Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles.

Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.

Hairpin-Spherical Nucleic Acids for Diagnosing COVID-19: a Simple Method to Generalize the Conventional PCR for Molecular Assays.

The COVID-19 pandemic revealed during the first global wave of this infectious disease that mass diagnostic testing was necessary to more rapidly detect infection in patients and control the pandemic. Therefore, extra research efforts to develop reliable and more accessible techniques for disease diagnosis are of supreme importance. Here, a target-responsive assembly of gold nanoparticle-core hairpin-spherical nucleic acids (AuNP-core H-SNAs) was implemented to modify the conventional polymerase chain reaction (PCR) assay for the "naked-eye" colorimetric detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Two hairpin DNA ligands are designed based on the two highly conserved regions within N and E genes of SARS-CoV-2 RNA by positioning two short palindromic arms (stem) on either side of a recognition sequence (loop). In the presence of a sequence-specific probe (activator), hairpin DNAs anchored to the surface of AuNPs unfold and expose the palindromic ends to the DNA-directed assembly of AuNPs. The sequence of the activator probes was chosen to be identical to the TaqMan probe in a real-time reverse transcription PCR (RT-PCR) assay for specifically targeting the N and E genes of SARS-CoV-2 RNA. They may either be degraded by the 5'-exonuclease activity of DNA polymerase during PCR cycles or stay intact depending on the presence or absence of the target template in the sample, respectively. Post-addition of H-SNA solutions to the final PCR products of some preconfirmed clinical samples for COVID-19 generated naked-eye-observable red and blue colors for positive and negative cases, respectively, with similar sensitivity to that of the real-time RT-PCR method.

Synthesis of biological based hennotannic acid-based salts over porous bismuth coordination polymer with phosphorous acid tags.

In this paper, a novel porous polymer capable of coordinating to bismuth (PCPs-Bi) was synthesized. The Bi-PCPs was then reacted with phosphorous acid to produce a novel polymer PCPs(Bi)N(CH2PO3H2)2 which is shown to act as an efficient and recyclable catalyst. The mentioned catalyst was applied for the efficient synthesis of new mono and bis naphthoquinone-based salts of piperidine and/or piperazine via the reaction of hennotannic acid with various aldehydes, piperidine and/or piperazine, respectively. The structure of the resulting mono and bis substituted piperazine or piperidine-based naphthoquinone salts was thoroughly characterized spectroscopically. The electrochemical behavior of the products was also investigated. The presented protocol has the advantages of excellent yields (82-95%), short reaction times (4-30 min) and simple work-up.

Novel nano-architectured carbon quantum dots (CQDs) with phosphorous acid tags as an efficient catalyst for the synthesis of multisubstituted 4H-pyran with indole moieties under mild conditions.

In this work, a new nano-structured catalyst with phosphorus acid moieties, synthesized by the reaction of carbon quantum dots (CQDs) and phosphorus acid under refluxing EtOH. The structure and morphology of CQDs-N(CH2PO3H2)2 were fully characterized using various techniques such as Fourier transform infrared (FT-IR) spectroscopy, transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, thermogravimetric (TG) analysis, fluorescence and X-ray diffraction (XRD) measurements. The new CQDs-N(CH2PO3H2)2 catalyst was successfully used for the synthesis of 2-amino-6-(2-methyl-1H-indol-3-yl)-4-phenyl-4H-pyran-3,5-dicarbonitriles by the one-pot reaction of various aromatic aldehydes, 3-(1H-indol-3-yl)-3-oxopropanenitrile derivatives and malononitrile in refluxing EtOH and/or ultrasonic irradiation conditions.

Conventional PCR assisted single-component assembly of spherical nucleic acids for simple colorimetric detection of SARS-CoV-2.

Continuous identification of suspected infectious cases is crucial to control the recent pandemic caused by the novel human coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Real-time polymerase chain reaction (real-time PCR) technology cannot be implemented easily and in large scale in some communities due to lack of resources and infrastructures. Here, we report a simple colorimetric strategy derived from linker-based single-component assembly of gold nanoparticle-core spherical nucleic acids (AuNP-core SNAs) for visual detection of PCR products of SARS-CoV-2 ribonucleic acid (RNA) template. A palindromic linker is designed based on SARS-CoV-2 specific E gene to program the identical colloidal SNAs into large assemblies along with a distinct red-to-purple color change. The linker acts as a probe of SARS-CoV-2 RNA in conventional PCR reaction. In the presence of the correct template the palindromic linker, which is complementary to a short region within the target amplicon, is cleaved by 5'-exonuclease activity of deoxyribonucleic acid (DNA) polymerase. Cleavage of the palindromic linker during the amplification process inhibits the single-component assembly formation of SNAs. So, positive and negative viral samples produce simply red and purple colors in the post PCR colorimetric test, respectively. Evaluation of the samples obtained from cases with laboratory-confirmed SARS-CoV-2 infection revealed that our assay can rival with real-time PCR method in sensitivity.

