Optical molecular imaging for systems biology: from molecule to organism

The development of highly efficient analytical methods capable of probing biological systems at system level is an important task that is required in order to meet the requirements of the emerging field of systems biology. Optical molecular imaging (OMI) is a very powerful tool for studying the temporal and spatial dynamics of specific biomolecules and their interactions in real time in vivo. In this article, recent advances in OMI are reviewed extensively, such as the development of molecular probes that make imaging brighter, more stable and more informative (e.g., FPs and semiconductor nanocrystals, also referred to as quantum dots), the development of imaging approaches that provide higher resolution and greater tissue penetration, and applications for measuring biological events from molecule to organism level, including gene expression, protein and subcellular compartment localization, protein activation and interaction, and low-mass molecule dynamics. These advances are of great significance in the field of biological science and could also be applied to disease diagnosis and pharmaceutical screening. Further developments in OMI for systems biology are also proposed.     

Molecular imprinting: a dynamic technique for diverse applications in analytical chemistry

Continuous advances in analyzing complex matrices, improving reliability and simplicity, and performing multiple simultaneous assays with extreme sensitivity are increasing. Several techniques have been developed for the quantitative assays of analytes at low concentrations (e.g., high-pressure liquid chromatography, gas chromatography, immunoassay and the polymerase chain reaction technique). To achieve highly specific and sensitive analysis, high affinity, stable, and specific recognition agents are needed. Although biological recognition agents are very specific and sensitive they are labile and/or have a low density of binding sites. During the past decade molecular imprinting has emerged as an attractive and highly accepted tool for the development of artificial recognition agents. Molecular imprinting is achieved by the interaction, either noncovalent or covalent, between complementary groups in a template molecule and functional monomer units through polymerization or polycondensation. These molecularly imprinted polymers have been widely employed for diverse applications (e.g., in chromatographic separation, drug screening, chemosensors, catalysis, immunoassays etc.) owing to their specificity towards the target molecules and high stability against physicochemical perturbations. In this review the advantages, applications, and recent developments in molecular imprinting technology are highlighted.     

High-density synthetic peptide microarrays: emerging tools for functional genomics and proteomics

New approaches for manufacturing and application of peptide arrays on planar surfaces are emerging, thereby opening advanced opportunities to probe the expression and function of the proteome. In complementing DNA and protein array analyses, peptide fragment screening directly addresses functional protein interaction sites, leading to a detailed insight into the discovered molecular recognition events, placing them in the context of the whole genome, and even allowing rapid determination of the chemical nature of these interactions. This information can then be transferred into powerful small peptide tools that interfere with these interactions in vivo and help to link targets with phenotypes. With the spreading of new peptide array tools, peptide screening will extend its impact on modern genome-driven molecular biology. This will advance the systematic discovery and validation of new pharmaceutical targets as well as the development of potent molecular diagnostics for medical and ecological monitoring.     

Analysis of drug interactions with serum proteins and related binding agents by affinity capillary electrophoresis: A review

Biomolecules such as serum proteins can interact with drugs in the body and influence their pharmaceutical effects. Specific and precise methods that analyze these interactions are critical for drug development or monitoring and for diagnostic purposes. Affinity capillary electrophoresis (ACE) is one technique that can be used to examine the binding between drugs and serum proteins, or other agents found in serum or blood. This article will review the basic principles of ACE, along with related affinity-based capillary electrophoresis (CE) methods, and examine recent developments that have occurred in this field as related to the characterization of drug–protein interactions. An overview will be given of the various formats that can be used in ACE and CE for such work, including the relative advantages or weaknesses of each approach. Various applications of ACE and affinity-based CE methods for the analysis of drug interactions with serum proteins and other binding agents will also be presented. Applications of ACE and related techniques that will be discussed include drug interaction studies with serum agents, chiral drug separations employing serum proteins, and the use of CE in hybrid methods to characterize drug binding with serum proteins.     

Synthetic polymer nanoparticle-polysaccharide interactions: a systematic study

The interaction between synthetic polymer nanoparticles (NPs) and biomacromolecules (e.g., proteins, lipids, and polysaccharides) can profoundly influence the NPs fate and function. Polysaccharides (e.g., heparin/heparin sulfate) are a key component of cell surfaces and the extracelluar matrix and play critical roles in many biological processes. We report a systematic investigation of the interaction between synthetic polymer nanoparticles and polysaccharides by ITC, SPR, and an anticoagulant assay to provide guidelines to engineer nanoparticles for biomedical applications. The interaction between acrylamide nanoparticles (~30 nm) and heparin is mainly enthalpy driven with submicromolar affinity. Hydrogen bonding, ionic interactions, and dehydration of polar groups are identified to be key contributions to the affinity. It has been found that high charge density and cross-linking of the NP can contribute to high affinity. The affinity and binding capacity of heparin can be significantly diminished by an increase in salt concentration while only slightly decreased with an increase of temperature. A striking difference in binding thermodynamics has been observed when the main component of a polymer nanoparticle is changed from acrylamide (enthalpy driven) to N-isopropylacryalmide (entropy driven). This change in thermodynamics leads to different responses of these two types of polymer NPs to salt concentration and temperature. Select synthetic polymer nanoparticles have also been shown to inhibit protein-heparin interactions and thus offer the potential for therapeutic applications.     

