for environmental monitoring of pathogenic bacteria and a wide array of biomolecules.

Adjusting the Structure of a Peptide Nucleic Acid (PNA) Molecular Beacon and Promoting Its DNA Detection by a Hybrid with Quencher-Modified DNA

In this study, we performed an elaborate adjustment of the structure of peptide nucleic acid (PNA) molecular beacons as probes for detecting nucleic acids. We synthesized the PNA beacons with various numbers of Glu, Lys, and dabcyl (Dab) quenchers in them, and we investigated their fluorescence changes (F1/1/F0) with and without full-match DNA. As the numbers of Glu/Lys or Dab increased, the F1/1/F0 tended to decrease. Among the different beacons, the PNA beacon with one Glu and one Lys (P1Q1) showed the largest F1/1/F0. On the other hand, a relatively large F1/1/F0 was obtained when the number of Glu/Lys and the number of Dab were the same, and the balance between the numbers of Glu/Lys and Dab seemed to affect the F1/1/F0. We also investigated the DNA detection by the prehybrid of P1Q1, which consists of the T790M base sequence, [P1Q1(T790M)], with quencher-modified DNA (Q-DNA). We examined the DNA detection with single-base mismatch by P1Q1(T790M), and we clarified that there was difficulty in detecting the sequence with P1Q1 alone, but that the sequence was successfully detected by the prehybrid of P1Q1 with the Q-DNA.

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.

A portable SERS sensor for pyocyanin detection in simulated wound fluid and through swab sampling

A portable surface-enhanced Raman spectroscopy (SERS) sensor for detecting pyocyanin (PYO) in simulated wound fluid and from bacteria samples was developed. Solution-phase SERS detection protocols are designed to be compatible with two different clinical practices for wound exudate collection, namely negative pressure liquid collection and swabbing. For citrate-coated metal nanoparticles of three different compositions, i.e. gold (AuNPs), alloyed silver/gold (AgAuNPs), and silver (AgNPs), we firstly confirmed their interaction with PYO in the complex wound fluid, using fluorescence quenching experiments, which rationalized the Raman enhancement effects. We then demonstrated the Raman enhancement effects of the metal nanoparticles in the order of AgNPs > AgAuNPs > AuNPs. The limit of detection (LOD) achieved for PYO is 1.1 μM (in a linear range of 0.1-25 μM by the AgNPs), 10.9 μM (in a linear range of 5-100 μM, by the AgAuNPs), and 17.7 μM (in a linear range of 10-100 μM by the AuNPs). The AgNP and AgAuNP sensors together cover the sensitivity and dynamic range requirements for the clinical detection of wound infection, where PYO is present at a concentration of 1-50 μM. In addition, sterilized cotton swabs were used to collect wound fluid and transfer samples into AgNP solution for SERS measurements. This detection protocol was completed within 5 minutes with a LOD of 23.1 μM (in a linear range of 15-100 μM). The SERS sensing protocol was validated by its successful detection of PYO in cultured Pseudomonas aeruginosa bacteria. The findings presented in this work pave the way towards point-of-care diagnostics of wound infections.

Gene editing and RNAi approaches for COVID-19 diagnostics and therapeutics

The novel coronavirus pneumonia (COVID-19) is a highly infectious acute respiratory disease caused by Severe Acute Respiratory Syndrome-Related Coronavirus (SARS-CoV-2) (Prec Clin Med 2020;3:9-13, Lancet 2020;395:497-506, N. Engl J Med 2020a;382:1199-207, Nature 2020;579:270-3). SARS-CoV-2 surveillance is essential to controlling widespread transmission. However, there are several challenges associated with the diagnostic of the COVID-19 during the current outbreak (Liu and Li (2019), Nature 2020;579:265-9, N. Engl J Med 2020;382:727-33). Firstly, the high number of cases overwhelms diagnostic test capacity and proposes the need for a rapid solution for sample processing (Science 2018;360:444-8). Secondly, SARS-CoV-2 is closely related to other important coronavirus species and subspecies, so detection assays can give false-positive results if they are not efficiently specific to SARS-CoV-2. Thirdly, patients with suspected SARS-CoV-2 infection sometimes have a different respiratory viral infection or co-infections with SARS-CoV-2 and other respiratory viruses (MedRxiv 2020a;1-18). Confirmation of the COVID-19 is performed mainly by virus isolation followed by RT-PCR and sequencing (N. Engl J Med 2020;382:727-33, MedRxiv 2020a, Turkish J Biol 2020;44:192-202). The emergence and outbreak of the novel coronavirus highlighted the urgent need for new therapeutic technologies that are fast, precise, stable, easy to manufacture, and target-specific for surveillance and treatment. Molecular biology tools that include gene-editing approaches such as CRISPR-Cas12/13-based SHERLOCK, DETECTR, CARVER and PAC-MAN, antisense oligonucleotides, antisense peptide nucleic acids, ribozymes, aptamers, and RNAi silencing approaches produced with cutting-edge scientific advances compared to conventional diagnostic or treatment methods could be vital in COVID-19 and other future outbreaks. Thus, in this review, we will discuss potent the molecular biology approaches that can revolutionize diagnostic of viral infections and therapies to fight COVID-19 in a highly specific, stable, and efficient way.

