Charge self-trapping in two strand biomolecules:Adiabatic polaron approach

We investigate the properties of the excess charge(electron, hole) introduced into a two-strand biomolecule. We consider the possibility that the stable soliton excitation can be formed due to interaction of excess charge with the phonon subsystem. The influence of overlap of the molecular orbitals between adjacent structure elements of the macromolecular chain on the soliton properties is discussed. Special attention is paid to the influence of the overlapping of the molecular orbitals between structure elements placed on the different chains. Using the literature values of the basic energy parameters of the two-chain biomolecular structures, possible types of soliton solutions are discussed.

Effect of Purified Paper Wasp Ropalidia marginata Venom Toxins on Different Biomolecules in Mice Serum

This study evaluated the effects of purified paper wasp Ropalidia marginata venoms on various biomolecules in the blood serum of albino mice. Changes in the concentration of some important macromolecules, i.e., proteins, free amino acids, uric acid, cholesterol, pyruvic acid, total lipids and glucose were noted down. These alterations were measured after intraperitoneal injection of 40% and 80% 24-hour LD50 purified Ropalidia marginata venom toxin. Serum total protein levels were found to decrease to 78% after 6 hrs, while serum free amino acid levels were significantly increased to 117% 6 hrs after venom injection compared to control. It was also found that serum uric acid levels increased to 138% after 8 hrs of venom injection compared to control. The increase in serum cholesterol i.e. (101% and 106%) and pyruvic acid increased significantly to a maximum value of 106% after 6 hrs of treatment at 40% LD50. Glycogen levels in the gastrocnemius muscle were found to decrease significantly (p-0.05) to 43% and 92% at LD50 after injection of purified Ropalidia marginata venom after 8 h and 80% at LD50 compared to control. Moreover, up to 71% and 81% were obtained at 10 hrs of treatment with the same dose. In the present study, the purified toxins significantly changed the levels of biomolecules in blood serum, indicating their wider effects on cellular physiology due to toxic effects and stress on the animal. These toxins can be good antigens and stimulate immune responses in experimental mice.

Transitional metal ions induced damage to biomolecules:role of ferryl and perferryl radicals

Objective:To investigate the effect of oxidized transitional metal（ferric and cupric） ions on the amino acids.Methods:25 mmol/L hydroxyproline and 25 mmol/L histidine were incubated with 50μL Fe3+ and Cu2+ ions at pH 7.4 and 37℃for 30 mins in separate test tubes.Then 500μL of 1% thiobarbituricacid（TBA） was added to the incubated amino acids followed by addition of 500μL of glacial acetic acid.The resultant mixture was vortexed and heated at 100℃for 30 min.Absorbance readings were noted after cooling to room temperature.The experiment was repeated in the presence of various reagents,like hydroxyl radical scavengers,antioxidant enzymes,and reducing agents and metal ion chelators.Results:The pink chromogen formed with the absorbance maxima at 524 nm,AND shifted to 560 nm in alkaline pH.The absorbance was expressed as TBAadduct in MDA units.The TBA-adduct decreased in the presence of reducing agents and metal ion chelators.Antioxidant enzymes and hydroxyl radical scavengers did not show any effect. Conclusion:Transitional metal ions in their oxidized state showed significant damage to amino acids,hydroxyproline and histidine.The results indicate the possible role played by high-valent oxo-iron species,ferryl and perferry radicals in damaging biomolecules.

Evaluation of attraction terms in equations of state on the prediction of solubility of some biomolecules in supercritical carbon dioxide

In the present work, effect of the attraction terms of four recently modified Peng-Robinson （MPR） equations of state on the prediction of solubility of caffeine, cholesterol, uracil and erythromycin was studied. The attraction terms of two of these equations are linear relative to the acentric factor and for the other two are exponential. It is found that the later show less deviation. Also interaction parameters for the studied systems are obtained and the percentage of average absolute relative deviation （%AARD） in each calculation is displayed.

