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Phages are one of the most diverse and widely distributed organisms on the earth today, and have great advantages in eliminating bacteria, especially multi-drug resistant bacteria that are widespread at present. At present, a variety of bacteriophage products have been well applied in the fields of breeding for food raw materials, farmed animals, foodborne pathogenic bacteria detection, and instant food sterilization. However, the narrow host range and complex interaction mechanism between bacteriophage and host bacteria greatly limit their development as new bacteriostatic agents. The specific binding between bacteriophages and host bacteria depends on the receptor binding proteins on the surface of bacteriophages. Studying the structure, function and mechanism of action of various bacteriophage receptor binding proteins will help in understanding the interaction process between bacteriophage and bacteria. On this basis, phage receptor binding protein modification by genetic engineering and induced culture methods to obtain high-quality broad-spectrum phages has become an important content of phage research. This paper summarizes the current research on different structures of phage receptor binding proteins and various host spectrum expansion schemes in an effort to provide theoretical support for the development and application of bacteriophages in the food industry.

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A cost-effective approach has been developed to synthesize Cu nanoparticles encapsulated into B and N double-doped carbon nanotubes (Cu@BCNNTs) by one-step pyrolysis. According to the specific binding of Cu–Cl and Cu–glutathione (GSH), we employed Cu@BCNNTs to build an electrochemical sensing platform to detect GSH. The unique space-confined structure can prevent Cu nanoparticles from agglomeration. In addition, B and N co-doped porous hollow tubes can improve the electrochemical conductivity, expand the number of active sites, enhance surface adsorption, and shorten the transport path. These favorable characteristics of Cu@BCNNTs make them have excellent electrocatalytic properties. These results display that the prepared sensor can detect GSH from 0.5 to 120 μM with a detection limit of 0.024 μM. The obtained sensors can be successfully applied in the human serum with recovery of GSH ranging from 100.2 to 103.9%. This work provides a new vision to synthesize nanoparticles confined in a hollow tube for the applications in biosensing and medical diagnostics. [ABSTRACT FROM AUTHOR]

The unique biodegradation and mineralization properties of nanosized CO 3 2−- containing hydroxyapatite (HCA)-coated BBG (nano-HCA@BG) make it a promising material for soft tissue repair. However, its single-function solid powder form makes it difficult to control drug release rates, limiting its potential in vivo application. To address this challenge, we designed a hierarchical multifunctional composite by incorporating gelatin with nano-HCA@BG loaded with AgNPs. The hierarchical composite achieved a high degree of structural fit from nanometer to micrometer scale, as demonstrated by structural characterization results. The composite showed improved encapsulation of nanodrug and controlled degradation, as confirmed by degradation and antimicrobial property results. Wound healing experiments in vivo revealed efficient encapsulation of nano-HCA@BG through specific combination of gelatin and nano-HCA@BG, leading to improved controlled degradation and biological activity of the glass. The study also developed a dynamic flowing drug loading method that integrated material preparation and drug loading, thus improving the efficiency of drug loading of the nano-HCA@BG. Overall, our study demonstrates a new method for the preparation of hierarchical functional biomaterials of bioglass, laying the foundation for nano-HCA@BG to play an important role in tissue repair. Moreover, our findings suggest that better understanding of the structure and biological properties of nano-HCA@BG could expand its application in other biomedical fields such as drug delivery. [ABSTRACT FROM AUTHOR]

Objective: There is increasing interest in simultaneous endovascular delivery of more than one drug from a drug-loaded stent into a diseased artery. There may be an opportunity to obtain a therapeutically desirable uptake profile of the two drugs over time by appropriate design of the initial drug distribution in the stent. Due to the non-linear, coupled nature of diffusion and reversible specific/non-specific binding of both drugs as well as competition between the drugs for a fixed binding site density, a comprehensive numerical investigation of this problem is critically needed. Methods: This paper presents numerical computation of dual drug delivery in a stent-artery system, accounting for diffusion as well as specific and non-specific reversible binding. The governing differential equations are discretized in space, followed by integration over time using a stiff numerical solver. Three different cases of initial dual drug distribution are considered. Results: For the particular case of sirolimus and paclitaxel, results show that competition for a limited non-specific binding site density and the significant difference in the forward/backward reaction coefficients play a key role in determining the nature of drug uptake. The nature of initial distribution of the two drugs in the stent is also found to influence the binding process, which can potentially be used to engineer a desirable dual drug uptake profile. Conclusions: These results help improve the fundamental understanding of endovascular dual drug delivery. In addition, the numerical technique and results presented here may be helpful for designing and optimizing other drug delivery problems as well. [ABSTRACT FROM AUTHOR]

Biologically active surfaces with spatio‐selective binding capabilities minimize nonspecific adsorption and are essential to fabricate biomedical devices. Chitosan is a potential material for such a functional surface because of its good biocompatibility. In this study, a chitosan‐based bioactive surface was prepared using a facile drop‐casting method. Nonbiofouling properties of the bare chitosan film were observed against fluorescent‐tagged proteins (streptavidin and bovine serum albumin). The interaction of streptavidin with biotin was used to assess the specific binding capabilities. Biotin was spatially and selectively immobilized onto the film through surface organic reactions. Fluorescence intensities of the streptavidin‐treated chitosan film proportionally changed with the biotin concentration, suggesting a good specific binding. Furthermore, the intrinsic amine groups in the chitosan coating provided antibacterial properties, which could be further enhanced by introducing quaternary ammonium cations. The combination of nonbiofouling, specific binding, and antibacterial properties renders chitosan a viable candidate for biomedical and analytical applications. [ABSTRACT FROM AUTHOR]