Programmable Engineering of DNA-AuNP Encoders Integrated Multimodal Coupled Analysis for Precision Discrimination of Multiple Metal Ions

A cross-responsive strategy (CRS) based on gold nanoparticles (AuNPs) through attaching various recognition receptors on the surface of AuNPs for identifying multiple analytes is presented, and the detection throughput and overall identification accuracy are improved. However, the CRS's recognition receptor cannot get comprehensive information from the target analytes limited in number and type, which determines the overall identification accuracy. Therefore, the practicability of the CRS runs into a bottleneck. Herein, we report a programmable DNA-AuNP encoder combined with a multimodal coupled analysis algorithm for high-throughput detection and accurate analysis of multiple metal ions. The programmable DNA-AuNP encoder breaks through the limitation of the recognition receptor's quantity. Furthermore, the multimodal signals from target metal ion-induced DNA-AuNP aggregation are related to and observed in the ultraviolet absorbance spectrum, surface potential, and particle diameter. The multimodal coupled analysis algorithm can reflect comprehensive information on the target analyte more completely. Finally, this study provides a highly generic tool for the cross-responsive strategy.

A sensitive "off-on" carbon dots-Ag nanoparticles fluorescent probe for cysteamine detection via the inner filter effect

In this study, we describe the construction of an "off-on" fluorescent probe based on carbon dots (CDs) and silver nanoparticles (AgNPs) mixture for sensitive and selective detection of cysteamine. By mixing AgNPs with CDs solution, the fluorescence of CDs was significantly decreased due to the inner filter effect (IFE). Upon addition of cysteamine to the mixed aqueous of CDs and AgNPs, the silver-sulfur bond between cysteamine and AgNPs caused AgNPs to aggregate, and the quenched fluorescence of CDs could in turn be recovered. The probe was employed to quantitatively detect cysteamine, and the results showed that it could detect cysteamine in a concentration range of 2-16 μM with the detection limit of 0.35 μM (signal-to-noise ratio of 3). The detection of cysteamine spiked into bovine serum samples showed high recovery rates ranging from 95.5 to 111.7%. More importantly, the developed probe had low cytotoxicity and was successfully used for in vivo imaging of HepG2 cells.

Paper-based DNA sensor enabling colorimetric assay integrated with smartphone for human papillomavirus detection

A colorimetric paper-based DNA sensor that relies on the inhibition of PNA-induced AuNPs aggregation was combined with a simple smartphone readout for the point-of-care detection of HPV type 16 DNA.

Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions

The fundamental interactions underlying citrate-mediated chemical stability of metal nanoparticles, and their surface characteristics dictating particle dispersion/aggregation in aqueous solutions, are largely unclear. Here, we developed a theoretical model to estimate the stoichiometry of small, charged ligands (like citrate) chemisorbed onto spherical metallic nanoparticles and coupled it with atomistic molecular dynamics simulations to define the uncovered solvent-accessible surface area of the nanoparticle. Then, we integrated coarse-grained molecular dynamics simulations and two-body free energy calculations to define dispersion state phase diagrams for charged metal nanoparticles in a range of medium’s ionic strength, a known trigger for aggregation. Ultraviolet-visible spectroscopy experiments of citrate-capped nanocolloids validated our predictions and extended our results to nanoparticles up to 35 nm. Altogether, our results disclose a complex interplay between the particle size, its surface charge density, and the ionic strength of the medium, which ultimately clarifies how these variables impact colloidal stability.

Citrate-stabilized metallic colloids are key materials towards chemosensing and catalysis applications. Here the authors introduce a new theoretical model to estimate how the stoichiometry of citrate molecules absorbed onto spherical metallic nanoparticles influences their aggregation phenomena.

Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions

The fundamental interactions underlying citrate-mediated chemical stability of metal nanoparticles, and their surface characteristics dictating particle dispersion/aggregation in aqueous solutions, are largely unclear. Here, we developed a theoretical model to estimate the stoichiometry of small, charged ligands (like citrate) chemisorbed onto spherical metallic nanoparticles and coupled it with atomistic molecular dynamics simulations to define the uncovered solvent-accessible surface area of the nanoparticle. Then, we integrated coarse-grained molecular dynamics simulations and two-body free energy calculations to define dispersion state phase diagrams for charged metal nanoparticles in a range of medium’s ionic strength, a known trigger for aggregation. Ultraviolet-visible spectroscopy experiments of citrate-capped nanocolloids validated our predictions and extended our results to nanoparticles up to 35 nm. Altogether, our results disclose a complex interplay between the particle size, its surface charge density, and the ionic strength of the medium, which ultimately clarifies how these variables impact colloidal stability.