A palindromic-based strategy for colorimetric detection of HIV-1 nucleic acid: Single-component assembly of gold nanoparticle-core spherical nucleic acids.

Gold nanoparticle-core spherical nucleic acids (AuNP core-SNAs), by virtue of the programmable nature of oligonucleotides, have yielded access to the innovative strategies for targeted biodiagnostics. Here, DNA-directed self-assembly of AuNP core-SNAs has been used to design a colorimetric method to sense HIV-1 viral nucleic acid. This strategy utilizes an oligonucleotide with sequence of 5'-untranslated region (5' UTR) of the HIV-1 RNA genome anchored on the surface of AuNPs and a complementary linker strand with a palindromic sequence tail. In the absence of HIV-1 target nucleic acid the complementary linker induces self-assembly of SNAs based on sequence symmetry in the free palindromic tail which can bridge two DNA double helices. While in the presence of the target DNA, due to linker-target duplex formation, the colloidal stability and the red color of the SNAs solution are preserved. Picomole amounts of target DNA can easily be detected with the naked eyes. A 95-mer synthetic DNA strand with the same sequence of HIV-1 viral RNA was utilized for positive control of HIV-1 RNA. The selectivity of the selected linker was satisfactory up to 90% match.

Nanodiamonds and Their Applications in Cells.

Diamonds owe their fame to a unique set of outstanding properties. They combine a high refractive index, hardness, great stability and inertness, and low electrical but high thermal conductivity. Diamond defects have recently attracted a lot of attention. Given this unique list of properties, it is not surprising that diamond nanoparticles are utilized for numerous applications. Due to their hardness, they are routinely used as abrasives. Their small and uniform size qualifies them as attractive carriers for drug delivery. The stable fluorescence of diamond defects allows their use as stable single photon sources or biolabels. The magnetic properties of the defects make them stable spin qubits in quantum information. This property also allows their use as a sensor for temperature, magnetic fields, electric fields, or strain. This Review focuses on applications in cells. Different diamond materials and the special requirements for the respective applications are discussed. Methods to chemically modify the surface of diamonds and the different hurdles one has to overcome when working with cells, such as entering the cells and biocompatibility, are described. Finally, the recent developments and applications in labeling, sensing, drug delivery, theranostics, antibiotics, and tissue engineering are critically discussed.

Nanodiamonds for In Vivo Applications.

Due to their unique optical properties, diamonds are the most valued gemstones. However, beyond the sparkle, diamonds have a number of unique properties. Their extreme hardness gives them outstanding performance as abrasives and cutting tools. Similar to many materials, their nanometer-sized form has yet other unique properties. Nanodiamonds are very inert but still can be functionalized on the surface. Additionally, they can be made in very small sizes and a narrow size distribution. Nanodiamonds can also host very stable fluorescent defects. Since they are protected in the crystal lattice, they never bleach. These defects can also be utilized for nanoscale sensing since they change their optical properties, for example, based on temperature or magnetic fields in their surroundings. In this Review, in vivo applications are focused upon. To this end, how different diamond materials are made and how this affects their properties are discussed first. Next, in vivo biocompatibility studies are reviewed. Finally, the reader is introduced to in vivo applications of diamonds. These include drug delivery, aiding radiology, labeling, and use in cosmetics. The field is critically reviewed and a perspective on future developments is provided.

H-point curve isolation method for determination of catechol in complex unknown mixtures.

In this work, the combination of H-point curve isolation method (HPCIM) and H-point standard additions method (HPSAM) was used for determination of catechol in the presence of phenolic interferents. Spectrophotometric multivariate calibration data constructed by successive standard additions of an analyte in an unknown matrix was used by the method. A cumulative spectrum for interferents in sample was extracted by HPCIM and then HPSAM is used for determination of the catechol concentration by obtained cumulative interferents spectrum. The method was tested with simulated data set. The spectrum obtained from applying HPCIM to the simulated data well agrees with the cumulative spectra of the interferents. The method was applied to the determination of catechol in the presence of highly overlapping interferents in synthetic ternary mixtures using spectrophotometric data. Moreover, the proposed method was successfully used for determination of catechol in real complicated matrices of tea and urine samples. Percent recoveries were between 95.4 and 113.6.

