HU is a most abundant DNA-binding protein in bacteria. This protein is conserved either in its heterodimeric form or in one of its homodimeric forms in all bacteria, in plant chloroplasts, and in some viruses. HU protein non-specifically binds and bends DNA as a hetero- or homodimer and can participate in DNA supercoiling and DNA condensation. It also takes part in some DNA functions such as replication, recombination, and repair. HU does not recognize any specific sequences but shows some specificity to cruciform DNA and to repair intermediates, e.g., nick, gap, bulge, 3'-overhang, etc. To understand the features of HU binding to DNA and repair intermediates, a fast and easy HU proteins purification procedure is required. Here we report overproduction and purification of the HU homodimers. The method of HU purification allows obtaining a pure recombinant non-tagged protein cloned in Escherichia coli. We applied this method for purification of Acholeplasma laidlawii HU and demonstrated that this protein possesses a DNA-binding activity and is free of contaminating nuclease activity. Besides that we have shown that expression of A. laidlawii ihf_hu gene in a slow-growing hupAB E. coli strain restores the wild-type growth indicating that aclHU can perform the basic functions of E. coli HU in vivo.
Surface plasmonic sensors have received considerable attention, found extensive applications, and outperformed conventional optical sensors. In this work, biopolymer chitosan (CS) was used to prepare the bilayer structure (CS/Au) of a plasmonic refractive index sensor for dopamine (DA) detection. The sensing characteristics of the developed plasmonic sensor were evaluated. Increasing DA concentrations significantly shifted the SPR dips. The sensor exhibited stability and a refractive index sensitivity of 8.850°/RIU in the linear range 0.1 nM to 1 µM with a detection limit of 0.007 nM and affinity constant of 1.383 × 108 M-1. The refractive index and thickness of the CS/Au structure were measured simultaneously by fitting the obtained experimental findings to theoretical data based on Fresnel equations. The fitting yielded the refractive index values n (1.5350 ± 0.0001) and k (0.0150 ± 0.0001) for the CS layer contacting 0.1 nM of DA, and the thickness, d was (15.00 ± 0.01) nm. Then, both n and d values increased by increasing DA concentrations. In addition, the changes in the FTIR spectrum and the variations in sensor surface roughness and structure obtained by AFM analysis confirmed DA adsorption on the sensing layer. Based on these observations, CS/Au bilayer has enhanced the performance of this plasmonic sensor, which showed promising importance as a simple, low-cost, and reliable platform for DA sensing.
Extracellular vesicles (EVs)-nanoscale phospholipid vesicles secreted by cells-present new opportunities for molecular diagnosis from non-invasive liquid biopsies. Single EV protein analysis can be extremely valuable in studying EVs as circulating cancer biomarkers, but it is technically challenging due to weak detection signals associated with limited amounts of epitopes and small surface areas for antibody labeling. Here, a new, simple method that enables multiplexed analyses of EV markers with improved sensitivities is reported. Specifically, plasmon-enhanced fluorescence detection is implemented that amplifies fluorescence signals using surface plasmon resonances excited by periodic gold nanohole structures. It is shown that fluorescence signals in multiple channels are amplified by one order of magnitude, and both transmembrane and intravesicular markers can be detected at the single EV level. This approach can offer additional insight into understanding subtypes, heterogeneity, and production dynamics of EVs during disease development and progression.
In this study, optical and thermal properties of normal grade and winter grade palm oil biodiesel were investigated. Surface Plasmon Resonance and Photopyroelectric technique were used to evaluate the samples. The dispersion curve and thermal diffusivity were obtained. Consequently, the variation of refractive index, as a function of wavelength in normal grade biodiesel is faster than winter grade palm oil biodiesel, and the thermal diffusivity of winter grade biodiesel is higher than the thermal diffusivity of normal grade biodiesel. This is attributed to the higher palmitic acid C(16:0) content in normal grade than in winter grade palm oil biodiesel.