Stoichiometric Tuning of PNA Probes to Au0.8Ag0.2 Alloy Nanoparticles for Visual Detection of Nucleic Acids in Plasma

Standard detection methods for nucleic acids, an important class of diagnostic biomarkers, are often laborious and cumbersome. In need for development of facile methodologies, localized surface plasmon resonance (LSPR) assays have been widely explored for both spectroscopic and visual detection of nucleic acids. Our sensing approach is based on monitoring changes in the LSPR band due to interaction between peptide nucleic acid (PNA) and plasmonic nanoparticles (NPs) in the presence/absence of target nucleic acid. We have investigated the importance of tuning the stoichiometry of PNA to NPs to enable "naked-eye" detection of nucleic acids at clinically relevant concentration ranges. Assaying in plasma is achieved by incorporation of silver in gold NPs (AuNPs) via an alloying process. The synthesized gold/silver alloy NPs reduce nonspecific adsorption of proteinaceous interferents in plasma. Furthermore, the gold/silver alloy NPs absorb in the most sensitive cyan to green transition zone (∼500 nm) yielding highly competitive visual limits of detection (LODs). The visual LOD (calculated objectively using the ΔE algorithm) for a model microRNA (mir21) using a productive combination of stoichiometric tuning of the PNA to NP ratio and compositional tuning of the NPs in buffer and plasma extract equals 200 pM (∼250 times lower than existing reports) and 3 nM, respectively. We envision that the proposed LSPR assay based on Au_0.8Ag_0.2NPs offers an avenue for rapid and sensitive on-site detection of nucleic acids in complex matrixes in combination with efficient target extraction kits.

Sequence-specific detection of single-stranded DNA with a gold nanoparticle-protein nanopore approach

Fast, cheap and easy to use nucleic acids detection methods are crucial to mitigate adverse impacts caused by various pathogens, and are essential in forensic investigations, food safety monitoring or evolution of infectious diseases. We report here a method based on the α-hemolysin (α-HL) nanopore, working in conjunction to unmodified citrate anion-coated gold nanoparticles (AuNPs), to detect nanomolar concentrations of short single-stranded DNA sequences (ssDNA). The core idea was to use charge neutral peptide nucleic acids (PNA) as hybridization probe for complementary target ssDNAs, and monitor at the single-particle level the PNA-induced aggregation propensity AuNPs during PNA–DNA duplexes formation, by recording ionic current blockades signature of AuNP–α-HL interactions. This approach offers advantages including: (1) a simple to operate platform, producing clear-cut readout signals based on distinct size differences of PNA-induced AuNPs aggregates, in relation to the presence in solution of complementary ssDNAs to the PNA fragments (2) sensitive and selective detection of target ssDNAs (3) specific ssDNA detection in the presence of interference DNA, without sample labeling or signal amplification. The powerful synergy of protein nanopore-based nanoparticle detection and specific PNA–DNA hybridization introduces a new strategy for nucleic acids biosensing with short detection time and label-free operation.

A peptide nucleic acid-regulated fluorescence resonance energy transfer DNA assay based on the use of carbon dots and gold nanoparticles

A convenient fluorometric method was developed for specific determination of DNA based on peptide nuclei acid (PNA)-regulated fluorescence resonance energy transfer (FRET) between carbon dots (CDs) and gold nanoparticles (AuNPs). In this system, CDs that display lake blue fluorescence with excitation/emission maxima at 345/445 nm were used as fluorometric reporter, while AuNPs were used as fluorescence nanoquencher. A neutral PNA probe, which is designed to recognize the target DNA, was used as a coagulant to control the dispersion and aggregation of AuNPs. Without DNA, PNA can induce immediate AuNP aggregation, thus leading to the recovery of the FRET-quenched fluorescence emission of CDs. However, the addition of the complementary target DNA can protect AuNPs from being aggregated due to the formation of DNA/PNA complexes, which subsequently produces a high fluorescence quenching efficiency of CDs by dispersed AuNPs. Under optimized conditions, quantitative evaluation of DNA was achieved in a linear range of 5-100 nM with a detection limit of 0.21 nM. This method exhibited an excellent specificity towards fully matched DNA. In addition, the application of this assay for sensitive determination of DNA in cell lysate demonstrates its potential for bioanalysis and biodetection. Graphical abstract A simple fluorometric biosensor for specific detection of DNA was developed based on peptide nuclei acid (PNA)-regulated fluorescence resonance energy transfer (FRET) between carbon dots (CDs) and gold nanoparticles (AuNPs).

