Matrix‐assisted peptide synthesis on nanoparticles

We report a new method for multistep peptide synthesis on polymeric nanoparticles of differing sizes. Polymeric nanoparticles were functionalized via their temporary embedment into a magnetic inorganic matrix that allows multistep peptide synthesis. The matrix is removed at the end of the process for obtaining nanoparticles functionalized with peptides. The matrix‐assisted synthesis on nanoparticles was proved by generating various biologically relevant peptides. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.     

Step‐by‐step monitoring of a magnetic and SERS‐active immunosensor assembly for purification and detection of tau protein

We report a bottom‐up synthesis of iron oxide and gold nanoparticles, which are functionalized and combined to form a nanohybrid serving as an immune sensor, which selectively binds to tau protein, a biomarker for diagnosis of Alzheimer's disease. Detection of the target analyte is achieved by surface‐enhanced Raman scattering originating from the diagnostic part of the nanohybrid that was prepared from Au nanoparticles functionalized with 5,5′‐dithiobis‐(2‐nitrobenzoic acid) as a Raman reporter and monoclonal anti‐tau antibody. The magnetic part consists of Fe_xO_y nanoparticles functionalized with polyclonal anti‐tau antibody and is capable to separate tau protein from a complex matrix such as cerebrospinal fluid. We further identified and validated a set of analytical tools that allow monitoring the success of both nanoparticle preparation and each functionalization step performed during the assembly of the two binding sites by an immune reaction. By applying UV/Vis spectroscopy, dynamic light scattering, zeta potential measurements, X‐ray diffraction, small‐angle X‐ray scattering, and transmission electron microscopy, we demonstrate a proof‐of‐concept for a controlled and step‐by‐step traceable synthesis of a tau protein‐specific immune sensor.     

Synthesis and characterizations of iso‐luminol‐functionalized,tadpole‐shaped,gold nanomaterials

Iso‐luminol functionalized gold nanomaterials were synthesized in high yield by a simple seeding approach, using the chemiluminescent reagent iso‐luminol as reductant in the presence of HAuCl₄, AgNO₃ and cetyltrimethylammonium bromide (CTAB). The morphology of as‐prepared gold nanoparticles was characterized by transmission electron microscopy and UV–vis spectroscopy, showing that gold nanotadpoles (AuNTps) were obtained. Subsequent experiments revealed that the amounts of seed colloids and AgNO₃ and the concentrations of iso‐luminol and CTAB in the growth solution play critical roles in the formation of well‐shaped AuNTps. The surface state of AuNTps was characterized by UV–vis spectroscopy and fluorescence spectroscopy, indicating that iso‐luminol and its oxidation product, 4‐aminophthalate, coexisted on the surface of AuNTps. The CL behaviour was studied by static injection CL experiments, demonstrating that AuNTps were of CL activity. Finally, the growth mechanism of AuNTps was also discussed. Copyright © 2012 John Wiley & Sons, Ltd.     

Functionalization of whole‐cell bacterial reporters with magnetic nanoparticles

We developed a biocompatible and highly efficient approach for functionalization of bacterial cell wall with magnetic nanoparticles (MNPs). Three Acinetobacter baylyi ADP1 chromosomally based bioreporters, which were genetically engineered to express bioluminescence in response to salicylate, toluene/xylene and alkanes, were functionalized with 18 ± 3 nm iron oxide MNPs to acquire magnetic function. The efficiency of MNPs functionalization of Acinetobacter bioreporters was 99.96 ± 0.01%. The MNPs‐functionalized bioreporters (MFBs) can be remotely controlled and collected by an external magnetic field. The MFBs were all viable and functional as good as the native cells in terms of sensitivity, specificity and quantitative response. More importantly, we demonstrated that salicylate sensing MFBs can be applied to sediments and garden soils, and semi‐quantitatively detect salicylate in those samples by discriminably recovering MFBs with a permanent magnet. The magnetically functionalized cells are especially useful to complex environments in which the indigenous cells, particles and impurities may interfere with direct measurement of bioreporter cells and conventional filtration is not applicable to distinguish and harvest bioreporters. The approach described here provides a powerful tool to remotely control and selectively manipulate MNPs‐functionalized cells in water and soils. It would have a potential in the application of environmental microbiology, such as bioremediation enhancement and environment monitoring and assessment.     