• Oligodiaminogalactose 4 mer (ODAGal4) stabilized duplex RNA. • Oligodiaminogalactose 4 mer (ODAGal4) did not stabilize duplex DNA. • Oligodiaminogalactose 4 mer (ODAGal4) bound to duplex RNA in the order of 105 M −1. • Oligodiaminogalactose 4 mer (ODAGal4) did not bind to duplex DNA. • Negative enthalpy, entropy, and heat capacity changes were observed upon binding. Duplex RNA stabilization is important for the application in the artificial silencing of gene expression. Excess usage of cationic molecules with low binding affinity to duplex RNA may cause cytotoxicity due to nonspecific binding. Cationic molecules specifically binding to duplex RNA with high binding affinity are necessary for duplex RNA stabilization. Here, UV melting and isothermal titration calorimetric analyses revealed that our previously designed cationic oligodiaminogalactose 4 mer (ODAGal4) specifically stabilized duplex RNA by binding to it with approximately 105 M −1 binding constant, without binding to duplex DNA. Temperature dependence of thermodynamic parameters, including negative enthalpy and entropy changes, revealed that the magnitude of negative heat capacity change was quite large for small molecules binding to duplex RNA, suggesting the influence of the hydrophobic effect on the binding process. Our results suggest the therapeutic application of ODAGal4 as a key molecule for duplex RNA-binding specificity to prevent any nonspecific binding. [Display omitted] [ABSTRACT FROM AUTHOR]

In the detection of biomolecules, surface plasmon resonance (SPR) sensors require high sensitivity. In this study, we propose a sensitivity-enhanced functionalized plasmonic interface based on Ag–TiO 2 –Co(OH) 2 nanosheets structure. Compared to unmodified SPR sensors, the sensitivity of the sensor decorated with TiO 2 and Co(OH) 2 nanosheets is increased by 130.84%, reaching 5764.27 nm/RIU. This enhancement is attributed to the high refractive index of the coating, as well as the high specific surface area and abundant active sites provided by the synthesized Co(OH) 2 nanosheets with a multi-grooved structure. Additionally, employing a double-antibody sandwich method, the antibody-functionalized plasmonic interface enables specific detection of human serum albumin (HSA). The linear response of this sensor was in the wide range of 0.4–150 μM, and the LOD reached 154.89 nM(K D is approximately 1.73 × 10−6 M). This novel SPR sensor offers a new strategy for biochemical sensing and provides a highly sensitive platform for immunoassays. [Display omitted] [ABSTRACT FROM AUTHOR]

This study is dealt with the two-phase binding (specific and nonspecific) of drug eluted from a half- embedded drug-eluting stent in presence of atherosclerotic plaque. The specific binding due to the interaction of drug molecules with specific receptors and nonspecific binding caused by the trapping of drug in the extra-cellular matrix have been paid due attention. An idealised wall consisting of a plaque and a healthy tissue region has been considered. Moreover, a Dirichlet release condition is imposed on the strut surface. In this investigation, a two-dimensional model governing drug transport and its two-phase binding in cylindrical polar coordinate system has been solved numerically by a finite-difference method. Our simulation predicts that plaque behaves like a physical barrier in two types of the binding process and there is an inverse relationship between bound drug concentration and plaque thickness. Simulations show that a single peak profile of drug is noted when the struts are situated one-strut radius apart and as the inter-strut distance increases, the peak concentration falls and distinct peak profiles over each strut are visualised. The model also reveals that in the region downstream of a strut, the concentration of both bound drug forms in the plaque and healthy regions increases, and eventually, the saturation length of binding sites increases. Predicted results show for smaller Damköhler number, the rapid saturation of binding sites takes place and the stent having thinner strut may perform well in terms of effectiveness as well as efficacy in the stent-based delivery. [ABSTRACT FROM AUTHOR]

[Display omitted] • A novel c-MYC G4 ligand was developed by migrating the benzene group on a carbazole-benzothiazolium scaffold. • The ligand exhibits considerable specificity to the c-MYC G4, which was distinguished from other small-molecule ligands. • The ligand may cause transcriptional inhibition of the c-MYC oncogene instead of other G4-mediated oncogenes. c-MYC is one of the most important oncogenes, which is overexpressed in many cancers, and is highly related to development, metastasis, and drug resistance of cancers. The G4 structure in the promoter of c-MYC oncogene contributes a lot to the gene transcriptional mechanism. Small-molecule ligands binding to the c-MYC G4 appear to be a new class of anticancer agents. However, selective ligands for the c-MYC G4 over other G4s have been rarely reported. In this study, we reported a novel fluorescent ligand by migrating the benzene group on a carbazole-benzothiazolium scaffold, which was demonstrated to exhibit considerable specificity to the c-MYC G4, which was distinguished from other small-molecule ligands. The further cellular experiments suggested that this ligand may indeed target the promoter G4 and cause apparent transcriptional inhibition of the c-MYC oncogene instead of other G4-mediated oncogenes, which thereby resulted in cancer cell growth inhibition. Collectively, this study provided a good example for developing specific c-MYC G4 ligands, which may further develop into an effective anticancer agent that inhibit the c-MYC expression. [ABSTRACT FROM AUTHOR]