Hard- and soft-modeling approaches for resolution of complex formation of Co2+ and Ni2+ with glycine.

Principal component analysis (PCA) was used to obtain information about the number of components in the complex formation equilibria of Co(2+) and Ni(2+) with glycine (Gly). In order to obtain a clearer insight into these complex formation systems, multivariate curve resolution-alternating least squares (MCR-ALS) was used. Using MCR-ALS as a soft-modeling method, well-defined concentration and spectral profiles were obtained under unimodality, non-negativity, and closure constraints. Based on the obtained results, an equilibrium model was proposed and subsequently, a hard-modeling method was used to resolve the complex formation equilibria completely. Due to the presence of multiple equilibria, the resolution of such systems is very difficult. The Co-Gly system was best described by a model consisting of M(GlyH), M(Gly), M(Gly)(2), M(Gly)(2)H, and M(Gly)(3) (M = Co(2+)) with the overall stability constants determined to be 7.10 ± 0.011, 5.14 ± 0.006, 9.28 ± 0.009, 13.75 ± 0.016, and 11.10 ± 0.010, respectively. On the other hand, the system of Ni-Gly was best fitted by a model containing M(GlyH), M(Gly), M(Gly)(2), M(Gly)(3), and M(Gly)(2)(OH) (M = Ni(2+)) with overall stability constants of 10.95 ± 0.04, 6.41 ± 0.03, 11.31 ± 0.03, 15.39 ± 0.06, and 14.32 ± 0.02, respectively.

Principle component analysis (PCA) and second-order global hard-modelling for the complete resolution of transition metal ions complex formation with 1,10-phenantroline.

Second-order global hard-modelling was applied to resolve the complex formation between Co(2+), Ni(2+), and Cd(2+) cations and 1,10-phenantroline. The highly correlated spectral and concentration profiles of the species in these systems and low concentration of some species in the individual collected data matrices prevent the well-resolution of the profiles. Therefore, a collection of six equilibrium data matrices including series of absorption spectra taken with pH changes at different reactant ratios were analyzed. Firstly, a precise principle component analysis (PCA) of different augmented arrangements of the individual data matrices was used to distinguish the number of species involved in the equilibria. Based on the results of PCA, the equilibria included in the data were specified and second-order global hard-modelling of the appropriate arrangement of six collected equilibrium data matrices resulted in well-resolved profiles and equilibrium constants. The protonation constant of the ligand (1,10-phenantroline) and spectral profiles of its protonated and unprotonated forms are the additional information obtained by global analysis. For comparison, multivariate curve resolution-alternating least squares (MCR-ALS) was applied to the same data. The results showed that second-order global hard-modelling is more convenient compared with MCR-ALS especially for systems with completely known model. It can completely resolve the system and the concentration profiles which are closer to correct ones. Moreover, parameters showing the goodness of fit are better with second-order global hard-modelling.

Application of multivariate curve resolution-alternating least squares (MCR-ALS) for secondary structure resolving of proteins.

Fourier transform infrared (FTIR) spectroscopy is the most common spectroscopic technique used for study of protein structure. Initially, band deconvolution techniques were applied to determine the secondary structure of proteins. Recently, several multivariate regression methods have been used to predict the secondary structure of proteins as an alternative to the previous methods. Multivariate curve resolution-alternating least squares (MCR-ALS) was applied on the FTIR spectra of proteins to resolve the fraction and spectral profiles of different structural motifs. Initial estimates of spectral profiles of different protein motifs were built using orthogonal projection approach (OPA). Predicted fractions of alpha-helix and beta-sheet obtained by MCR-ALS technique were compared with those from partial least squares (PLS) modeling which revealed superiority of the former. If we consider the possibility of pure spectra prediction in addition to the prediction of secondary structure from the data set, MCR-ALS can be proposed as a very valuable alternative for qualitative and quantitative study of protein structures.

Application of soft- and hard-modelling approaches to resolution of kinetics of electron donor-acceptor complex formation of 2,3-dichloro-5,6-dicyano-1,4-benzoquinone with imipramine in different solutions.