Efficient Gene Therapy of Pancreatic Cancer via a Peptide Nucleic Acid (PNA)-Loaded Layered Double Hydroxides (LDH) Nanoplatform

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest malignant tumors with extremely poor prognosis due to the later stage diagnosis when surgical resection is no longer applicable. Alternatively, the traditional gene therapy which drives pancreatic cancer cells into an inactive state and inhibiting the proliferation and metastasis, presents potentials to safely inhibit pancreatic cancer progression, but unfortunately has received limited success to date. Here, an efficient gene therapy of pancreatic cancer is shown via a peptide nucleic acid (PNA)-loaded layered double hydroxides (LDHs) nanoplatform. Compared with the traditional DNA- or RNA-based gene therapies, the gene therapy using PNA features great advantages in recognizing and hybridizing with the target mutant sequences to form PNA-DNA hybrids with significantly enhanced stability due to the absence of electrostatic repulsion, and the constrained flexibility of the polyamide backbone. Moreover, ultrasmall LDHs are engineered to load PNA and the obtained PNA-loaded LDH platform (LDHs/PNA) is capable of efficiently and selectively targeting the intranuclear mutant sequences thanks to the proton sponge effect. Treatments with LDHs/PNA demonstrate markedly inhibited growth of pancreatic cancer xenografts via a cancer cell proliferation suppression mechanism. The results demonstrate the great potentials of LDHs/PNA as a highly promising gene therapy agent for PDAC.

Sensors, Biosensors, and Analytical Technologies for Aquaculture Water Quality

In aquaculture industry, fish, shellfish, and aquatic plants are cultivated in fresh, salt, or brackish waters. The increasing demand of aquatic products has stimulated the rapid growth of aquaculture industries. How to effectively monitor and control water quality is one of the key concerns for aquaculture industry to ensure high productivity and high quality. There are four major categories of water quality concerns that affect aquaculture cultivations, namely, (1) physical parameters, e.g., pH, temperature, dissolved oxygen, and salinity, (2) organic contaminants, (3) biochemical hazards, e.g., cyanotoxins, and (4) biological contaminants, i.e., pathogens. While the physical parameters are affected by climate changes, the latter three are considered as environmental factors. In this review, we provide a comprehensive summary of sensors, biosensors, and analytical technologies available for monitoring aquaculture water quality. They include low-cost commercial sensors and sensor network setups for physical parameters. They also include chromatography, mass spectrometry, biochemistry, and molecular methods (e.g., immunoassays and polymerase chain reaction assays), culture-based method, and biophysical technologies (e.g., biosensors and nanosensors) for environmental contamination factors. According to the different levels of sophistication of various analytical techniques and the information they can provide (either fine fingerprint, highly accurate quantification, semiquantification, qualitative detection, or fast screening), we will comment on how they may be used as complementary tools, as well as their potential and gaps toward current demand of real-time, online, and/or onsite detection.

Using gold nanoparticles to detect single-nucleotide polymorphisms: toward liquid biopsy

The possibility of detecting genetic mutations rapidly in physiological media through liquid biopsy has attracted the attention within the materials science community. The physical properties of nanoparticles combined with robust transduction methods ensure an improved sensitivity and specificity of a given assay and its implementation into point-of-care devices for common use. Covering the last twenty years, this review gives an overview of the state-of-the-art of the research on the use of gold nanoparticles in the development of colorimetric biosensors for the detection of single-nucleotide polymorphism as cancer biomarker. We discuss the main mechanisms of the assays that either are assisted by DNA-based molecular machines or by enzymatic reactions, summarize their performance and provide an outlook towards future developments.

Sensing of circulating cancer biomarkers with metal nanoparticles

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

In-Solution Molecular Recognition Comparison of Aptamers against the Herbicide Atrazine

Atrazine is a common herbicide that is widely used to control weed growth in both agricultural and residential settings. It has been shown to act as an endocrine disruptor that affects aquatic organisms. Rapid and low-cost monitoring methods for atrazine is the first step to mitigate its widespread persistency. Aptamers are small synthetic oligonucleotides that can assume a 3D structure to act as the molecular recognition element for a specific target of interest. Two different atrazine binding aptamers (R12.23 Trunc. and R12.45 Trunc.) have been identified from the same library design but with fundamentally different in vitro selection methodologies. While the R12.23 Trunc. has been utilized in immobilized biosensing platforms, it is unclear if in-solution-based applications would be suitable for both atrazine binding aptamers. This study provides the first insight of comparative in-solution binding profiles of the two atrazine binding aptamers. Based on our results, this information will be useful for future biosensing platform development utilizing the two aptamers.