Excess adsorption of biomolecules on soft surfaces: Adsorption of DNA, proteins and lactose on fatty surfaces

Insoluble fatty surfaces are involved in many important interactions such as in biomembranes with soluble biological macro and micromolecules. In this paper we have studied the adsorption interaction of aqueous solution of DNA, some proteins and lactose on several sparingly soluble fatty substances namely milk fat, stearic acid, palmitic acid, phosphatidyl choline and cholesterol surfaces by measuring the depletion of the adsorbates by analytical methods. Adsorption () of DNA on the soft surfaces of stearic acid, milk fat, phosphatidyl choline, palmitic acid and cholesterol was measured as a function of DNA concentration C2. In each case was found to increase with C2 until it reached the maximum value at a critical concentration . For different surfaces stands in the order: stearic acid > milk fat > phosphatidyl choline > cholesterol > palmitic acid. DNA forms multilayers on stearic acid surface. Adsorption of hemoglobin on cholesterol surface is found to be negative or zero but that of BSA on cholesterol is positive. Adsorption of gelatin on cholesterol surface is significantly higher than that of BSA. Lysozyme on cholesterol surface forms multilayers and on casein forms bilayer. The lowering of free energies ?DGo for all systems have been calculated using integrated form of the Gibbs adsorption and their values have been compared with each other. It is concluded that despite differences in the adsorption behavior of the biomolecules on various soft surfaces, free energy change expressed as Bull’s free energy change (Δ) remain nearly constant except for BSA-fatty acid interaction which may be likely due a specific interaction.

Mesophilic Process and Kinetics Studies of Selected Biomolecules as Potential Enhancers of Biomethanization of Cow Dung in an Anaerobic Tubular Batch Reactor

Mesophilic biogas production and substrate decomposition is one of the significant limiting steps in biogas generation. The rate of generation and quality often affect the viability of biogas systems. This study assessed the potential for biogas process catalysis using powdered Sorghum bicolor L., Zea mays, and Pennisetum glaucum. The kinetics and biogas generation processes were studied. Experiments were conducted in 1 m3 tubular batch reactors, where batches were dosed with various organic biomolecules. Results show that the use of P. glaucum L. and S. bicolor L. reduced the biogas retention times significantly. Biogas generation commenced after the first day for digesters fed with S. bicolor L. and P. glaucum L. while one with Z. mays and control occurred on day two. The rate of biomethanation and methane content were enhanced. S. bicolor L. led to the highest methane content. Findings reveal that locally available organic biomolecules improved biogas quality and quantity.

Oxidative Consumption of Oral Biomolecules by Therapeutically-Relevant Doses of Ozone

In view of its potent microbicidal actions, ozone (O3) offers much potential for application as a therapeutic agent in oral health, e.g. in the treatment of dental caries. This oxidant is extremely reactive towards biomolecules present in the oral environment, and in this study we have employed high-resolution proton (1H) nuclear magnetic resonance (NMR) spectroscopy to determine the nature and extent of the oxidation of biomolecules known to be present in carious dentin, plaque and saliva. Phosphate-buffered (pH 7.00) aqueous solutions containing sodium pyruvate, α-D-glucose, L-cys teine and L-methionine (5.00 mM) were treated with gaseous O3 (4.48 mmol.) delivered by a therapeutic O3 generating device. Attack of O3 on methionine and cysteine generated the corresponding primary oxidation products of these substrates, specifically methionine sulphoxide [98% ± 4% (mean ± SEM) yield] and cystine (95% ± 6% yield) respectively, and treatment of pyruvate with this oxidant produced acetate and CO2 via an oxidative decarboxylation process (93% ± 4% yield). Reaction of O3 with α-D-glucose gave rise to formate as a major product (24% ± 2% yield). In conclusion, multicomponent 1H NMR analysis of appropriate chemical model systems provides valuable molecular information regarding the reactivity of O3 towards biomolecules present in the oral environment, information which is of much relevance to its therapeutic mechanisms of action. Moreover, in view of the much higher concentrations of these O3-scavenging biomolecules in oral fluid and/or soft tissue environments than that of O3 applied, they may also serve to offer protection against putative adverse effects inducible by any of this oxidant which escapes from its site of therapeutic application (e.g., at primary root carious lesions).

Living Matter in Crash Test:How Biomolecules Respond to Mecha nical Forces

The Group on Protein Mechanics and Evolution at the CAS-MPG Partner Institute for Computational Biology,Shanghai,was established in January 2007 and headed by Dr.Frauke Gr?ter.The Klaus Tschira Lab has continued the eff orts of this former Independent Junior Research Group,since Dr.Gr?ter took up a position at the Heidelberg Institute of Theoretical Studies(HITS)in Heidelberg,Germany。

Investigation of photon energy absorption properties for some biomolecules

The mass energy absorption coefficient (len=q), effective atomic number (ZPEAeff ), and electron density (NPEAeff ) of some biomolecules with potential application in radiation dosimetry were calculated for their photon energy absorption (PEA) in the energy region of 1–20 MeV. It was noticed that the values of len=q, ZPEAeff , and NPEAeff vary with the energy and composition of the biomolecules. The results for ZPEAeff were compared with effective atomic numbers (ZPIeff ) owing to the photon interaction (PI). Significant differences were noted between ZPEAeff and ZPIeff in the energy region of 10–150 keV for all of the biomolecules involved. A maximum difference of 45.36% was observed at 50 keV for creatinine hydrochloride. Moreover, the studied attenuation parameters were found to be sharply affected at the K-absorption edge of relatively high-Z elements present in the biomolecules.