The binding between cinnamycin and the phosphatidylethanolamine (PE)-included vesicles was monitored using cyclic voltammetry (CV) measurements and interpreted in terms of the composition of the vesicles and the monolayer binding site. The monolayer was composed of pure 11-mercapto-1-undecanol (MUD) to 90% MUD/10% 16-mercaptohexadecanoic acid (MHA) on a gold surface. Cinnamycin was immobilized on each monolayer. The vesicles, prepared at the desired ratio of the phospholipids, were injected on the cinnamycin-immobilized surface. CV experiments were performed for each step. For the pure-dipalmitoylphosphatidyl-choline (DPPC) vesicles on all of monolayers and the DPPC/dipalmitoylphosphatidyl-ethanolamine (DPPE) vesicles on the pure-MUD monolayer, the electric property of the surface was little changed. However, the vesicles made with 90% DPPC/10% DPPE on the monolayer prepared with 99% MUD/1% MHA to 90% MUD/10% MHA showed a consistent decrease in the CV response. Additionally, in the 95% DPPC/5% DPPE vesicles and the 99.5% MUD/0.5% MHA monolayer, variances in the responses were observed. [ABSTRACT FROM AUTHOR]

Transcription factors (TFs) bind to specific DNA motifs to regulate the expression of target genes. To reach their binding sites, TFs diffuse in 3D and perform local motions such as 1D sliding, hopping, or intersegmental transfer. TF–DNA interactions depend on multiple parameters, such as the chromatin environment, TF partitioning into distinct subcellular regions, and cooperativity with other DNA-binding proteins. In this review, how current understanding of the search process has initially been shaped by prokaryotic studies is discussed, as well as what is known about the parameters regulating TF search efficiency in the context of the complex eukaryotic chromatin landscape. Transcription factors (TFs) search their specific sites through both 3D diffusion and local motions. TF search efficiency depends on TFs' biochemical properties and local concentrations. Eukaryotic TFs vary strongly in their nonspecific DNA association and search efficiency. Progress in temporal and spatial resolution of single-molecule microscopy will be required to better describe the nanoscale movements of TFs on chromatin. [ABSTRACT FROM AUTHOR]

Imprinting polymerization is an exciting technique since it leads to specific binding sites, which are the basis of a variety of applications, such as sensors, detectors, and catalysts. The specific binding sites are created using templates and then fixing the structure of the binding site with crosslinking. The literature review of imprinting polymerizations shows that the crosslinking density governs the physical properties of the resulting molecularly imprinted polymer (MIP). It is also a factor governing the capacity and the selectivity of MIPs. Reviewing polymer science data and theory, the crosslinking density commonly used in MIP synthesis is unusually high. The data reviewed here suggest that more research is needed to determine the optimal crosslinking density for MIPs.

The binding between cinnamycin and the phosphatidylethanolamine (PE)-included vesicles was monitored using cyclic voltammetry (CV) measurements and interpreted in terms of the composition of the vesicles and the monolayer binding site. The monolayer was composed of pure 11-mercapto-1-undecanol (MUD) to 90% MUD/10% 16-mercaptohexadecanoic acid (MHA) on a gold surface. Cinnamycin was immobilized on each monolayer. The vesicles, prepared at the desired ratio of the phospholipids, were injected on the cinnamycin-immobilized surface. CV experiments were performed for each step. For the pure-dipalmitoylphosphatidyl-choline (DPPC) vesicles on all of monolayers and the DPPC/dipalmitoylphosphatidyl-ethanolamine (DPPE) vesicles on the pure-MUD monolayer, the electric property of the surface was little changed. However, the vesicles made with 90% DPPC/10% DPPE on the monolayer prepared with 99% MUD/1% MHA to 90% MUD/10% MHA showed a consistent decrease in the CV response. Additionally, in the 95% DPPC/5% DPPE vesicles and the 99.5% MUD/0.5% MHA monolayer, variances in the responses were observed.

Inefficient sample preparation methods hinder the performance of high-throughput single-molecule force spectroscopy (H-SMFS) for viscous damping among reactants and unstable linkage. Here, we demonstrated a sample preparation method for H-SMFS systems to achieve a higher ratio of effective target molecules per sample cell by gas-phase silanization and reactant hydrophobization. Digital holographic centrifugal force microscopy (DH-CFM) was used to verify its performance. The experimental result indicated that the DNA stretching success ratio was improved from 0.89% to 13.5%. This enhanced efficiency preparation method has potential application for force-based DNA stretching experiments and other modifying procedures. [ABSTRACT FROM AUTHOR]

Graphical abstract Abstract Bisphenol A molecular imprinted adsorbent (BMIA) was successfully synthesized by a sol-gel process and showed a good specific binding performance in the water. The further studies showed that the mass transfer process was controlled by in-diffusion, and the synthesis conditions would effect on the amount of imprinting sites. Scatchard model analysis evidenced that the high binding affinity sites and the low binding affinity sites were both on BMIA, and the high binding affinity sites played a key role in the specific binding process. Scatchard model analysis of temperature effect experiments and dosage effect experiments proved that the specific binding sites with high binding affinity and the unexpressed specific binding sites with low binding affinity were the two different states of the imprinting binding sites. The conversion between the two different states depended on the reaction driving force, and the increasing reaction driving force would increase the number of specific binding sites. Especially, the temperature showed a linear positive correlation with the amount of specific binding sites. Finally, a possible model was put forward to explain the two different states conversion mechanism of the imprinting sites. [ABSTRACT FROM AUTHOR]