Bioanalytical interaction studies executed by preincubation affinity capillary electrophoresis

The versatility of CE is beneficial for the study of many types of molecular interactions, because different experimental designs can be made to suit the characteristics of a particular interaction. A very versatile starting point is the preequilibration type of affinity CE that has been used extensively for characterizing biomolecular interactions in the last 15 years. We review this field here and include a comprehensive overview of the existing preincubation ACE modes including their advantages and limitations as well as the methodological developments and applications within the bioanalytical field.     

Developments in the production of biological and synthetic binders for immunoassay and sensor-based detection of small molecules

The need for chemical and biological entities of predetermined selectivity and affinity towards target analytes is greater than ever, in applications such as environmental monitoring, bioterrorism detection and analysis of natural toxin contaminants in the food chain.In this review, we focus on advances in the production of specific binders, in terms of both natural entities (e.g., antibodies) and synthetic binders (e.g., molecularly-imprinted polymers). We discuss the potential of emerging technologies for integration into immunoassay and sensing techniques. We place special emphasis on use of these technologies in bioanalytical applications.     

Applications of affinity interactions in capillary electrophoresis

Capillary electrophoresis (CE) has proven useful for the study of reversible molecular interactions. This is because highly efficient and reproducible separations take place in an environment where molecular interactions may contribute to selectivity without being inhibited by adverse buffer conditions. Affinity CE may be used to estimate quantitative binding data (binding constants and in some cases binding stoichiometries and rate constants) for various molecular interactions. Specific binding interactions (e.g., based on antibodies or aptamers) may also be utilized to quantitatively measure specific analytes using CE. Applications within these areas are here reviewed with focus on the last three years and with emphasis on novel concepts as well as innovative methodology and technology. It is concluded that the affinity CE approach is of growing versatility and will continue to play an integral role in discovering, characterizing, and exploiting biomolecular interactions.     

Metallacarboranes and their interactions: theoretical insights and their applicability

This tutorial review will deal with the study of metallacarboranes and their interactions with other molecules from a theoretical point of view. This contribution is devoted to guide experimental chemists through calculations that some years ago were reserved to theoretical specialists. The widespread availability of fast computers enables nowadays studies of complex compounds (e.g. metallacarboranes) from different perspectives including simulation of NMR, infrared or Raman spectra and calculation of other properties such as atomic charges or inter-/intramolecular interactions. The insights gained on the basis of theoretical calculations are crucial for either finding novel or improving existing applications of metallacarboranes. For example, in the case of enzyme inhibitors, the interactions of the metallacarboranes with the surrounding protein and how the interaction affects the efficiency are difficult problems to study experimentally. The use of theoretical tools can provide a detailed understanding of the physico-chemical basis of the interactions and thus offers a chance to control the overall process.     

Mass spectrometry-based proteomics: existing capabilities and future directions

Mass spectrometry (MS)-based proteomics is emerging as a broadly effective means for identification, characterization, and quantification of proteins that are integral components of the processes essential for life. Characterization of proteins at the proteome and sub-proteome (e.g., the phosphoproteome, proteoglycome, or degradome/peptidome) levels provides a foundation for understanding fundamental aspects of biology. Emerging technologies such as ion mobility separations coupled with MS and microchip-based-proteome measurements combined with MS instrumentation and chromatographic separation techniques, such as nanoscale reversed phase liquid chromatography and capillary electrophoresis, show great promise for both broad undirected and targeted highly sensitive measurements. MS-based proteomics increasingly contribute to our understanding of the dynamics, interactions, and roles that proteins and peptides play, advancing our understanding of biology on a systems wide level for a wide range of applications including investigations of microbial communities, bioremediation, and human health.     

Determining nanomaterials in food

Nanotechnology has emerged as one of the most innovative technologies and has the potential to improve food quality and safety. However, there are a few studies demonstrating that nanomaterials (NMs) are not inherently benign.This review highlights some current applications of NMs in food, food additives and food-contact materials, and reviews analytical approaches suitable to address food-safety issues related to nanotechnology.We start with a preliminary discussion on the current regulatory situation with respect to nanotechnology in relation to foods. We cover sample preparation, imaging techniques (e.g., electron microscopy, scanning electron microscopy and X-ray microscopy), separation methods (e.g., field-flow fractionation and chromatographic techniques) and detection or characterization techniques (e.g., light scattering, Raman spectroscopy and mass spectrometry). We also show the first applications of the analysis of NMs in food matrices.     