We propose a surface plasmon resonance (SPR) sensor based on photonic crystal fiber (PCF) with selectively filled analyte channels. Silver is used as the plasmonic material to accurately detect the analytes and is coated with a thin graphene layer to prevent oxidation. The liquid-filled cores are placed near to the metallic channel for easy excitation of free electrons to produce surface plasmon waves (SPWs). Surface plasmons along the metal surface are excited with a leaky Gaussian-like core guided mode. Numerical investigations of the fiber's properties and sensing performance are performed using the finite element method (FEM). The proposed sensor shows maximum amplitude sensitivity of 418 Refractive Index Units (RIU-1) with resolution as high as 2.4 × 10(-5) RIU. Using the wavelength interrogation method, a maximum refractive index (RI) sensitivity of 3000 nm/RIU in the sensing range of 1.46-1.49 is achieved. The proposed sensor is suitable for detecting various high RI chemicals, biochemical and organic chemical analytes. Additionally, the effects of fiber structural parameters on the properties of plasmonic excitation are investigated and optimized for sensing performance as well as reducing the sensor's footprint.
Over the past decade, science has experienced a growing rise in nanotechnology with ground-breaking contributions. Through various laborious technologies, nanomaterials with different architectures from 0 D to 3 D have been synthesized. However, the 3 D flower-like organic-inorganic hybrid nanomaterial with the most direct one-pot green synthesis method has attracted widespread attention and instantly become research hotspot since its first allusion in 2012. Mild synthesis procedure, high surface-to-volume ratio, enhanced enzymatic activity and stability are the main factor for its rapid development. However, its lower mechanical strength, difficulties in recovery from the reaction system, lower loading capacity, poor reusability and accessibility of enzymes are fatal, which hinders its wide application in industry. This review first discusses the selection of non-enzymatic biomolecules for the synthesis of hybrid nanoflowers followed by the innovative advancements made in organic-inorganic hybrid nanoflowers to overcome aforementioned issues and to enhance their extensive downstream applications in transduction technologies. Besides, the role of hybrid nanoflower has been successfully utilized in many fields including, water remediation, biocatalyst, pollutant adsorption and decolourization, nanoreactor, biosensing, cellular uptake and others, accompanied with several quantification technologies, such as ELISA, electrochemical, surface plasmon resonance (SPR), colorimetric, and fluorescence were comprehensively reviewed.
Evaluation of binding between analytes and its relevant ligands on surface plasmon resonance (SPR) biosensor is of considerable importance for accurate determination and screening of an interference in immunosensors. Dengue virus serotype 2 was used as a case study in this investigation. This research work compares and interprets the results obtained from analytical analysis with the experimental ones. Both the theoretical calculations and experimental results are verified with one sample from each category of dengue serotypes 2 (low, mid, and high positive), which have been examined in the database of established laboratorial diagnosis. In order to perform this investigation, the SPR angle variations are calculated, analyzed, and then validated via experimental SPR angle variations. Accordingly, the error ratios of 5.35, 6.54, and 3.72% were obtained for the low-, mid-, and high-positive-specific immune globulins of patient serums, respectively. In addition, the magnetic fields of the biosensor are numerically simulated to show the effect of different binding mediums.
We used 40 ± 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 °C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 µg ml(-1) swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.
Cardiovascular disease (CVD) has become one of the leading causes of morbidity and mortality in both men and women. According to the World Health Organization (WHO), ischemic heart disease is the major issue due to the narrowing of the coronary artery by plaque formation on the artery wall, which causes an inadequate flow of oxygen and blood to the heart and is called 'coronary artery disease'. The CVD death rate increased by up to 15% in 2016 (~17.6 million) compared to the past decade. This tremendous increment urges the development of a suitable biomarker for rapid and early diagnosis. Currently, C-reactive protein (CRP) is considered an outstanding biomarker for quick and accurate outcomes in clinical analyses. Various techniques have also been used to diagnose CVD, including surface plasmon resonance (SPR), colorimetric assay, enzyme-linked immunosorbent assay (ELISA), fluoro-immunoassays, chemiluminescent assays, and electrical measurements. This review discusses such diagnostic strategies and how current, cutting-edge technologies have enabled the development of high-performance detection methodologies. Concluding remarks have been made concerning the clinical significance and the use of nanomaterial in medical diagnostics towards nanotheranostics.