Novel materials based on DNA‐CTMA and lanthanide (Ce3+, Pr3+)

New, deoxyribonucleic acid (DNA) based compounds, functionalized with hexadecyltrimethylammonium chloride (CTMA) and lanthanide hydroxide nanoparticles were synthesized. The spectral measurements suggest that between the DNA‐CTMA complex and the lanthanide (III) ions a chemical interaction takes place. The obtained materials exhibit an improved fluorescence efficiency, showing a potential interest for application in photonics, and more particularly, in light emitting devices. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 613–617, 2016.     

Fluorescence modulation of 1,7‐bis(4‐hydroxy‐3‐methoxyphenyl)‐1,6‐heptadiene‐3,5‐dione by silver nanoparticles and its possible analytical application

The effects of silver nanoparticles on the photophysical properties of 1,7‐bis(4‐hydroxy‐3‐methoxyphenyl)‐1,6‐heptadiene‐3,5‐dione, popularly known as curcumin, have been investigated using optical absorption and fluorescence techniques. Although absorption spectroscopy suggests a ground‐state complex formation, fluorescence quenching data confirms a simultaneous static and dynamic quenching, inferring ground as well as excited‐state complex formation. The recovery of fluorescence quenching of the curcumin–silver nanoparticle complex in the presence of ascorbic acid or uric acid emphasizes a strong interaction between the silver nanoparticles and ascorbic acid/uric acid, suggesting that fluorescence recovery after the quenching of curcumin–silver nanoparticle complexes has potential for ascorbic acid or uric acid assay development. Copyright © 2011 John Wiley & Sons, Ltd.     

Thermoluminescence of mercaptoethanol‐capped ZnS:Mn nanoparticles

The thermoluminescence (TL) of nanoparticles has become a matter of keen interest in recent times but is rarely reported. This article reports the synthesis of ZnS:Mn nanocrystals using a chemical route, with mercaptoethanol (ME) as the capping agent. The particle sizes for the nanocrystals were measured by X‐ray diffraction (XRD) and also by studying transmission electron microscopy (TEM) patterns. The particle sizes of the synthesized samples were found to be between 1 and 3 nm. For samples with different concentrations of the capping agent, it was found that the TL intensity of the ZnS:Mn nanoparticles increased as the particle size decreased. A shift in the peak position of the TL glow curve was also seen with decreasing particle size. The TL intensity was found to be maximal for samples with 1.2% of Mn. A change in the peak position was not found for samples with different concentrations of Mn. The half‐width glow peak curve method was used to determine the trap‐depth. The frequency factor of the synthesized samples was also calculated. The stability of the charge carriers in the traps increases with decreasing nanoparticle size. The higher stability may be attributed to the higher surface/volume ratio and also to the increase in the trap‐depth with decreasing particle size. Copyright © 2014 John Wiley & Sons, Ltd.     

Concanavalin A‐immobilized magnetic nanoparticles for selective enrichment of glycoproteins and application to glycoproteomics in hepatocelluar carcinoma cell line

Protein glycosylation is one of the most important PTMs in biological organism. Lectins such as concanavalin A (Con A) have been widely applied to N‐glycosylated protein investigation. In this study, we developed Con A‐immobilized magnetic nanoparticles for selective separation of glycoproteins. At first, a facile immobilization of Con A on aminophenylboronic acid‐functionalized magnetic nanoparticles was performed by forming boronic acid‐sugar‐Con A bond in sandwich structure using methyl α‐D ‐mannopyranoside as an intermedium. The selective capture ability of Con A‐modified magnetic nanoparticles for glycoproteins was tested using standard glycoproteins and cell lysate of human hepatocelluar carcinoma cell line 7703. In total 184 glycosylated sites were detected within 172 different glycopeptides corresponding to 101 glycoproteins. Also, the regeneration of the protein‐immobilized nanoparticles can easily be performed taking advantage of the reversible binding mechanism between boronic acid and sugar chain. The experiment results demonstrated that Con A‐modified magnetic nanoparticles by the facile and low‐cost synthesis provided a convenient and efficient enrichment approach for glycoproteins, and are promising candidates for large‐scale glycoproteomic research in complicated biological samples.     