Real-Time and Spatial Electroanalysis of Biomolecules in One Living Cell Using Liquid-Phase Modified Nanopipette

The well-developed solid-phase modified strategy at the electrode has enabled the preparation of biosensors for the detection of multiple analytes,even in single living cells.However,limited assay elements can be modified at the solid surface,restricting the types of molecules that can be analyzed and the sensitivity of detection.Here,a novel liquid-phase modified strategy at the tip of a nanopipette is designed to realize real-time and local analysis of biomolecules inside the cell that are barely detectable using solid-phase modified nanoelectrodes.This design utilizes the nanotip structure at a platinized carbon open nanopipette to stably retain a nanodroplet that contains the required reagents with high reactivity for the assay of the target analyte.The generated hydrogen peroxide is electrochemically quantified at the Pt layer to carry out the real-time measurement in a living cell with a spatial resolution of 70 nm.Taking advantage of highly spatial and real-time detection,uneven distribution of sphingomyelinase(SMase)in the living CT26 cell is unprecedentedly shown to exhibit the significance in the establishment of liquid-phase modified nanopipette.This new modification strategy opens up a new direction for sensor design and consequently advances the development of biosensors in the chemical and biological research.

Advances in probing single biomolecules: From DNA bases to glycans

Imaging biomolecules in real space is crucial for gaining a comprehensive understanding of the properties and functions of biological systems at the most fundamental level.Among the various imaging techniques available for biomolecules and their assembled nanostructures,scanning probe microscopy(SPM)provides a powerful and nondestructive imaging option.SPM is unique in visualizing intrinsically disordered biomolecules at the nanometer scale(e.g.,glycans).This review highlights recent achievements in studying biomolecules using SPM technique,focusing on DNA bases,amino acids,proteins,and glycans.The atomic-level analysis of biomolecules made possible by SPM allows for a more accurate definition of the local structure–property relationship.High-resolution SPM imaging of single biomolecules offers a new way to study basic processes of life at the molecular level.

Manipulation and detection of single nanoparticles and biomolecules by a photonic nanojet

Optical methods to manipulate and detect nanoscale objects are highly desired in both nanomaterials and molecular biology fields.Optical tweezers have been used to manipulate objects that range in size from a few hundred nanometres to several micrometres.The emergence of near-field methods that overcome the diffraction limit has enabled the manipulation of objects below 100 nm.A highly free manipulation with signal-enhanced real-time detection,however,remains a challenge for single sub-100-nm nanoparticles or biomolecules.Here we show an approach that uses a photonic nanojet to perform the manipulation and detection of single sub-100-nm objects.With the photonic nanojet generated by a dielectric microlens bound to an optical fibre probe,three-dimensional manipulations were achieved for a single 85-nm fluorescent polystyrene nanoparticle as well as for a plasmid DNA molecule.Backscattering and fluorescent signals were detected with the enhancement factors up to~103 and~30,respectively.The demonstrated approach provides a potentially powerful tool for nanostructure assembly,biosensing and single-biomolecule studies.

Recent advances in molecular fluorescent probes for organic phosphate biomolecules recognition

Organic phosphate biomolecules(OPBs) are indispensable components of eukaryotes and prokaryotes,such as acting as the fundamental components of cell membranes and important substrates for nucleic acids. They play pivotal roles in various biological processes, such as energy conservation, metabolism,and signal modulation. Due to the difficulty of detection caused by variety OPBs, investigation of their respective physiological effects in organisms has been restrained by the lack of efficient tools. Many small fluorescent probes have been employed for selective detection and monitoring of OPBs in vitro or in vivo due to the advantages of tailored properties, biodegradability and in situ high temporal and spatial resolution imaging. In this review, we summarize the recent advances in fluorescent probes for OPBs,such as nucleotides, NAD(P)H, FAD/FMN and PS. Importantly, we describe their identification mechanisms in detail and discuss the general strategies for these OPBs probe designs, which provide new insights and ideas for the future probe designs.