Recent advances on noncovalent molecular imprints for affinity separations

Molecularly imprinted polymers (MIPs) are tailor-made synthetic materials capable of selectively rebinding a target analyte, or a group of structurally related compounds based on a combination of recognition mechanisms including size, shape, and functionality. Among the advantageous properties of MIPs are the achievable specific affinity, the relative ease of preparation, and their mechanical and chemical robustness, which renders them ideal materials for applications as stationary phase (e. g., affinity chromatography or SPE), or as antibody mimics (e. g., biomimetic assays). Here, we review recent advancements on the application of MIPs in affinity separations and biomimetic assays, which have focused on the synthesis of size- and shape-uniform particles facilitating reproducibility, improved binding site accessibility, and enhanced affinity. While MIPs certainly offer promising potential as selective separation phase in a variety of applications, deeper understanding of the fundamental interactions governing imprinting, and rational understanding of the imprinting mechanism has yet to be achieved for providing rational guidelines in deliberately designing next-generation MIP materials.     

色谱技术在药物-血浆蛋白相互作用研究中的应用进展

小分子药物进入人体血液循环系统后与人血清白蛋白(HSA)、α₁ -酸性糖蛋白(AGP)等血浆蛋白存在广泛的相互作用,这些相互作用深刻影响药物在体内的分布及其与靶标蛋白的结合,进而影响药物效应的发挥。深入探究药物与血浆蛋白间的相互作用对于候选药物的成药性优化、新药研发、联合用药的风险评控等意义重大。而发展高效、灵敏、准确的分析检测方法是开展药物-血浆蛋白相互作用研究的关键。近年来,色谱技术由于其高通量、高分离性能、高灵敏度等特点在该领域得到了广泛的应用,包括测定血浆蛋白翻译后修饰对药物结合的影响,多种药物的竞争性结合等。其中,高效亲和色谱(HPAC)和毛细管电泳(CE)应用最为广泛,能够通过多种分析方法获取结合常数、结合位点数、解离速率常数等相互作用信息。该文着重综述了HPAC和CE在药物-血浆蛋白相互作用研究中的常用策略及最新研究进展,包括HPAC中常用的前沿色谱法、竞争洗脱法、超快亲和提取法、峰值分析法和峰衰减分析法,以及CE中常用的亲和毛细管电泳法(ACE)和毛细管电泳前沿分析法(CE-FA)等。最后,该文还对当前色谱方法存在的不足进行了总结,并对色谱技术在药物-血浆蛋白相互作用研究领域的应用前景和发展方向进行了展望。     

Affinity capillary electrophoresis on microchips

The present study shows that the application of the method of affinity capillary electrophoresis (ACE) to investigate interactions between ligands and their substrates can be realized on microchips. With ACE it is possible to characterize non-covalent molecular interactions (complexation and partition equilibria). Binding constants (K(B)) provide a measured value of the affinity of a ligand molecule to a substrate, which is basic information for the understanding of hormones, drugs and their targets, e.g. receptors in the human body. A microchip electrophoresis instrument equipped with a UV-detector and a home-built chip-station with electrochemical detection were used. ACE could be achieved with model solutions of neurotransmitters using sulfated beta-cyclodextrin (sCD) as substrate in a background buffer. This paper describes the advantages of microchip-ACE (MC-ACE) to traditional affinity capillary electrophoresis on a capillary. The results show that MC-ACE has great potential as a tool for fast scanning of interactions and to calculate binding constants of ligands with their substrates.     

Direct optical sensors: principles and selected applications

In the field of bio and chemosensors a large number of detection principles has been published within the last decade. These detection principles are based either on the observation of fluorescence-labelled systems or on direct optical detection in the heterogeneous phase. Direct optical detection can be measured by remission (absorption of reflected radiation, opt(r)odes), by measuring micro-refractivity, or measuring interference. In the last case either Mach–Zehnder interferometers or measurement of changes in the physical thickness of the layer (measuring micro-reflectivity) caused, e.g., by swelling effects in polymers (due to interaction with analytes) or in bioassays (due to affinity reactions) also play an important role. Here, an overview of methods of microrefractometric and microreflectometric principles is given and benefits and drawbacks of the various approaches are demonstrated using samples from the chemo and biosensor field. The quality of sensors does not just depend on transduction principles but on the total sensor system defined by this transduction, the sensitive layer, data acquisition electronics, and evaluation software. The intention of this article is, therefore, to demonstrate the essentials of the interaction of these parts within the system, and the focus is on optical sensing using planar transducers, because fibre optical sensors have been reviewed in this journal only recently. Lack of selectivity of chemosensors can be compensated either by the use of sensor arrays or by evaluating time-resolved measurements of analyte/sensitive layer interaction. In both cases chemometrics enables the quantification of analyte mixtures. These data-processing methods have also been successfully applied to antibody/antigen interactions even using cross-reactive antibodies. Because miniaturisation and parallelisation are essential approaches in recent years, some aspects and current trends, especially for bio-applications, will be discussed. Miniaturisation is especially well covered in the literature.     