Luminescent and hydrophilic LaF3–polymer nanocomposite for DNA detection

Luminescent LaF₃–Ce³⁺/Tb³⁺ nanocrystals have been successfully prepared via a simple wet chemical technique. For the next bioapplication, these nanoparticles dispersed in cyclohexane have also been functionalized with poly(St‐co‐MAA), based on a designed oil‐in‐water microemulsion system. These polymer‐coated nanospheres are water‐soluble and bioconjugable. Unlike semiconductor quantum dots, the as‐prepared lanthanum fluoride nanocrystals possess non‐size‐dependent emissions and completely stable photocycles. With functionalized LaF₃ nanospheres as fluorescence probes, a fluorescence method was developed for the rapid quantitative analysis of DNA, due to the quenching effect of fluorescence by the DNA. Under optimum conditions, the fluorescence intensity was proportional to the concentration of the introduced DNA over the range 2.5–35 µg/mL for calf thymus DNA (ctDNA) and 2.5–30 µg/mL for fish sperm DNA (fsDNA), respectively. Copyright © 2008 John Wiley & Sons, Ltd.     

Synthesis and characterization of cysteine functionalized silver nanoparticles for biomolecule immobilization

A facile method for the aqueous phase synthesis of cysteine-functionalized silver nanoparticles by potato extract has been reported in the present work. These functionalized nanoparticles were then used for the covalent immobilization of a biomolecule, alkaline phosphatase, on its surface through carbodiimide coupling. Different reaction parameters such as cysteine concentration, reducing agent concentration, temperature, pH and reaction time were varied during the nanoparticles’ formation, and their effects on plasmon resonance were studied using Ultraviolet–visible spectroscopy. Fourier transform infrared spectroscopy was used to confirm the surface modification of silver nanoparticles by cysteine and the particle size analysis was done using particle size analyzer, which showed the average nanoparticles’ size of 61 nm for bare silver nanoparticles and 201 nm for the enzyme-immobilized nanoparticles. The synthesized nanoparticles were found to be highly efficient for the covalent immobilization of alkaline phosphatase on its surface and retained 67 % of its initial enzyme activity (9.44 U/mg), with 75 % binding efficiency. The shelf life of the enzyme-nanoparticle bioconjugates was found to be 60 days, with a 12 % loss in the initial enzyme activity. With a simple synthesis strategy, high immobilization efficiency and enhanced stability, these enzyme-coated nanoparticles have the potential for further integration into the biosensor technology.     

Helping decision making for reliable and cost‐effective 2b‐RAD sequencing and genotyping analyses in non‐model species

High‐throughput sequencing has revolutionized population and conservation genetics. RAD sequencing methods, such as 2b‐RAD, can be used on species lacking a reference genome. However, transferring protocols across taxa can potentially lead to poor results. We tested two different IIB enzymes (AlfI and CspCI) on two species with different genome sizes (the loggerhead turtle Caretta caretta and the sharpsnout seabream Diplodus puntazzo) to build a set of guidelines to improve 2b‐RAD protocols on non‐model organisms while optimising costs. Good results were obtained even with degraded samples, showing the value of 2b‐RAD in studies with poor DNA quality. However, library quality was found to be a critical parameter on the number of reads and loci obtained for genotyping. Resampling analyses with different number of reads per individual showed a trade‐off between number of loci and number of reads per sample. The resulting accumulation curves can be used as a tool to calculate the number of sequences per individual needed to reach a mean depth ≥20 reads to acquire good genotyping results. Finally, we demonstrated that selective‐base ligation does not affect genomic differentiation between individuals, indicating that this technique can be used in species with large genome sizes to adjust the number of loci to the study scope, to reduce sequencing costs and to maintain suitable sequencing depth for a reliable genotyping without compromising the results. Here, we provide a set of guidelines to improve 2b‐RAD protocols on non‐model organisms with different genome sizes, helping decision‐making for a reliable and cost‐effective genotyping.     

Nanotechnology‐based molecular photoacoustic and photothermal flow cytometry platform for in‐vivo detection and killing of circulating cancer stem cells

In‐vivo multicolor photoacoustic (PA) flow cytometry for ultrasensitive molecular detection of the CD44+ circulating tumor cells (CTCs) is demonstrated on a mouse model of human breast cancer. Targeting of CTCs with stem‐like phenotype, which are naturally shed from parent tumors, was performed with functionalized gold and magnetic nanoparticles. Results in vivo were verified in vitro with a multifunctional microscope, which integrates PA, photothermal (PT), fluorescent and transmission modules. Magnet‐induced clustering of magnetic nanoparticles in individual cells significantly amplified PT and PA signals. The novel noninvasive platform, which integrates multispectral PA detection and PT therapy with a potential for multiplex targeting of many cancer biomarkers using multicolor nanoparticles, may prospectively solve grand challenges in cancer research for diagnosis and purging of undetectable yet tumor‐initiating cells in circulation before they form metastasis. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Mode‐coupling Smoluchowski dynamics of a double‐stranded DNA oligomer