Glassy dynamics of water at interface with biomolecules: A Mode Coupling Theory test

We study the slow dynamics of hydration water upon cooling in two different biological aqueous solutions,one containing a molecule of lysozyme and another with trehalose molecules.In particular we test if the glassy behaviour of these solutions fulfils the predictions of the popular Mode Coupling Theory of glassy dynamics.In particular we test the Time Temperature Superposition Principle and the matching of the exponents of the theory.Our results confirm that this theory is able to describe the dynamical behaviour of supercooled water also in non ideal cases as the ones under investigation in the region of mild supercooling.

Advances in the pathogenesis and clinical application prospects of tumor biomolecules in keloid

Keloid scarring is a kind of pathological healing manifestation after skin injury and possesses various tumor properties,such as the Warburg effect,epithelial-mesenchymal transition(EMT),expression imbalances of apoptosis-related genes and the presence of stem cells.Abnormal expression of tumor signatures is critical to the initiation and operation of these effects.Although previous experimental studies have recognized the potential value of a single or several tumor biomolecules in keloids,a comprehensive evaluation system for multiple tumor signatures in keloid scarring is still lacking.This paper aims to summarize tumor biomolecules in keloids from the perspectives of liquid biopsy,genetics,proteomics and epigenetics and to investigate their mechanisms of action and feasibility from bench to bedside.Liquid biopsy is suitable for the early screening of people with keloids due to its noninvasive and accurate performance.Epigenetic biomarkers do not require changes in the gene sequence and their reversibility and tissue specificity make them ideal therapeutic targets.Nonetheless,given the ethnic specificity and genetic predisposition of keloids,more large-sample multicenter studies are indispensable for determining the prevalence of these signatures and for establishing diagnostic criteria and therapeutic efficacy estimations based on these molecules.

One-dimensional and two-dimensional nanomaterials for the detection of multiple biomolecules

The complexity of biological samples determines that the detection of a single biomolecule is unable to satisfy actual needs. Moreover, the "false positives" results caused by a single biomolecule detections easily leads to erroneous clinical diagnosis and treatment. Thus, it is important for the homogenous quantification of multiple biomolecules in not only basic research but also practical application. As a consequent, a large number of literatures have been exploited to monitor multiple biomolecules in homogenous solution, enabling facilitating the development of the disease diagnosis, treatment as well as drug discovery. One-dimensional nanomaterials and two-dimensional nanomaterials have special physical and chemical properties, such as good electrochemical properties, stable structure, large specific surface area, and biocompatibility, which are widely used in electrochemical and fluorescent detection of biomolecules. This tutorial review highlights the recent development for the detection of multiple biomolecules by using nanomaterials including one-dimensional materials(1DMs) as well as twodimensional materials(2DMs).

Super-assembled sandwich-like Au@MSN@Ag nanomatrices for high-throughput and efficient detection of small biomolecules

Small biomolecules(m/z<500)are the material basis of organisms and participate in life activities,but their comprehensive and accurate detection in complex samples remains a challenge.Matrix-assisted laser desorption/ionization mass spectrometry(MALDI-MS)is a powerful detection tool for molecular analysis with high throughput.The development of a new matrix is essential to improve the efficiency of the MALDI-MS for molecular compound detection.In this work,the sandwich-like gold nanoparticles@mesoporous silica nanocomposite@silver nanoparticles(Au@MSN@Ag)nanospheres were prepared by layer-by-layer super-assembly strategy,and can be used as a novel matrix for the quantitative detection and enrichment of small biomolecules by LDI-MS.The sandwich-like nanospheres form a unique plasma resonant cavity that effectively absorbs the laser energy,while the homogeneous mesoporous structure of MSN can lock the analyte,which is essential for efficient LDI of small molecules.Compared to traditional matrices,Au@MSN@Ag shows the advantages of low background,wide application range,high sensitivity,super high salt and protein tolerance,and good stability.For example,the detection limit of glucose was as low as 5 fmol,and showed a good linear relationship in the range of 1−750μg/mL.Au@MSN@Ag assisted LDI-MS allows the enrichment and detection of small molecules in traditional Chinese medicine(TCM)without derivatization and purification,classification of herbs using the accurate quantitative results oligosaccharides,and identification of gelatin by amino acid content.This research could help in designing more efficient nanostructure matrices and further explored the application of LDI-MS.