High sensitivity and capturing ratio are strongly demanded for surface plasmon resonance (SPR) sensors when applied in detection of small molecules. Herein, an SPR sensor is combined with a novel smart material, namely, MoS2 nanoflowers (MNFs), to demonstrate programmable adsorption/desorption of small bipolar molecules, i.e., amino acids. The MNFs overcoated on the plasmonic gold layer increase the sensitivity by 25% compared to an unmodified SPR sensor, because of the electric field enhancement at the gold surface. Furthermore, as the MNFs have rich edge sites and negatively charged surfaces, the MNF-SPR sensors exhibit not only much higher bipolar-molecule adsorption capability, but also efficient desorption of these molecules. It is demonstrated that the MNF-SPR sensors enable controllable detection of amino acids by adjusting solution pH according to their isoelectric points. In addition, the MNFs decorated on the plasmonic interface can be as nanostructure frameworks and modified with antibody, which allows for specific detection of proteins. This novel SPR sensor provides a new simple strategy for pre-screening of amino acid disorders in blood plasma and a universal high-sensitive platform for immunoassay.
A gold nanoparticle (AuNP) has a localized surface plasmon resonance peak depending on its size, which is often utilized for surface-enhanced Raman scattering (SERS). To obtain information on the cholesterol (Chol)-incorporated lipid membranes by SERS, AuNPs (5, 100 nm) were first functionalized by 1-octanethiol and then modified by lipids (AuNP@lipid). In membrane surface-enhanced Raman spectroscopy (MSERS), both signals from 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and Chol molecules were enhanced, depending on preparation conditions (size of AuNPs and lipid/AuNP ratio). The enhancement factors (EFs) were calculated to estimate the efficiency of AuNPs on Raman enhancement. The size of AuNP100nm@lipid was 152.0 ± 12.8 nm, which showed an surface enhancement Raman spectrum with an EF2850 value of 111 ± 9. The size of AuNP5nm@lipid prepared with a lipid/AuNP ratio of 1.38 × 104 (lipid molecule/particle) was 275.3 ± 20.2 nm, which showed the highest enhancement with an EF2850 value of 131 ± 21. On the basis of fluorescent probe analyses, the membrane fluidity and polarity of AuNP@lipid were almost similar to DOPC/Chol liposome, indicating an intact membrane of DOPC/Chol after modification with AuNPs. Finally, the membrane properties of AuNP@lipid systems were also discussed on the basis of the obtained MSERS signals.
In this work, natural sunlight successfully induced the deposition of gold (Au), silver (Ag), and palladium (Pd) nanoparticles (NPs) with 17.10, 9.07, and 12.70 wt% onto the surface of graphitic carbon nitride (g-C3N4). The photocatalytic evaluation was carried out by adopting Bisphenol A (BPA) as a pollutant under natural sunlight irradiation. The presence of noble metals was confirmed by EDX, HRTEM, and XPS analysis. The deposition of Ag NPs (7.9 nm) resulted in the degradation rate which was 2.15-fold higher than pure g-C3N4 due to its relatively small particle size, contributing to superior charge separation efficiency. Au/g-C3N4 unveiled inferior photoactivity because the LSPR phenomenon provided two pathways for electron transfer between Au NPs and g-C3N4 further diminished the performance. The improved degradation lies crucially on the particle size and Schottky barrier formation at the interface of M/g-C3N4 (M=Au, Ag, and Pd) but not the visible light harvesting properties. The mechanism insight revealed the holes (h+) and superoxide radical (•O2-) radical actively involved in photocatalytic reaction for all composites.