The local dynamics of a double‐stranded DNA d(TpCpGpCpG)₂ is obtained to second order in the mode‐coupling expansion of the Smoluchowski diffusion theory. The time correlation functions of bond variables are derived and the ¹³C‐nmr spin–lattice relaxation times T₁ of different ¹³C along the chains are calculated and compared to experimental data from the literature at three frequencies. The DNA is considered as a fluctuating three‐dimensional structure undergoing rotational diffusion. The fluctuations are evaluated using molecular dynamics simulations, with the ensemble averages approximated by time averages along a trajectory of length 1 ns. Any technique for sampling the configurational space can be used as an alternative. For a fluctuating three‐dimensional (3D) structure using the three first‐order vector modes of lower rates, higher order basis sets of second‐rank tensor are built to give the required mode coupling dynamics. Second‐ and even first‐order theories are found to be in close agreement with the experimental results, especially at high frequency, where the differences in T₁ for ¹³C in the base pairs, sugar, and backbone are well described. These atomistic calculations are of general application for studying, on a molecular basis, the local dynamics of fluctuating 3D structures such as double‐helix DNA fragments, proteins, and protein–DNA complexes. © 1999 John Wiley & Sons, Inc. Biopoly 50: 613–629, 1999     

Reaction mechanism of surfactant‐sensitized chemiluminescence of bis(2,4,6‐trichlorophyenyl) oxalate and hydrogen peroxide induced by gold nanoparticles

The chemiluminescence (CL) of bis(2,4,6‐trichlorophyenyl) oxalate with hydrogen peroxide in the present of cationic surfactant and gold nanoparticles was studied. The CL emission was obviously enhanced in the presence of surfactant at a suitable concentration, with a synergetic catalysis effect exhibited. Different sizes of gold nanoparticles (15 and 50 nm) showed different effects on CL intensity. Mechanisms of the CL reaction and sensitization effect are discussed. Copyright © 2008 John Wiley & Sons, Ltd.     

Steady‐state and time‐resolved fluorescence of tetramethylrhodamine attached to DNA: correlation with DNA sequences

Time‐resolved fluorescence as well as steady‐state absorption and fluorescence were detected in order to study the interactions between tetramethylrhodamine (TAMRA) and DNA when TAMRA was covalently labeled on single‐ and double‐stranded oligonucleotides. Fluorescence intensity quenching and lifetime changes were characterized and correlated with different DNA sequences. The results demonstrated that the photoinduced electron transfer interaction between guanosine residues and TAMRA introduced a short lifetime fluorescence component when guanosine residues were at the TAMRA‐attached terminal of the DNA sequences. The discrepancy of two‐state and three‐state models in previous studies was due to the DNA sequence selection and sensitivity of techniques used to detect the short lifetime component. The results will help the design of fluorescence‐based experiments related to a dye labeled probe. Copyright © 2012 John Wiley & Sons, Ltd.     

Microscopic insight into the DNA condensation process of a zwitterion‐functionalized polycation

Zwitterion‐functionalized polycations are ideal gene carriers with long circulation, high cellular uptaking and low cell viability. However, the trade‐off between the DNA condensation efficiency and the cell viability must be addressed. The purpose of this study is to provide a microscopic insight into the DNA condensation process and to explore the effect of a zwitterionic block of zwitterion‐functionalized polycation, which is of great significance in designing novel gene delivery systems. Poly[2‐(dimethylamino)ethyl methacrylate‐b‐(sulfobetaine methacrylate)] (PDMAEMA‐b‐PSBMA) copolymers were synthesized and used as the model systems. Different from the conventional concept that the PSBMA zwitterionic block act only as the “stealthy” groups, the subtle differences in physical and colloidal characteristics between the polycation/DNA polyplexes show that the PSBMA segment is capable of wrapping DNA attributed to the quaternary ammonium cations, without compromising the DNA condensation capability. On the other hand, the incorporation of PSBMA block reduces the surface charge of the polyplexes, which substantially result in the inefficient transfection and the reduced cytotoxicity.     