Bovine herpesvirus 1 (BoHV-1) is a highly contagious viral pathogen which causes infectious bovine rhinotracheitis in cattle worldwide. Currently, there is no antiviral prophylactic treatment available capable of mitigating the disease impact and facilitating recovery from latent infection. In this study, we have engineered a novel recombinant anti-BoHV-1 immunotoxin construct termed “BoScFv-PE38” that consists of a single-chain monoclonal antibody fragment (scFv) fused with an active domain of Pseudomonas exotoxin A as a toxic effector (PE38). The recombinant BoScFv-PE38 immunotoxin expressed in a prokaryotic expression system has specific binding affinity for BoHV-1 glycoprotein D (gD) with a dissociation constant (Kd) of 12.81 nM and for BoHV-1 virus particles with a Kd value of 97.63 nM. We demonstrate that the recombinant BoScFv-PE38 is internalized into MDBK cell compartments that inhibit BoHV-1 replication with a half-maximal inhibitory concentration (IC50) of 4.95 ± 0.33 nM and a selective index (SI) of 456 ± 31. Furthermore, the BoScFv-PE38 exerted a cytotoxic effect through the induction of ATP and ammonia, leading to apoptosis of BoHV-1-infected cells and the inhibition of BoHV-1 replication in MDBK cells. Collectively, we show that BoScFv-PE38 can potentially be employed as a therapeutic agent for the treatment of BoHV-1 infection.

Swine leukocyte antigen (SLA) class I molecules play a crucial role in generating specific cellular immune responses against viruses and other intracellular pathogens. They mainly bind and present antigens of intracellular origin to circulating MHC I-restricted cytotoxic T lymphocytes (CTLs). Binding of an appropriate epitope to an SLA class I molecule is the single most selective event in antigen presentation and the first step in the killing of infected cells by CD8+ CTLs. Moreover, the antigen epitopes are strictly restricted to specific SLA molecules. In this study, we constructed SLA class I complexes in vitro comprising viral epitope peptides, the extracellular region of the SLA-1 molecules, and β2-microglobulin (β2m) using splicing overlap extension polymerase chain reaction (SOE-PCR). The protein complexes were induced and expressed in an Escherichia coli prokaryotic expression system and subsequently purified and refolded. Specific binding of seven SLA-1 proteins to one classical swine fever virus (CSFV) and four porcine reproductive and respiratory syndrome virus (PRRSV) epitope peptides was detected by enzyme-linked immunosorbent assay (ELISA)-based method. The SLA-1∗13:01, SLA-1∗11:10, and SLA-1∗11:01:02 proteins were able to bind specifically to different CTL epitopes of CSFV and PRRSV and the MHC restrictions of the five epitopes were identified. The fixed combination of Asn151Val152 residues was identified as the potentially key amino acid residues influencing the binding of viral several CTL epitope peptides to SLA-1∗13:01 and SLA-1∗04:01:01 proteins. The more flexible pocket E in the SLA-1∗13:01 protein might have fewer steric limitations and therefore be able to accommodate more residues of viral CTL epitope peptides, and may thus play a critical biochemical role in determining the peptide-binding motif of SLA-1∗13:01. Characterization of the binding specificity of peptides to SLA class I molecules provides an important basis for epitope studies of infectious diseases in swine, and for the rational development of novel porcine vaccines, as well as for detailed studies of CTL responses in pigs used as animal models.

It is important to obtain the targeted nanocarriers during cancer treatment. Herein, mannosylated liposomes encapsulating carbon dots (CDs) are provided for targeted recognition of liver cancer HepG2 cells, which is based on the specific interaction between D -mannose and glycoprotein on the surface of HepG2 cells. CDs were prepared by hydrothermal method. Then, they were encapsulated into liposomes by hydrophobic force. The encapsulation of CDs into liposomes increases their stability and fluorescence intensity. Furthermore, D -mannose can also be inserted into liposomes by the aldehyde amine reaction between aldehyde groups of mannose molecules and amino groups of liposomes. The obtained D -mannose-CDs-liposomes (Man-CDs-liposomes) exhibit selectively tracking and efficiently labelling for cancer cells. The work highlights the potential application of CDs for bioimaging and diagnostic. [ABSTRACT FROM AUTHOR]

Bovine herpesvirus 1 (BoHV-1) is a highly contagious viral pathogen which causes infectious bovine rhinotracheitis in cattle worldwide. Currently, there is no antiviral prophylactic treatment available capable of mitigating the disease impact and facilitating recovery from latent infection. In this study, we have engineered a novel recombinant anti-BoHV-1 immunotoxin construct termed "BoScFv-PE38" that consists of a single-chain monoclonal antibody fragment (scFv) fused with an active domain of Pseudomonas exotoxin A as a toxic effector (PE38). The recombinant BoScFv-PE38 immunotoxin expressed in a prokaryotic expression system has specific binding affinity for BoHV-1 glycoprotein D (gD) with a dissociation constant (Kd) of 12.81 nM and for BoHV-1 virus particles with a Kd value of 97.63 nM. We demonstrate that the recombinant BoScFv-PE38 is internalized into MDBK cell compartments that inhibit BoHV-1 replication with a half-maximal inhibitory concentration (IC50) of 4.95 ± 0.33 nM and a selective index (SI) of 456 ± 31. Furthermore, the BoScFv-PE38 exerted a cytotoxic effect through the induction of ATP and ammonia, leading to apoptosis of BoHV-1-infected cells and the inhibition of BoHV-1 replication in MDBK cells. Collectively, we show that BoScFv-PE38 can potentially be employed as a therapeutic agent for the treatment of BoHV-1 infection. [ABSTRACT FROM AUTHOR]