Label-free peptide nucleic acid biosensor for visual detection of multiple strains of influenza A virus suitable for field applications

Accurate and rapid diagnosis of Influenza A viruses (IAVs) is challenging because of multiple strains circulating in humans and animal populations, and the emergence of new strains. In this study, we demonstrate a simple and rapid strategy for visual detection of multiple strains of IAVs (H1 to H16 subtypes) using peptide nucleic acid (PNA) as a biosensor and unmodified gold nanoparticles (AuNPs) as a reporter. The design principle of the assay is based on the color change on account of free PNA-induced aggregation of AuNPs in the presence of non-complementary viral RNA sequence and vice-versa. The assay could detect IAV RNA with a visual limit of detection of 2.3 ng. The quantification of RNA with a considerable accuracy on a simple spectrophotometer was achieved on plotting the PNA-induced colorimetric changes (absorption ratio of A₆₄₀/A₅₂₀) in the presence of a varying concentration of complementary RNA. As a proof-of-concept, the visual assay was validated on 419 avian clinical samples and receiver operating characteristic (ROC) curve analysis showed a high diagnostic specificity (96.46%, 95% CI = 93.8 to 98.2) and sensitivity (82.41%, 95% CI = 73.9 to 89.1) when RT-qPCR was used as reference test. Hence, the simplicity, rapidity, and universality of this strategy make it a potential candidate visual assay for clinical diagnosis and surveillance of IAVs, especially in the resource-limited settings. The proposed strategy establishes new avenues for developing a simple and rapid diagnostic system for viral infections and biomolecules.

Paper-based point-of-care test with xeno nucleic acid probes

Bridging the unmet need of efficient point-of-care testing (POCT) in biomedical engineering research and practice with the emerging development in artificial synthetic xeno nucleic acids (XNAs), this review summarized the recent development in paper-based POCT using XNAs as sensing probes. Alongside the signal transducing mode and immobilization methods of XNA probes, a detailed evaluation of probe performance was disclosed. With these new aspects, both researchers in synthetic chemistry / biomedical engineering and physicians in clinical practice could gain new insights in designing, manufacturing and choosing suitable reagents and techniques for POCT.

Delivery of antisense peptide nucleic acid by gold nanoparticles for the inhibition of virus replication

Aim: We aim to use peptide nucleic acid (PNA) for antisense therapy against bovine viral diarrhea virus (BVDV), a surrogate model of human hepatitis C virus, and introduce an optimal approach for delivering PNA into the cell. Materials & methods: PNA was designed for hybridization to the 5'-untranslated region of BVDV RNA in order to form a heteroduplex structure and inhibit the translation and replication of virus. Gold nanoparticles (AuNPs) were used as a delivery system for PNA. Results: The cellular uptake of PNA-AuNPs and inhibition of BVDV infection in the middle stage of viral replication were found. Conclusion: Further research is warranted to develop AuNPs as a potential vehicle for delivering PNA in order to remove viruses from the infected cells.

Colorimetric detection of single base-pair mismatches based on the interactions of PNA and PNA/DNA complexes with unmodified gold nanoparticles

Rapid and sensitive single nucleotide polymorphisms (SNPs) genotyping is of particular important for early diagnosis, prevention, and treatment of specific human diseases. A simple and low-cost SNP detection method would be valuable for routine analysis in resource-limited settings. Here, we demonstrated a novel and convenient gold nanoparticle (AuNPs) based colorimetric approach for efficient screening of SNPs at room temperature without instrumentation. SNP detection is performed in a single tube with one set of unmodified AuNPs, a label-free peptide nucleic acid (PNA) probe, a single exonuclease (S1 nuclease), and the target to be tested. S1 nuclease could digest DNAs in DNA/PNA duplexes involving a mismatch into small fragments, while DNAs in the fully-matched DNA/PNA duplexes can be effectively protected by PNA from enzymatic degradation. This difference could be easily discriminated by color changes associated with gold aggregation. PNA oligomers can induce immediate AuNP aggregation even in the presence of nucleoside monophosphates (dNMPs), the digestion products of DNA. Whereas PNA/DNA duplexes can effectively stabilize unmodified AuNPs, and the stabilization effect of PNA/DNA is better than single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). Without the need of precise temperature control and extra salt addition, SNPs are detected with a detection limit of 2.3 nM in cell lysate. Moreover, this system can effectively discriminate a range of different mismatches even in spiked cell lysate, demonstrate the potential use of this biosensor for biological samples.

A physical-based interpretation of mechanism and kinetics of Cr(VI) reduction in aqueous solution by zero-valent iron nanoparticles

The aim of this paper is to show the results obtained by investigating the reduction of hexavalent Chromium [Cr(VI)] by iron nano-particles in aqueous solution, interpreted in light of the particle-grain model. The diffusional and geometric parameters that govern and describe the reacting system were estimated from the evidences deriving from the characterization and the experiments conducted, allowing assumptions based on physical principles. Such procedure rendered the particle-grain model a valid choice for the interpretation of the results obtained. The model, used in its dimensionless form, was tested according to a preliminary procedure aimed at analyzing the sensitivity of the system, by varying within wide ranges the ratio between the reaction rate, the diffusive mass transfer rate, and the particle-grain radius, to show how reliable its potential application may be. Subsequently, a non-linear regression procedure was used to estimate the two main parameters of the model that affect the reduction process: (i) the diffusion coefficient within the solid layer produced along with the reaction, D^p_c (6.02 E-13 m² s^-1), and (ii) the kinetic constant of the surface reaction, k_c (0.21 m s^-1). The values found for the parameters were perfectly in line with theoretical considerations and experimental evidences.