Synthesis of New exo‐ and endo‐3,8‐Dihydro‐β‐santalols and Other Norbornyl‐Derived Alcohols

Several new and differently functionalized cis‐2,3‐dimethylnorbornane derivatives presenting diverse side‐chain lengths were prepared, the structures of which are related to the natural fragrance β‐santalol. In particular, exo‐ and endo‐3,8‐dihydro‐β‐santalols, with either (E) or (Z) C?C‐bond configuration on the side chain, were synthesized in seven steps and 21–24% overall yields. Several other exo‐ and endo‐norbornyl alcohols with shorter side chains were also prepared in high yields. The olfactory evaluation indicated woody, sandalwood, as well as fruity notes for some of the derivatives.     

The effect of temperature on antibacterial activity of biosynthesized silver nanoparticles

The purpose of this study was the evaluation of two different temperatures on antibacterial activity of the biosynthesized silver nanoparticles. 38 silver nanoparticles-producing bacteria were isolated from soil and identified. Biosynthesis of silver nanoparticles by these bacteria was verified through visible light spectrophotometry. Two strains were relatively active for production of silver nanoparticles. These strains were subjected for molecular identification and recognized as Bacillus sp. and Acinetobacter schindleri. In the present study, the effect of temperatures was evaluated on structure and antimicrobial properties of the silver nanoparrticles by transmission electron microscopy (TEM), X-ray diffraction (XRD) analysis and antimicrobial Agar well diffusion methods. The silver nanoparticles showed antibacterial activity against all the pathogenic bacteria; however, this property was lost after treatment of the silver nanoparticles by high temperatures (100 and 300 °C). TEM images showed that the average sizes of heated silver nanoparticles were >100 nm. However, these were <100 nm for non-heated silver nanoparticles. Although, XRD patterns showed the crystalline structure of heated silver nanoparticles, their antibacterial activities were less. This was possible because of the sizes and accordingly less penetration of the particles into the bacterial cells. In addition, elimination of the capping agents by heat might be considered another reason.     

Effect of capping agent concentration on thermoluminescence and photoluminescence of copper‐doped zinc sulfide nanoparticles

Copper‐doped zinc sulfide (ZnS:Cu) nanoparticles with varying concentrations of capping agent were prepared using a chemical route technique. These particles were characterized by scanning electron microscopy (SEM), transmission electron microscopy and X‐ray diffraction (XRD). Optical absorption studies showed that the absorption edge shifted towards the blue region as the concentration of the capping agent increased. Using effective mass approximation, calculation of the nanoparticle size indicated that effective band gap energy increases with decreasing particle size. The thermoluminescence (TL) properties of sodium hexameta phosphate (SHMP)‐passivated ZnS:Cu nanoparticles were investigated after UV irradiation at room temperature. The TL glow curve of capped ZnS:Cu showed variations in TL peak position and intensity with the change in capping agent concentration. The photoluminescence (PL) spectra of ZnS:Cu nanoparticles excited at 254 nm exhibited a broad green emission band peaking around 510 nm, which confirmed the characteristic feature of Zn²⁺ as well as Cu²⁺ ions as the luminescent centres in the lattice. The PL spectra of ZnS:Cu nanoparticles with increasing capping agent concentrations revealed that the emission becomes more intense and shifted towards shorter wavelengths as the sizes of the samples were reduced. Copyright © 2014 John Wiley & Sons, Ltd.     

Effect of enzyme dehydration on alcalase‐catalyzed dipeptide synthesis in near‐anhydrous organic media

The effect of enzyme dehydration by molecular sieves on the coupling of phenylalanine amide and the carbamoylmethyl ester of N‐protected phenylalanine in near‐anhydrous tetrahydrofuran was investigated. This coupling was catalyzed by Alcalase covalently immobilized onto macroporous acrylic beads (Cov); these immobilized enzymes were hydrated prior to use. The dehydration kinetics of Cov by molecular sieve powder were determined by incubating Cov with different amounts of molecular sieve powder for different periods of time (0–80 h). Subsequently, the remaining coupling activity of Cov was measured. Dehydration‐induced inactivation of Cov by molecular sieve powder was found to occur in three phases: (1) an initial, rapid, major dehydration‐induced inactivation that takes place during the first activity measurement, (2) a phase of first‐order inactivation, and (3) a plateau phase in activity. These dehydration kinetics were incorporated into a previously found reaction kinetics model. The resulting model was then used to fit progress curve data of the coupling in the presence of different amounts of molecular sieve powder. Upon establishment of parameter values, the model was used to predict independent data sets and found to work well. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:870–875, 2013