Silatranes: a review on their synthesis, structure, reactivity and applications

This critical review summarizes progress of the rapidly developing and very active field of silatrane chemistry. The first part of the review deals with general synthetic approaches used to synthesize different silatranes. The most interesting feature of silatranes, i.e., variation of Si-N bond length on the basis of the axial substituent of Si, and other structural features, are described in the second part with special emphasis on crystallographic and theoretical studies. It is followed by a discussion on the reactivity of various silatranes. Silatranes have now gained acceptance for a wide variety of applications which are summarized in the last section of review. Some of them have extensive interest due to their medical use to heal wounds or stimulate hair-growth (pilotropic activity), biological properties, pharmacological properties e.g. antitumor, anticancer, antibacterial, anti-inflammatory, fungicidal activity, stimulating effect in animal production and seed germination effects. The review focuses on the extended potential of silatranes in sol-gel processes, mesoporous zeotypes, atomic force microscopy, commercial products such as adhesion promoters, polymer formation and rubber compositions. This critical review will be helpful for general researchers, experts, advanced undergraduates and newcomers working on silatrane chemistry as this review presents greater emphasis on synthesis and characterization, structural properties, reactivity and applications of silatranes in the field of biology, material science, sol-gel chemistry, pharmaceutics, agriculture and medicine (311 references).     

Determination of the binding parameters for antithrombin-heparin fragment systems by affinity and frontal analysis continuous capillary electrophoresis

The suitability of affinity capillary electrophoresis (ACE) and frontal analysis continuous capillary electrophoresis (FACCE) for binding constant determination was investigated for complexes between heparin fragments and antithrombin III, one of the main target proteins in the coagulation cascade. In a 100 mM ionic strength phosphate buffer (pH 7.4), ACE was suitable to determine weak to medium interactions developed by short oligomeric heparin fragments, but it failed for decasaccharide, which presents a more complex irreversible interaction. However FACCE allowed evaluating the binding constant for these longer oligomeric fragments. Both experimental approaches were complementary for a wide variety of heparinic fragments.     

Paper-based enzyme-free immunoassay for rapid detection and subtyping of influenza A H1N1 and H3N2 viruses

Development of rapid screening in the ambulatory environment is the most pressing needs for the control of spread of infectious disease. Despite there are many methods to detect the immunoassay results, quantitative measurement in rapid disease screening is still a great challenge for point-of-care applications. In this work, based on the internal structural protein, i.e., nucleoprotein (NP), and outer surface glycoproteins, i.e., H1 and H3, of the influenza viruses, specific and sensitive immunoassay on paper-based platform was evaluated and confirmed. Detection and subtyping of influenza A H1N1 and H3N2 viruses found in people were demonstrated by colorimetric paper-based sandwich immunoassay. Concentration-dependent response to influenza viruses was shown and the detection limits could achieve 2.7 × 10³ pfu/assay for H1 detection and 2.7 × 10⁴ pfu/assay for H3 detection, which are within the clinical relevant level. Moreover, detection of influenza virus from infected cell lysate and clinical samples was demonstrated to further confirm the reliability of the paper-based immunoassay. The use of paper for the development of diagnostic devices has the advantages of lightweight, ease-of-use, and low cost and paper-based immunoassay is appropriate to apply for rapid screening in point-of-care applications.     

Nonadditivity of polymeric and charged surface interactions: consequences for doped lamellar phases

We explore theoretically the modifications to the interactions between charged surfaces across an ionic solution caused by the presence of dielectric polymers. Although the chains are neutral, the polymer physics and the electrostatics are coupled; the intrasurface electric fields polarize any low-permittivity species (e.g., polymer) dissolved in a high-permittivity solvent (e.g., water). This coupling enhances the polymer depletion from the surfaces and increases the screening of electrostatic interactions with respect to a model which treats polymeric and electrostatic effects as independent. As a result, the range of the ionic contribution to the osmotic interaction between surfaces is decreased while that of the polymeric contribution is increased. These changes modify the total interaction in a nonadditive manner. Building on the results for parallel surfaces, we investigate the effect of this coupling on the phase behavior of polymer-doped smectics.