Strand displacement amplification-coupled dynamic light scattering method to detect urinary telomerase for non-invasive detection of bladder cancer

Despite huge successes achieved by strand displacement amplification (SDA) and gold nanoparticles (AuNPs) in biomolecules sensing, the strategy of combination of SDA and AuNPs-based dynamic light scattering (DLS) for a biomolecule sensing is unexplored. Here we developed a non-invasive, SDA-based DLS method for the diagnosis of bladder cancer by detecting telomerase activity in human urine. In the presence of telomerase, the telomerase substrate (TS) primer was elongated with repeating sequences of (TTAGGG)n, and the resulting product triggers SDA between the hairpin deoxyribonucleic acid (DNA) and the Primer. The SDA product can be recognized by the oligonucleotide-modified AuNPs probes, resulting in DLS measurable AuNPs aggregation. The assay displayed a detection limit of 3 MCF-7 cells with a signal-to-noise ratio of 3 in a dynamic range of 5-1000 cells. The method was simple, reliable and has been successfully applied in the detection of telomerase in urine with good accuracy, selectivity and reproducibility. Moreover, only urine samples from bladder cancer patients induced a significant change in the average hydrodynamic diameter, indicating practical applicability of the method for the non-invasive diagnosis of bladder cancer.

Nano-Cellulose/MOF Derived Carbon Doped CuO/Fe₃O₄ Nanocomposite as High Efficient Catalyst for Organic Pollutant Remedy

Metal–organic framework (MOF)-based derivatives are attracting increased interest in various research fields. In this study, nano-cellulose MOF-derived carbon-doped CuO/Fe₃O₄ nanocomposites were successfully synthesized via direct calcination of magnetic Cu-BTC MOF (HKUST-1)/Fe₃O₄/cellulose microfibril (CMF) composites in air. The morphology, structure, and porous properties of carbon-doped CuO/Fe₃O₄ nanocomposites were characterized using SEM, TEM, powder X-ray diffraction (PXRD), X-ray photoelectron spectroscopy (XPS), and vibrating sample magnetometry (VSM). The results show that the as-prepared nanocomposite catalyst is composed of Fe₃O₄, CuO, and carbon. Compared to the CuO/Fe₃O₄ catalyst from HKUST-1/Fe₃O₄ composite and CuO from HKUST-1, this carbon-doped CuO/Fe₃O₄ nanocomposite catalyst shows better catalytic efficiency in reduction reactions of 4-nitrophenol (4-NP), methylene blue (MB), and methyl orange (MO) in the presence of NaBH₄. The enhanced catalytic performance of carbon-doped CuO/Fe₃O₄ is attributed to effects of carbon preventing the aggregation of CuO/Fe₃O₄ and providing high surface-to-volume ratio and chemical stability. Moreover, this nanocomposite catalyst is readily recoverable using an external magnet due to its superparamagnetic behavior. The recyclability/reuse of carbon-doped CuO/Fe₃O₄ was also investigated.

Colorimetric human papillomavirus DNA assay based on the retardation of avidin-induced aggregation of gold nanoparticles

A colorimetric assay for human papillomavirus (HPV) DNA was developed based on the retardation of the avidin-induced aggregation of gold nanoparticles (AuNPs) by HPV DNA. Positively charged avidin acts as a coagulant for AuNP aggregation. In the presence of the target DNA, however, the aggregation of AuNPs is retarded owing to electrosteric stabilization as a result of the hybridization of the target and probe DNA. In the absence of HPV DNA, the stabilization effect caused by the biotinylated probe DNA is weak, resulting in NP aggregation and a color change from red to purple. Aggregation may be easily observed with bare eyes or spectrophotometrically at about 560 nm. The visual detection limit is 1 nM. The assay was used for the determination of HPV DNA after polymerase chain reaction (PCR) amplification without any further purification. Graphical abstract Schematic presentation of the avidin-induced aggregation of unmodified gold nanoparticles (AuNPs) which leads to a color change from red to purple. In the presence of dsDNA, however, the aggregation is remarkably retarded.

Understanding and improving aggregated gold nanoparticle/dsDNA interactions by molecular spectroscopy and deconvolution methods

It is well known that single-stranded DNA (ssDNA) is easily able to adsorb on citrate-capped, non-functionalized gold nanoparticles (AuNPs). However, the affinity of double-stranded DNA (dsDNA) for them is much more limited. The present work demonstrates that long dsDNA suffers from a bending conformational change when anionic nanoparticles are present in solution. A striking decrease in the persistence length of the double helix in the absence of salt is observed through dynamic light scattering (DLS), viscometric, and atomic force microscopy (AFM) methods. Long dsDNA is therefore shown to be able to interact with anionic gold nanoparticles. To date, only ssDNA detection has been described by making use of interparticle cross-linking aggregation mechanisms; however, the data shown in this work allow for the development of new methods for detecting dsDNA in solution by using aggregated AuNPs as a starting point. The aggregation state is induced by the controlled addition of an inert electrolyte. A deconvolution procedure of the experimental plasmon shows how individual bands corresponding to aggregated nanoclusters diminish as the DNA concentration increases in the presence of 0.075 M NaCl.