The leaves of the Mitragynine speciosia tree (also known as Kratom) have long been chewed, smoked, or brewed into a tea by people in Southeastern Asian countries, such as Malaysia and Thailand. Just this past year, the plant Kratom gained popularity in the United States as a "legal opioid" and scheduling it as a drug of abuse is currently pending. The primary alkaloid found in Kratom is a μ-opioid receptor agonist, mitragynine, whose structure contains a promising scaffold for immunopharmacological use. Although Kratom is regarded as a safe opioid alternative, here we report the LD50 values determined for its two main psychoactive alkaloids, mitragynine and 7-hydroxymitragynine, as comparable to heroin in mice when administered intravenously. Given Kratom's recent emergence in the U.S., there is currently no diagnostic test available for law enforcement or health professionals, so we sought to design such an assay. Mitragynine was used as a starting point for hapten design, resulting in a hapten with an ether linker extending from the C9 position of the alkaloid. Bacterial flagellin (FliC) was chosen as a carrier protein for active immunization in mice, yielding 32 potential monoclonal antibodies (mAbs) for assay development. Antimitragynine mAbs in the range of micro- to nanomolar affinities were uncovered and their utility in producing a convenient lateral flow detection assay of human fluid samples was examined. Antibodies were screened for binding to mitragynine, 7-hydroxymitragynine, and performance in lateral flow assays. Two monoclonal antibodies were subcloned and further purified with 93 and 362 nM affinity to mitragynine. Test strip assays were optimized with a detection cut off of 0.5 μg/mL for mitragynine in buffer and urine (reflecting projected clinically relevant levels of drug in urine), which could be beneficial to law enforcement agencies and health professionals as the opioid epidemic in America continues to evolve.
Paratyphoid fever is caused by the bacterium Salmonellaenterica serovar Paratyphi (A, B and C), and contributes significantly to global disease burden. One of the major challenges in the diagnosis of paratyphoid fever is the lack of a proper gold standard. Given the absence of a licensed vaccine against S. Paratyphi, this diagnostic gap leads to inappropriate antibiotics use, thus, enhancing antimicrobial resistance. In addition, the symptoms of paratyphoid overlap with other infections, including the closely related typhoid fever. Since the development and utilization of a standard, sensitive, and accurate diagnostic method is essential in controlling any disease, this review discusses a new promising approach to aid the diagnosis of paratyphoid fever. This advocated approach is based on the use of surface plasmon resonance (SPR) biosensor and DNA probes to detect specific nucleic acid sequences of S. Paratyphi. We believe that this SPR-based genoassay can be a potent alternative to the current conventional diagnostic methods, and could become a rapid diagnostic tool for paratyphoid fever.
Surface plasmon resonance (SPR) is a label-free optical spectroscopy that is widely used for biomolecular interaction analysis. In this work, SPR was used to characterize the binding properties of highly sensitive nanocrystalline cellulose-graphene oxide based nanocomposite (CTA-NCC/GO) towards nickel ion. The formation of CTA-NCC/GO nanocomposite has been confirmed by FT-IR. The SPR analysis result shows that the CTA-NCC/GO has high binding affinity towards Ni2+ from 0.01 until 0.1 ppm with binding affinity constant of 1.620 × 103 M-1. The sensitivity for the CTA-NCC/GO calculated was 1.509° ppm-1. The full width at half maximum (FWHM), data accuracy (DA), and signal-to-noise ratio (SNR) have also been determined using the obtained SPR curve. For the FWHM, the value was 2.25° at 0.01 until 0.08 ppm and decreases to 2.12° at 0.1 until 10 ppm. The DA for the SPR curves is the highest at 0.01 until 0.08 ppm and lowest at 0.1 until 10 ppm. The SNR curves mirrors the curves of SPR angle shift where the SNR increases with the Ni2+ concentrations. For the selectivity test, the CTA-NCC/GO has the abilities to differentiate Ni2+ in the mixture of metal ions.
Reporting biomolecular interactions has become part and parcel of many applications of science towards an in-depth understanding of disease and gene regulation. Apart from that, in diagnostic applications where biomolecules (antibodies and aptamers) are vastly applied, meticulous monitoring of biomolecular interaction is vital for clear-cut diagnosis. Several currently available methods of analyzing the interaction of the ligands with the appropriate analytes are aided by labeling using fluorescence or luminescence techniques. However, labeling is cumbersome and can occupy important binding sites of interactive molecules to be labeled, which may interfere with the conformational changes of the molecules and increase non-specificity. Optical-based sensing can provide an alternative way as a label-free procedure for monitoring biomolecular interactions. Optical sensors affiliated with different operating principles, including surface plasmon changes, scattering and interferometry, can impart a huge impact for in-house and point-of-care applications. This optical-based biosensing permits real-time monitoring, obviating the use of hazardous labeling molecules such as radioactive tags. Herein, label-free ways of reporting biomolecular interactions by various optical biosensors were gleaned.