Carrageenans are a family of sulphated cell wall polysaccharides extracted from seaweeds and are widely used in different industrial sectors. Relative to κ-carrageenan (κ-car) and ι-carrageenan (ι-car), the ionic binding behavior of λ -carrageenan ( λ -car) is far less studied. In this work, the interaction and binding behavior between λ -car and metal ions of different valency (Na + , K + , Mg 2+ , Ca 2+ , Fe 2+ , Fe 3+ , Al 3+ , Cr 3+ ) have been investigated. In contrast to the non-specific interaction of the monovalent and divalent cations, specific binding has been identified between λ -car and Fe 3+ /Al 3+ . The specific binding could lead to either precipitation or gelation of λ -car, depending on the way of introducing Fe 3+ /Al 3+ ions. Fe 3+ and Al 3+ exhibit the same binding stoichiometry of [M 3+ ]/[repeating unit] = 1.0, with the former having a relatively larger binding constant. Cr 3+ , though having very similar physical properties with Fe 3+ /Al 3+ , is incapable of binding specifically to Cr 3+ . The phenomena could not be interpreted in terms of counterion condensation, and are rather attributable to a mechanism in which hexa-coordination of Fe 3+ /Al 3+ and entropy-driven cation dehydration play crucial roles in driving the binding of the trivalent metal ions to λ -car. [ABSTRACT FROM AUTHOR]

Three different series of brush polymers bearing glucosyl, maltosyl, or maltotriosyl moiety at the bristle end are successfully prepared by using cationic ring-opening polymerization and two sequential postmodification reactions. All brush polymers, except for the polymer containing 100 mol% maltotriosyl moiety, demonstrate the formation of multibilayer structure in films, always providing saccharide-enriched surface. These self-assembling features are remarkable, regarding the bulkiness of saccharide moieties and the kink in the bristle due to the triazole linker. The saccharide-enriched film surfaces reveal exceptionally high specific binding affinity to concanavalin A but suppress nonspecific binding of plasma proteins severely. Overall, the brush polymers bearing saccharide moieties of various kinds in this study are highly suitable materials for biomedical applications including biosensors. [ABSTRACT FROM AUTHOR]

2D aligned films prepared from engineered M13 bacteriophages (phage) have potential applications in tissue-regeneration and energy devices. TBP54–M13 phage specifically binds to acid-alkali treated titanium (Ti) surface. In this study, polyvinyl pyrrolidone–treated TBP54–M13 phage films were fabricated on Ti surfaces. The resultant film exhibited uniform nanostructure and favorable stability. This film has potential applications in surface multi–functionalization and patterning of Ti implants. [ABSTRACT FROM AUTHOR]

We validated the structure and performed synthesis of eight new peptides that are analogues of proglyprol, with the common formula of Pro(X)-A-Pro(Y). Here we present data on the molecular ligand-receptor activity of these peptide compounds; in particular, we present data on their ability to compete with the tripepetide Pro-Gly-Pro for specific binding sites on the plasma membranes of brain cells. The experiments were performed using a wide range of peptide concentrations, including low and ultralow, down to 10 mol/L. It has been shown that the peptides with substitution of the second amino acid and/or containing Ala on the C-terminus of the peptide blocked binding of tritium-labeled Pro-Gly-Pro. Regardless of the structure of the second amino acid in the composition of the modified peptide, 5-oxo-Pro-analogues induced a concentration-dependent increase in the number of binding sites of the radioactive ligand. Elongation of the peptide sequence due to addition of Ala to the C-terminus of the peptide probably increases the affinity of the analogues to the low-affinity binding sites on plasma membranes of brain cells. Taking these data into account, it is possible to consider the studied candidate peptides, i.e., synthetic modifications of the simplest glyproline, as biologically active synthetic molecules. [ABSTRACT FROM AUTHOR]

Whispering Gallery Mode (WGM) microresonators have recently been studied as a means to achieve real-time label-free detection of biological targets such as virus particles, specific DNA sequences, or proteins. Due to their high quality (Q) factors, WGM resonators can be highly sensitive. A biosensor also needs to be selective, requiring proper functionalization of its surface with the appropriate ligand that will attach the biomolecule of interest. In this paper, WGM microdisks are used as biosensors for detection of Staphylococcus aureus. The microdisks are functionalized with LysK, a phage protein specific for staphylococci at the genus level. A binding event on the surface shifts the resonance peak of the microdisk resonator towards longer wavelengths. This reactive shift can be used to estimate the surface density of bacteria that bind to the surface of the resonator. The limit of detection of a microdisk with a Q-factor around 104 is on the order of 5 pg/mL, corresponding to 20 cells. No binding of Escherichia coli to the resonators is seen, supporting the specificity of the functionalization scheme. [ABSTRACT FROM AUTHOR]