Fluorescent and colorimetric dual-mode aptasensor for thrombin detection based on target-induced conjunction of split aptamer fragments

Since the lack of detection diversity of the single-signal readout strategy, it is urgent to develop fast and multisignal assay strategies. A highly selective and sensitive assay method with colorimetric and fluorometric dual signals readouts is presented in this paper. It is based on the principle that the target induced conjunction of split aptamer fragments assembled on the surface of Au nanoparticles (AuNPs). In the presence of targets, the color of solution changed from wine red to blue and can be measured both visual inspection and spectrophotometry because of the aggregation of AuNPs. At the same time, the report probes which are original hybrid with the anchoring aptamer fragments on the AuNPs surface can be released and recovers the fluorescence. By use of this detection strategy, the limit of detection for thrombin (TMB), as a model of analyte, were 0.45 and 0.16nM, respectively. Furthermore, this protocol can discriminate TMB from other analogue with high selectivity and can be used to detect TMB in human serum samples. The results came from the two signals were well consistent with each other, which demonstrated that it has application potential for detection of TMB in complex matrix.

Development of a new method based on unmodified gold nanoparticles and peptide nucleic acids for detecting bovine viral diarrhea virus-RNA

A simple colorimetric assay is presented for detecting bovine viral diarrhea virus (BVDV)-RNA based on aggregation of gold nanoparticles (AuNPs) in the presence of charge-neutral peptide nucleic acids (PNA). Free charge-neutral PNA oligomers tended to be adsorbed onto AuNPs and act as a coagulant, whereas hybridizing complementary RNA with PNA disrupted PNA-induced AuNP aggregation, and the NPs remained stable. However, non-complementary RNA did not have this effect, and PNA induced aggregation of the AuNPs that resulted in a color change of the reaction from red to blue. The label-free colorimetric assay developed was estimated to have a 10.48 ng/reaction BVDV-RNA detection limit for the visual assay and 1.05 ng/reaction BVDV-RNA using a spectrophotometer. Diagnostic sensitivity and specificity for the assay was in accordance with real-time reverse transcriptase–polymerase chain reaction (RT-PCR) and nested RT-PCR results were 98 and 100%, respectively. Absorption of the 520/620 nm ratio was linear, along with an increase in the target RNA concentration of 1.64–52.4 ng/reaction (R² = 0.992), which showed a linear correlation for the quantitative assay. This study established a rapid visual label and enzyme-free diagnostic assay for detecting BVDV that is applicable in any clinical laboratory.

Nanoparticles assemblies on demand: Controlled aggregation of Ag(0) mediated by modified peptoid sequences

Assemblies of metal nanoparticles (NPs) have been broadly used for the construction of materials with distinct spectroscopic properties towards sensing applications. On the other hand, well-dispersed NPs are exploit for applications in catalysis and medicine. Biopolymers or biomimetic oligomers can serve both as efficient stabilizers of NPs and as useful aggregation mediators that can lead to assemblies with unique properties. Controlling aggregation processes, however, is still challenging and often relies on trial and error rather than on defined thumb rules. Herein we develop specific guidelines for the controlled aggregation of Ag(0) NPs at room temperature in water near neutral pH and without any additives. We use short peptide mimics, N-substituted glycine oligomers called peptoids, as mediators, and investigate the influence of sequences variations on the NPs assembly. Spectroscopic and electron microscopy data reveal that both the length of the peptoids and their sequences have an effect on the NPs aggregation. Thus, we demonstrate that we can control both the degree of aggregation and the aggregates sizes by tuning these properties. Specifically we show that longer peptoid sequences as well as sequences consisting of aromatic side chains are required for the formation of uniform NPs assemblies in an average size of 70nm, while a short hydrophilic sequence can stabilize well-dispersed Ag(0) NPs. Moreover, the catalytic activity of Ag(0) NPs towards the reduction of 4-nitrophenol to 4-aminophenol can be also controlled by varying the properties of the peptoid mediators.