Kinetics of electron donor-acceptor (EDA) complex formation of imipramine and 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) was investigated spectrophotometrically in acetonitrile, 1,2-dichloroethane, and chloroform solutions using soft- and hard-modelling approaches. From the results of exploratory analysis of kinetic data and the spectral changes by soft-modelling approaches, evolving factor analysis (EFA) and orthogonal projection approach (OPA), a consecutive two-steps reaction with two intermediates was proposed for the process in acetonitrile and 1,2-dichloroethane media and one with a single intermediate in chloroform solution. Secondly, by applying, multivariate nonlinear least squares hard-modelling approach on the collected experimental kinetic data matrix, the nonlinear parameters (rate constants) as well as the linear parameters (spectral profiles) were obtained by fitting the collected experimental kinetic data matrix to the proposed model. Small values of standard deviation in the resulting parameters and sum of squares of the residuals (ssq) obtained showed the proper selection of the model. Furthermore, the values of lack of fit and percent of explained variance confirmed the correct identified models. Identification of the model with the aid of soft-modelling approaches followed by application of the hard-modelling approaches decreases significantly the rotational ambiguity associated with the obtained concentration and spectral profiles. Variations in the kinetic constants were in complete agreement with the model proposed and the solvent polarities.

Evaluation of feed-forward back propagation and radial basis function neural networks in simultaneous kinetic spectrophotometric determination of nitroaniline isomers.

Mixtures of 2-, 3-, and 4-nitoroanilines, are simultaneously analyzed with spectrophotometry, based on their different kinetic properties. These nitroanilines react differentially with 1,2-naphtoquinone-4-sulphonate (NQS) at pH 7 in micellar medium to produce colored product. The differential kinetic spectra were monitored and recorded at 500 nm, and the data obtained from the experiments were processed by chemometric approaches, such as back-propagation neural networks (BPNNs), radial basis function neural networks (RBFNNs), and partial least squares (PLS). Experimental conditions were optimized and training the network was performed using principal components (PCs) of the original data. A set of synthetic mixtures of nitroanilines was evaluated and the results obtained by the application of these chemometric approaches were discussed and compared. The analytical performance of the models was characterized by relative standard errors. It was found that the artificial neural networks model affords relatively better results than PLS. The proposed method was applied to the determination of considered nitroanilines in water samples.

Application of principal component-artificial neural network models for simultaneous determination of phenolic compounds by a kinetic spectrophotometric method.

A multicomponent analysis method based on principal component analysis-artificial neural network models (PC-ANN) is proposed for the determination of phenolic compounds. The method relies on the oxidative coupling of phenols (phenol, 2 chlorophenol, 3-chlorophenol and 4-chlorophenol) to N,N-diethyl-p-phenylenediamine in the presence of hexacyanoferrate(III). The reaction monitored at analytical wavelength 680 nm of the dye formed. Phenols can be determined individually over the concentration range 0.1-7.0 microg ml(-1). Differences in the kinetic behavior of the four species were exploited by using PC-ANN, to resolve mixtures of phenol. After reducing the number of kinetic data using principal component analysis, an artificial neural network consisting of three layers of nodes was trained by applying a back-propagation learning rule. The optimized ANN allows the simultaneous quantitation of four analytes in mixtures with relative standard errors of prediction in the region of 5% for four species. The results show that PC-ANN is an efficient method for prediction of the four analytes.

Spectrophotometric resolution of ternary mixtures of tryptophan, tyrosine, and histidine with the aid of principal component-artificial neural network models.

A simple and sensitive spectrophotometric method to resolve ternary mixtures of tryptophan (Trp), tyrosine (Tyr), and histidine (His) in synthetic and water samples is described. It relies on the different kinetic rates of the analytes in their oxidative reaction with potassium ferricyanide (K(3)Fe(CN)(6)) in alkaline medium. The absorbance data were monitored on the analytical wavelength (420 nm) of K(3)Fe(CN)(6) spectrum. Synthetic mixtures of the three amino acids were analyzed, and the data obtained were processed by principal component-artificial neural network (PC-ANN) models. After reducing the number of spectral data using principal component analysis, an artificial neural network consisting of three layers of nodes was trained by applying a back-propagation learning rule. Tangent and sigmoidal transfer function were used in the hidden and output layers, respectively. The analytical performance of this method was characterized by relative standard error. The method allowed the determination of Trp, Tyr, and His at concentrations between 10 and 55, 10 and 60, and 10 and 40 microg ml(-1), respectively. The results show that the PC-ANN is an efficient method for prediction of the three analytes.