Fluorescent nanodiamonds (NDs) are remarkable objects. They possess unique mechanical and optical properties combined with high surface areas and controllable surface reactivity. They are non-toxic and hence suited for use in biological environments. NDs are also readily available and commercially inexpensive. Here, the exceptional capability of controlling and tailoring their surface chemistry is demonstrated. Small, bright diamond nanocrystals (size ˜30 nm) are conjugated to protein filaments of actin (length ˜3-7 µm). The conjugation to actin filaments is extremely selective and highly target-specific. These unique features, together with the relative simplicity of the conjugation-targeting method, make functionalised nanodiamonds a powerful and versatile platform in biomedicine and quantum nanotechnologies. Applications ranging from using NDs as superior biological markers to, potentially, developing novel bottom-up approaches for the fabrication of hybrid quantum devices that would bridge across the bio/solid-state interface are presented and discussed. [ABSTRACT FROM AUTHOR]

In our study, electrospray ionization mass spectrometry (ESI–MS) was used to investigate the formation and recognition of human telomere G-quadruplex. Among the six small molecules studied, homobarringtonie (shortened as P1 ), one of the antineoplastic alkaloids separated from Chinese cephalotaxus fortunei, was examined having the highest binding ability with the human telomere G-quadruplex. And the most superiority of P1 was the good binding preference for the G-quadruplex than the duplex DNA. CD melting experiment results implied that P1 could enhance the thermo stability of the G-quadruplex. Moreover, Autodock analysis gave the result that P1 has the biggest docked energy to the telomere G-quadruplex, which was consistent with the result of ESI–MS. The high specificity and binding affinity of P1 to the telomere G-quadruplex make it potential for drug design and cancer relief. [ABSTRACT FROM AUTHOR]

The binding of chlorin p 6 , a model photosensitizer for photodynamic therapy (PDT), to the Sudlow’s site II of Human Serum Albumin (HSA) has been monitored by different spectroscopic methods. Displacement of Dansyl- l -Proline (DP) from its conjugate with HSA is manifested in the spectral shift and decrease in its fluorescence intensity as well as the emergence of component with lifetime of 2–3 ns, which is characteristic of free DP. As DP is known to bind specifically to the Sudlow’s site II of human serum albumin, its displacement by chlorin p 6 indicates the residence of the photosensitizer in the same site, in addition to Sudlow’s site I. The binding constants for Sudlow’s site II, determined by the stopped-flow technique, are found to be two orders of magnitude smaller than that for Sudlow’s site I. [ABSTRACT FROM AUTHOR]

Here we studied the role of peptide anxiolytics (Selank and its short fragment, Arg-Pro-Gly-Pro) in the occurrence of direct and indirect changes in the basic parameters of the specific ligand-receptor interactions of γ-aminobutyric acid (GABA) with the plasma membranes of nerve cells in the brain. We found that in the presence of the studied peptides the amount of the specifically bound ligand, [H] GABA, varied. Preliminary intranasal administration of Selank also induced changes in the number of specific binding sites of [H] GABA but did not affect the affinity of the receptors. More complex and delayed effects were caused by the preliminary intranasal administration of Arg-Pro-Gly-Pro (RPGP). The data that were obtained in the research also indicate the impact of the peptides on cellular regulatory mechanisms that are not associated with the ligand-receptor interaction of studied peptides in the places of their action. Thus, the biological effects of Selank were apparently due to a combination of the direct modulating action of the peptide on the target receptor and the initiation of the biochemical cellular mechanisms that determine the molecular basis of the physiological effect of the peptide. [ABSTRACT FROM AUTHOR]

Molecular aspects of the biological mechanism of action of the synthetic peptide HFRWPGP, including an assessment of the stability to membrane proteolytic enzymes and the determination of several intermolecular interaction parameters of the peptide and rat-brain cytoplasmic membranes. It was hypothesized based on the results that the peptide apparently acts as an allosteric activity modulator for several receptor systems and can after the nature of signal transfer to cells. It was established that heptapeptide HFRWPGP in the presence of cerebellum and hippocampus cytoplasmic membranes was degraded in a manner similar to that of Semax proteolysis (used as a reference peptide) under the same incubation conditions. [ABSTRACT FROM AUTHOR]

Whispering Gallery Mode (WGM) microresonators have recently been studied as a means to achieve real-time label-free detection of biological targets such as virus particles, specific DNA sequences, or proteins. Due to their high quality (Q) factors, WGM resonators can be highly sensitive. A biosensor also needs to be selective, requiring proper functionalization of its surface with the appropriate ligand that will attach the biomolecule of interest. In this paper, WGM microdisks are used as biosensors for detection of Staphylococcus aureus. The microdisks are functionalized with LysK, a phage protein specific for staphylococci at the genus level. A binding event on the surface shifts the resonance peak of the microdisk resonator towards longer wavelengths. This reactive shift can be used to estimate the surface density of bacteria that bind to the surface of the resonator. The limit of detection of a microdisk with a Q-factor around 104 is on the order of 5 pg/mL, corresponding to 20 cells. No binding of Escherichia coli to the resonators is seen, supporting the specificity of the functionalization scheme.