Synergistic integration of metal nanoclusters and biomolecules as hybrid systems for therapeutic applications

Therapeutic nanoparticles are designed to enhance efficacy,real-time monitoring,targeting accuracy,biocompatibility,biodegradability,safety,and the synergy of diagnosis and treatment of diseases by leveraging the unique physicochemical and biological properties of well-developed bio-nanomaterials.Recently,bio-inspired metal nanoclusters(NCs)consisting of several to roughly dozens of atoms(<2 nm)have attracted increasing research interest,owing to their ultrafine size,tunable fluorescent capability,good biocompatibility,variable metallic composition,and extensive surface bio-functionalization.Hybrid coreeshell nanostructures that effectively incorporate unique fluorescent inorganic moieties with various biomolecules,such as proteins(enzymes,antigens,and antibodies),DNA,and specific cells,create fluorescently visualized molecular nanoparticle.The resultant nanoparticles possess combinatorial properties and synergistic efficacy,such as simplicity,active bio-responsiveness,improved applicability,and low cost,for combination therapy,such as accurate targeting,bioimaging,and enhanced therapeutic and biocatalytic effects.In contrast to larger nanoparticles,bio-inspired metal NCs allow rapid renal clearance and better pharmacokinetics in biological systems.Notably,advances in nanoscience,interfacial chemistry,and biotechnologies have further spurred researchers to explore bio-inspired metal NCs for therapeutic purposes.The current review presents a comprehensive and timely overview of various metal NCs for various therapeutic applications,with a special emphasis on the design rationale behind the use of biomolecules/cells as the main scaffolds.In the different hybrid platform,we summarize the current challenges and emerging perspectives,which are expected to offer in-depth insight into the rational design of bio-inspired metal NCs for personalized treatment and clinical translation.

Bioelectronic modulation of single-wavelength localized surface plasmon resonance (LSPR) for the detection of electroactive biomolecules

The simplification of localized surface plasmon resonance(LSPR) detection can further promote the development of optical biosensing application in point-of-care testing. In this study, we proposed a simple light emitting diode(LED) based single-wavelength LSPR sensor modulated with bio-electron transfers for the detection of electroactive biomolecules. Indium tin oxide electrode loaded with nanocomposites of polyaniline coated gold nanorod was used as LSPR chip, and the applied electric potential was scanned at the LSPR chip for single-wavelength LSPR biosensing. Under the scanning of applied potentials, biological electron transfer of redox reaction was employed to demonstrate the bioelectronic modulation of single-wavelength LSPR for selective electroactive biomolecule detection. Without any additional recognition material, electroactive biomolecules uric acid and dopamine were detected directly with a sensitivity of 5.05 μmol/L and 7.11 μmol/L at their specific oxidation potentials, respectively. With the simplified optical configuration and selective bioelectronic modulation, the single-wavelength LSPR sensor is promising for the development of simple, low-cost, and high specificity optical biosensor for point-of-care testing of electroactive biomolecules.

3D RNA nanocage for encapsulation and shielding of hydrophobic biomolecules to improve the in vivo biodistribution

Ribonucleic acid(RNA)nanotechnology platforms have the potential of harboring therapeutics for in vivo delivery in disease treatment.However,the nonspecific interaction between the harbored hydrophobic drugs and cells or other components before reaching the diseased site has been an obstacle in drug delivery.Here we report an encapsulation strategy to prevent such nonspecific hydrophobic interactions in vitro and in vivo based on a self-assembled three-dimensional(3D)RNA nanocage.By placing an RNA three-way junction(3WJ)in the cavity of the nanocage,the conjugated hydrophobic molecules were specifically positioned within the nanocage,preventing their exposure to the biological environment.The assembly of the nanocages was characterized by native polyacrylamide gel electrophoresis(PAGE),atomic force microscopy(AFM),and cryogenic electron microscopy(cryo-EM)imaging.The stealth effect of the nanocage for hydrophobic molecules in vitro was evaluated by gel electrophoresis,flow cytometry,and confocal microscopy.The in vivo sheathing effect of the nanocage for hydrophobic molecules was assessed by biodistribution profiling in mice.The RNA nanocages with hydrophobic biomolecules underwent faster clearance in liver and spleen in comparison to their counterparts.Therefore,this encapsulation strategy holds promise for in vivo delivery of hydrophobic drugs for disease treatment.