Multiplex Paper-Based Colorimetric DNA Sensor Using Pyrrolidinyl Peptide Nucleic Acid-Induced AgNPs Aggregation for Detecting MERS-CoV, MTB, and HPV Oligonucleotides

The development of simple fluorescent and colorimetric assays that enable point-of-care DNA and RNA detection has been a topic of significant research because of the utility of such assays in resource limited settings. The most common motifs utilize hybridization to a complementary detection strand coupled with a sensitive reporter molecule. Here, a paper-based colorimetric assay for DNA detection based on pyrrolidinyl peptide nucleic acid (acpcPNA)-induced nanoparticle aggregation is reported as an alternative to traditional colorimetric approaches. PNA probes are an attractive alternative to DNA and RNA probes because they are chemically and biologically stable, easily synthesized, and hybridize efficiently with the complementary DNA strands. The acpcPNA probe contains a single positive charge from the lysine at C-terminus and causes aggregation of citrate anion-stabilized silver nanoparticles (AgNPs) in the absence of complementary DNA. In the presence of target DNA, formation of the anionic DNA-acpcPNA duplex results in dispersion of the AgNPs as a result of electrostatic repulsion, giving rise to a detectable color change. Factors affecting the sensitivity and selectivity of this assay were investigated, including ionic strength, AgNP concentration, PNA concentration, and DNA strand mismatches. The method was used for screening of synthetic Middle East respiratory syndrome coronavirus (MERS-CoV), Mycobacterium tuberculosis (MTB), and human papillomavirus (HPV) DNA based on a colorimetric paper-based analytical device developed using the aforementioned principle. The oligonucleotide targets were detected by measuring the color change of AgNPs, giving detection limits of 1.53 (MERS-CoV), 1.27 (MTB), and 1.03 nM (HPV). The acpcPNA probe exhibited high selectivity for the complementary oligonucleotides over single-base-mismatch, two-base-mismatch, and noncomplementary DNA targets. The proposed paper-based colorimetric DNA sensor has potential to be an alternative approach for simple, rapid, sensitive, and selective DNA detection.

Rapid label-free visual detection of KRAS mutations using peptide nucleic acid and unmodified gold nanoparticles

Colorectal cancer (CRC) is among the most commonly diagnosed cancers worldwide.

Collapse of chain anadiplosis-structured DNA nanowires for highly sensitive colorimetric assay of nucleic acids

In this work, we have proposed a chain anadiplosis-structured DNA nanowire by using two well-defined assembly strands (AS1 and AS2).

Rapid Naked-Eye Discrimination of Cytochrome P450 Genetic Polymorphism through Non-Crosslinking Aggregation of DNA-Functionalized Gold Nanoparticles

Involvement of single-nucleotide polymorphism (SNP) genotyping in healthcare should allow for more effective use of pharmacogenomics. However, user-friendly assays without the requirement of a special instrument still remain unavailable. This study describes naked-eye SNP discrimination in exon 5 of the human cytochrome P450 2C19 monooxygenase gene, CYP2C19*1 (the wild-type allele) and CYP2C19*2 (the variant allele with G681A point mutation). The present assay is composed of allele-specific single-base primer extension and salt-induced aggregation of DNA-modified gold nanoparticles (DNA-AuNPs). Genetic samples extracted from human hair roots are subjected to this assay. The results are verified by direct sequencing. This study should promise the prospective use of DNA-AuNPs in gene diagnosis.

Mechanism of adsorption of single and double stranded DNA on gold and silver nanoparticles: Investigating some important parameters in bio-sensing applications

The mechanism of adsorption of single and double stranded DNAs on colloidal gold and silver nanoparticles has been studied by measuring the resistance of the nanoparticles, surrounded by various oligonucleotides, against salt induced aggregation. It is shown that both single and double stranded DNAs can be adsorbed on the metal nanoparticles and the adsorption strength is determined by the interaction between various bases of DNA and the nanoparticles. By changing the salt concentration, the difference between adsorption of various DNA strands on the nanoparticles can be specified. The results indicate that a key parameter in success of a sensing assay of DNA hybridization is the salt concentration which should be greater than a minimum threshold depending on the nanoparticles characteristics. We have also investigated the interaction mechanism between various DNA bases with the metal nanoparticles. For both gold and silver nanoparticles, adenine has the highest and thymine has the lowest attachment to the nanoparticles. From surface enhanced Raman spectroscopy (SERS) data of various bases in the presence of gold nanoparticles, the probable interaction points in the bases with the nanoparticles have been determined, which are mainly the nitrogen sites of these oligonucleotides.

Colorimetric plasmon sensors with multilayered metallic nanoparticle sheets

Colorimetric plasmon sensors for naked-eye detection of molecular recognition events have been proposed. Here, 3-layered Ag nanoparticle (NP) sheets on a Au substrate fabricated using the Langmuir-Schaefer method were utilized as the detection substrates. A drastic color change was observed following the binding of Au NPs via avidin-biotin interactions at less than 30% surface coverage. The color change was attributed not only to the localized surface plasmon resonance (LSPR) of the adsorbed Au NPs but also to the multiple light trapping effect derived from the stratified Au and Ag NPs, as predicted by a finite-difference time-domain (FDTD) simulation. This plasmonic multi-color has great potential in the development of simple and highly sensitive diagnostic systems.

Enhanced heat diffusion in nanofluid via DNA mediated aggregation

Thermal diffusivity increases with different shapes, concentration of gold nanoparticles and also with the addition of ssDNA while the addition of dsDNA found to be ineffective in causing any kind of change in the thermal diffusivity.