A high throughput screening system involving a linear ion trap (LTQ) analyzer, a house-made platform and a desorption electrospray ionization (DESI) source was established to screen ligands with a high affinity for proteins with anion-binding sites. The complexes were analyzed after incubation, ultrafiltration, washing, and displacement. A new anionic region inhibited dissociation (ARID) mechanism that was suitable for a protein with anion-binding site was proposed. We utilized the differences in detectable dissociation of protein-ligand complexes, combined with displacement experiments, to distinguish free ligands displaced from anion-binding sites from liberated ligands dissociated from nonspecific interactions. The method was validated by α-acid glycoprotein (AGP) and (R), (S)-amlodipine. Site-specific enantioselectivity shown in our experiments was consistent with earlier studies. Obtaining all of the qualitative information of 15*3 samples in 2.3 min indicates that the analysis process is no longer the time-limiting step in the initial stage of drug discovery. Quantitative information verified that our method was at least a semiquantitative method. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Human epidermal growth factor receptor 2 (HER2) expression has been shown to be increased in several types of human tumours. In this study, for the imaging of HER2-related tumours, a modified RNA aptamer with HER2-specific targeting was labelled with 99mTc, by using hydrazino nicotinamide (HYNIC) as the chelator in the presence of tricine or ethylenediamine- N,N′-diacetic acid (EDDA) as the co-ligand. Stability testing of the radiolabelled aptamers in the serum was performed through SDS-PAGE. The aptamer-radionuclide conjugate was evaluated for its cellular HER2-specific binding in ovarian cancer cells (SKOV-3), and its biodistribution properties were assessed in normal and SKOV-3 tumour-bearing mice. In the presence of either tricine or EDDA, the HYNIC-RNA aptamers were labelled with 99mTc at a high yield and radiochemical purity. Cellular experiments confirmed the specific binding of the RNA aptamer to the HER2 receptor. In the animal biodistribution study, uptake of the EDDA-co-liganded 99mTc-HYNIC-RNA aptamer by the liver and spleen was remarkably lower than that of the aptamer with tricine. Tumours also showed a higher accumulation of radioactivity with the EDDA-co-liganded aptamer complex. This study demonstrated EDDA to be better than tricine for use as a co-ligand with the RNA aptamer, which can be a potential tool for the molecular imaging of HER2-overexpressing cancers. [ABSTRACT FROM AUTHOR]

Agonist binding of A2A adenosine receptor (A2AAR) shows protective effects against inflammatory and immune. Efforts are exerted in understanding the general mechanism and developing A2AAR selectively binding agonists. Using molecular dynamics (MD) simulations, we have studied the interactions between A2AAR and its agonist (adenosine), and analyzed the induced dynamic behaviors of the receptor. Key residues interacting with adenosine are identified: A632:61, I662:64, V843:32, L853:33, T883:36, F1685:29, M1775:38, L2496:51, H2506:52, and N2536:55 interacting with adenosine with affinities larger than 0.5 kcal/mol. Moreover, no interaction between adenosine and L1675:28 is observed, which supports our previous findings that L1675:28 is an antagonist specific binding reside. The dynamic behaviors of agonist bound A2AAR are found to be different from apo-A2AAR in three typical functional switches: (i) tight "ionic lock" forms in adenosine-A2AAR, but it is in equilibrium between formation and breakage in apo-A2AAR; (ii) the rotamer toggle switch", T883:36/F2426:44/W2466:48, adopted different rotameric conformations in adenosine-A2AAR and apo-A2AAR; (iii) adenosine-A2AAR has a flexible intracellular loop 2 (IC2) and α-helical IC3, while apo-A2AAR preferred α-helical IC2 and flexible IC3. Our results indicate that agonist binding induced different conformational rearrangements of these characteristic functional switches in adenosine-A2AAR and apo-A2AAR. [ABSTRACT FROM AUTHOR]

Abstract: A modified RNA aptamer with HER2-specific binding was conjugated to hynic and labeled with 99mTc, for potential use as a radiopharmaceutical for diagnostic imaging of ovarian cancer cells (SKOV-3) with high HER2 expression. The aptamer was radiolabeled with 99mTc by using hynic as the chelator and tricine as the co-ligand. Stability testing of the radioconjugated aptamer was performed via ITLC and SDS-PAGE in normal saline and serum. The aptamer-radionuclide conjugate was evaluated for cellular HER2-specific binding, saturation affinity, and cellular internalization in SKOV-3 and MCF-7 cells, and its biodistribution properties were assessed in normal and SKOV-3 tumor-bearing mice. Radiolabeling of the aptamer was achieved with high yield and radiochemical purity, and the 99mTc-hynic-RNA aptamer was highly stable in normal saline and serum. Cellular experiments showed specific binding of the aptamer to the HER2 receptor with a dissociation constant of 27nM. Rapid blood clearance was observed after injection of the 99mTc-hynic-RNA aptamer, and the main excretion route was via the hepatobilary system. While the radioconjugated aptamer bound specifically to the HER2 receptor on cells in vitro, it did not show any significant tumor-to-blood or tumor-to-muscle ratios in mice. Modifications to radiolabeled aptamer will require improving its pharmacokinetic properties and tumor uptake in vivo. [Copyright &y& Elsevier]