Surface plasmon resonance (SPR) sensing is recently emerging as a valuable technique for measuring the binding constants, association and dissociation rate constants, and stoichimetry for a binding interaction kinetics in a number of emerging biological areas. This technique can be applied to the study of immune system diseases in order to contribute to improved understanding and evaluation of binding parameters for a variety of interactions between antigens and antibodies biochemically and clinically. Since the binding constants determination of an anti-protein dengue antibody (Ab) to a protein dengue antigen (Ag) is mostly complicated, the SPR technique aids a determination of binding parameters directly for a variety of particular dengue Ag_Ab interactions in the real-time. The study highlights the doctrine of real-time dengue Ag_Ab interaction kinetics as well as to determine the binding parameters that is performed with SPR technique. In addition, this article presents a precise prediction as a reference curve for determination of dengue sample concentration.
In this study, the authors investigated the effects of a single layer graphene as a coating layer on top of metal thin films such as silver, gold, aluminum and copper using finite-difference time domain method. To enhance the resolution of surface plasmon resonance (SPR) sensor, it is necessary to increase the SPR reflectivity and decrease the full-width-half maximum (FWHM) of the SPR curve so that there is minimum uncertainty in the determination of the resonance dip. Numerical data was verified with analytical and experimental data where all the data were in good agreement with resonance angle differing in <10% due to noise present in components such as humidity and temperature. In further analysis, reflectivity and FWHM were compared among four types of metal with various thin film thicknesses where graphene was applied on top of the metal layers, and data was compared against pure conventional metal thin films. A 60 nm-thick Au thin film results in higher performance with reflectivity of 92.4% and FWHM of 0.88° whereas single layer graphene-on-60 nm-thick Au gave reflectivity of 91.7% and FWHM of 1.32°. However, a graphene-on-40 nm-thick Ag also gave good performance with narrower FWHM of 0.88° and reflection spectra of 89.2%.
In this paper, we report the effects of a side-polished fiber (SPF) coated with titanium (Ti) films in different thicknesses, namely 5 nm, 13 nm, and 36 nm, protected by a thin layer of transition metal dichalcogenides (TMDCs) such as molybdenum disulfide (MoS2) and tungsten disulfide (WS2), which provide ultra-sensitive sensor-based surface plasmon resonance (SPR) covering from the visible to mid-infrared region. The SPF deposited with Ti exhibits strong evanescent field interaction with the MoS2 and WS2, and good optical absorption, hence resulting in high-sensitivity performance. Incremental increases in the thickness of the Ti layer contribute to the enhancement of the intensity of transmission with redshift and broad spectra. The findings show that the optimum thickness of Ti with 36 nm combined with MoS2 causes weak redshifts of the longitudinal localized surface plasmon resonance (LSPR) mode, while the same thickness of Ti with WS2 causes large blueshifts. The redshifts are possibly due to a reduced plasmon-coupling effect with the excitonic region of MoS2. The observed blueshifts of the LSPR peak position are possibly due to surface modification between WS2 and Ti. Changing the relative humidity from 58% to 88% only elicited a response in Ti/MoS2. Thus, MoS2 shows more sensitivity on 36-nm thickness of Ti compared with WS2. Therefore, the proposed fiber-optic sensor with integration of 2D materials is capable of measuring humidity in any environment.
Widefield surface plasmon resonance (WSPR) microscopy provides high resolution imaging of interfacial interactions. We report the application of the WSPR imaging system in the study of the interaction between keratinocytes and liquid crystals (LC). Imaging of fixed keratinocytes cultured on gold coated surface plasmon substrates functionalized with a thin film of liquid crystals was performed in air using a 1.45NA objective based system. Focal adhesion of the cells adhered to glass and LC were further studied using immunofluorescence staining of the vinculin. The imaging system was also simulated with 2×2 scattering matrix to investigate the optical reflection of the resonant plasmonic wave via the glass/gold/cell and glass/gold/LC/cell layers. WSPR imaging indicated that keratinocytes are less spread and formed distinct topography of cell-liquid crystal couplings when cultured on liquid crystal coated substrates. The simulation indicates that glass/LC shifted the surface plasmon excitation angle to 75.39° as compared to glass/air interface at 44°. The WSPR microcopy reveals that the cells remodelled their topography of adhesion at different interfaces.