Kinetic spectrophotometric determination of Fe(II) in the presence of Fe(III) by H-point standard addition method in mixed micellar medium.

The H-point standard addition method was applied to kinetic data for simultaneous determination of Fe(II) and Fe(III) or selective determination of Fe(II) in the presence of Fe(III). The method is based on the difference in the rate of complex formation between iron in two different oxidation states and methylthymol blue (MTB) at pH 3.5 in mixed cetyltrimethylammonium bromide (CTAB) and Triton X-100 micellar medium. Fe(II) can be determined in the range 0.25-2.5 microg ml(-1) with satisfactory accuracy and precision in the presence of excess Fe(III) and other metal ions that rapidly form complexes with MTB under working condition. The proposed method was successfully applied to the simultaneous determination of Fe(II) and Fe(III) or selective determination of Fe(II) in the presence of Fe(III) in spiked real environmental and synthetic samples with complex composition.

A kinetic spectrophotometric method for simultaneous determination of glycine and lysine by artificial neural networks.

A spectrophotometric method for simultaneous analysis of glycine and lysine is proposed by application of neural networks on the spectral kinetic data. The method is based on the reaction of glycine and lysine with 1,2-naphthoquinone-4-sulfonate (NQS) in slightly basic medium. On the basis of the difference in the rate between the two reactions, these two amino acids can be determined simultaneously in binary mixtures. Feed-forward neural networks have been trained to quantify considered amino acids in mixtures under optimum conditions. In this way, a one-layer network was trained. Sigmoidal and linear transfer functions were used in the hidden and output layers, respectively. Linear calibration graphs were obtained in the concentration range of 1 to 25microgml(-1) for glycine and 1 to 19microgml(-1) for lysine. The analytical performance of this method was characterized by the relative standard error. The proposed method was applied to the determination of considered amino acids in synthetic samples.

Spectrophotometric study of interaction of iodine with 4'-aminobenzo-15-crown-5 in chloroform, dichloromethane and 1,2-dichloroethane solutions.

The formation of charge transfer complex between 4'-aminobenzo-15-crown-5 (AB15C5) and iodine is investigated spectrophotometrically in chloroform, dichloromethane (DCM) and 1,2-dichloroethane (DCE) solutions at 25 degrees C. The continuous variation method clearly revealed the formation of 1:1 charge transfer complex in solution. The observed time dependence of the charge transfer band and subsequent formation of I 3- in solution were related to the slow transformation of the initially formed 1:1 AB15C5.I2 outer complex to an inner electron donor-acceptor (EDA) complex, followed by fast reaction of the inner complex with iodine to form a triiodide ion. The pseudo-first-order rate constants for the transformation process were evaluated from the absorbance-time data and found to vary in the order of 1,2-DCE>DCM>CHCl3. The values of the formation constant, KDA, for each complex are evaluated from Benesi-Hilebrand equation. Stability of the resulting complex in three solvents was also found to vary in the order of 1,2-DCE>DCM>CHCl3.

A spectrophotometric and thermodynamic study of the charge-transfer complexes of iodine with 2-aminomethyl-15-crown-5 in chloroform and 1,2-dichloroethane solutions.

Interaction of 2-aminomethyl-15-crown-5 (AM15C5) with iodine has been investigated spectrophotometrically in chloroform and 1,2-dichloroethane (1,2-DCE) solutions. The observed time dependence of the charge-transfer band and subsequent formation of I(3)(-) in solution were related to the slow transformation of the initially formed 1:1 AM15C5.I(2) outer complex to an inner electron donor-acceptor (EDA) complex, followed by fast reaction of the inner complex with iodine to form a triiodide ion. The pseudo-first-order rate constants were evaluated from the absorbance- and conductivity-time data. The stoichiometry and formation constants of the resulting EDA complexes have also been determined. Thermodynamic parameters, Delta H degrees and Delta S degrees , of the complexes have been determined from the temperature dependence of stability constants by Van't Hoff equation. The results indicate that iodine complexes of AM15C5 in both solvents are enthalpy stabilized but entropy destabilized. The influence of solvent properties on the kinetics and stability of the resulting charge-transfer complexes are discussed.