Transcription factors (TFs) interact dynamically in vivo with chromatin binding sites. Here we summarize and compare the four different techniques that are currently used to measure these kinetics in live cells, namely fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), single molecule tracking (SMT) and competition ChIP (CC). We highlight the principles underlying each of these approaches as well as their advantages and disadvantages. A comparison of data from each of these techniques raises an important question: do measured transcription kinetics reflect biologically functional interactions at specific sites (i.e. working TFs) or do they reflect non-specific interactions (i.e. playing TFs)? To help resolve this dilemma we discuss five key unresolved biological questions related to the functionality of transient and prolonged binding events at both specific promoter response elements as well as non-specific sites. In support of functionality, we review data suggesting that TF residence times are tightly regulated, and that this regulation modulates transcriptional output at single genes. We argue that in addition to this site-specific regulatory role, TF residence times also determine the fraction of promoter targets occupied within a cell thereby impacting the functional status of cellular gene networks. Thus, TF residence times are key parameters that could influence transcription in multiple ways. [ABSTRACT FROM AUTHOR]

Under certain conditions, repetitive DNA motifs have the potential to adopt non- B-form DNA structures, such as hairpins, triplexes, Z- DNA, quadruplexes, and i-motifs. Some non- B-form DNAs have been proposed to cause mutations and, consequently, participate in several biologically important processes, including regulation, evolution, and human disease. Advancement in the knowledge of specific interactions between molecules and non- B-form DNAs at the molecular level in living cells is important for understanding their biological functions. In this review, we describe the latest studies on molecules that target non- B-form DNAs in vivo, with a focus on Z- DNA, G-quadruplexes, triplexes, i-motifs, and hairpins. [ABSTRACT FROM AUTHOR]

Highlights: [•] Current study focuses on electrostatic interaction of carmoisine with HSA and BSA. [•] Primarily electrostatic interaction, binding strength is independent of pH. [•] Dye–protein interaction is significantly reduced with increasing ionic strength. [•] The work is important in protein mediated purification of similar dyes. [•] Possibility of health hazards arising out of use of such food colorants. [Copyright &y& Elsevier]

The article discusses the results of a study which identifies amino-acid residues of cell-surface protein CD36 after interaction with oxidized low-density lipoprotein (oxLDL) in mouse model. The study showed the presence of both hydrophilic and hydrophobic amino-acid residues 149-168 after conducting oxLDL specific binding analysis of several synthetic CD36 peptides. It mentioned that hydrophobic residues, Phe153, Leu158, and Leu161, played a critical role in specific binding interaction.

Abstract: To provide complete characterization of immunoassay on silicon biosensor surfaces, atomic force microscopy, (angle-resolved) X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry were applied to examine Si3N4 surfaces modified with (3-aminopropyl)triethoxysilane, coated with gamma globulins (IgG), blocked with bovine serum albumin and then reacted with anti-IgG antibody for two complementary pairs (rabbit and mouse IgG) at various concentrations (from 0.3nM to 330nM). Protein coverage, as reflected in (amine to total N1s) XPS signal ratio and determined from ARXPS, decreases slightly due to blocking and then increases monotonically for anti-IgG antibody concentrations higher than 1nM. AFM images reveal hardly any change of lateral nanostructure due to blocking but response to antibody solutions, based on both the mean size (from autocorrelation) and dominant spacing (from Fourier analysis) of surface features, similar to that given by ARXPS. AFM height histograms provided information about the vertical nanostructure and the parameters of height distribution (average height, spread – roughness and skewness) were distinctly influenced by coating, blocking and immunoreaction. Average protein layer thickness values determined based on protein structure (molecular weight, dimensions) and surface coverage provided from ARXPS were in accord with average height of protein layer determined from AFM. TOF-SIMS analysis indicated that BSA blocks free surface sites and in addition replaces some already adsorbed IgGs. [Copyright &y& Elsevier]

The article presents a study which aims to detect the binding of oxidized low-density lipoprotein (oxLDL) and CD36 with the use of a synthetic assay system from peptide. The study uses Alexa Fluor® (AFL) for fluorescence labeling of oxLDL. Results show that AFL-oxLDL bound to biotin-CD36149-168 were immobilized on assay plates.

Abstract: Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag+ ion stabilized a C:C mismatched base pair duplex DNA. A C–Ag–C metal-mediated base pair was supposed to be formed by the binding between the Ag+ ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C–Ag–C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag+ ion. Isothermal titration calorimetry demonstrated that the Ag+ ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 106 M−1, which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag+ ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag+ ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C–Ag–C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C–Ag–C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences. [Copyright &y& Elsevier]

Abstract: Trefoil factor family 2 (TFF2) participates in mucus stabilization and repair, apoptosis, and inflammatory responses. Previously published reports have indicated that several growth factors and basal transcription factors are associated with the expression of TFF2. However, the detailed mechanisms that regulate TFF2 expression are not fully understood. The present study was designed to assess the essential role of the transcription factor SP3 with respect to TFF2 expression. We first demonstrated that there was a negative correlation between the expression levels of SP3 and TFF2. Thus, in the examined cells, the overexpression of SP3 decreased the expression level of TFF2, whereas the inhibition of SP3 increased the expression level of TFF2. Moreover, we discovered two GC boxes in the TFF2 promoter and confirmed the specific binding of SP3 to this promoter. On the whole, this study indicated that Sp3 was a major regulator of TFF2 expression. This knowledge should contribute to our understanding of the role that is played by SP3 in the regulation of TFF2 expression. [Copyright &y& Elsevier]