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Biomolecular Interactions (biomolecular + interaction)
Selected AbstractsProbing Biomolecular Interactions at Conductive and Semiconductive Surfaces by Impedance Spectroscopy: Routes to Impedimetric Immunosensors, DNA-Sensors, and Enzyme BiosensorsELECTROANALYSIS, Issue 11 2003Eugenii Katz Abstract Impedance spectroscopy is a rapidly developing electrochemical technique for the characterization of biomaterial-functionalized electrodes and biocatalytic transformations at electrode surfaces, and specifically for the transduction of biosensing events at electrodes or field-effect transistor devices. The immobilization of biomaterials, e.g., enzymes, antigens/antibodies or DNA on electrodes or semiconductor surfaces alters the capacitance and interfacial electron transfer resistance of the conductive or semiconductive electrodes. Impedance spectroscopy allows analysis of interfacial changes originating from biorecognition events at electrode surfaces. Kinetics and mechanisms of electron transfer processes corresponding to biocatalytic reactions occurring at modified electrodes can be also derived from Faradaic impedance spectroscopy. Different immunosensors that use impedance measurements for the transduction of antigen-antibody complex formation on electronic transducers were developed. Similarly, DNA biosensors using impedance measurements as readout signals were developed. Amplified detection of the analyte DNA using Faradaic impedance spectroscopy was accomplished by the coupling of functionalized liposomes or by the association of biocatalytic conjugates to the sensing interface providing biocatalyzed precipitation of an insoluble product on the electrodes. The amplified detections of viral DNA and single-base mismatches in DNA were accomplished by similar methods. The changes of interfacial features of gate surfaces of field-effect transistors (FET) upon the formation of antigen-antibody complexes or assembly of protein arrays were probed by impedance measurements and specifically by transconductance measurements. Impedance spectroscopy was also applied to characterize enzyme-based biosensors. The reconstitution of apo-enzymes on cofactor-functionalized electrodes and the formation of cofactor-enzyme affinity complexes on electrodes were probed by Faradaic impedance spectroscopy. Also biocatalyzed reactions occurring on electrode surfaces were analyzed by impedance spectroscopy. The theoretical background of the different methods and their practical applications in analytical procedures were outlined in this article. [source] Tuning Specific Biomolecular Interactions Using Electro-Switchable Oligopeptide SurfacesADVANCED FUNCTIONAL MATERIALS, Issue 16 2010Chun L. Yeung Abstract The ability to regulate biomolecular interactions on surfaces driven by an external stimuli is of great theoretical interest and practical impact in the biomedical and biotechnology fields. Herein, a new class of responsive surfaces that rely on electro-switchable peptides to control biomolecular interactions on gold surfaces is presented. This system is based upon the conformational switching of positively charged oligolysine peptides that are tethered to a gold surface, such that bioactive molecular moieties (biotin) incorporated on the oligolysines can be reversibly exposed (bio-active state) or concealed (bio-inactive state) on demand, as a function of surface potential. The dynamics of switching the biological properties is studied by observing the binding events between biotin and fluorescently labeled NeutrAvidin. Fluorescence microscope images and surface plasmon resonance spectral data clearly reveal opposite binding behaviors when +0.3 V or ,0.4 V vs. SCE are applied to the surface. High fluorescence intensities are observed for an applied positive potential, while minimal fluorescence is detected for an applied negative potential. Surface plasmon resonance spectroscopy (SPR) results provided further evidence that NeutrAvidin binding to the surface is controlled by the applied potential. A large SPR response is observed when a positive potential is applied on the surface, while a negative applied potential induces over 90% reduction in NeutrAvidin binding. [source] Functionalization of Gold and Glass Surfaces with Magnetic Nanoparticles Using Biomolecular InteractionsBIOTECHNOLOGY PROGRESS, Issue 1 2006Bala G. Nidumolu Advances in nanotechnology have enabled the production and characterization of magnetic particles with nanometer-sized features that can be functionalized with biological recognition elements for numerous applications in biotechnology. In the present study, the synthesis of and interactions between self-assembled monolayers (SAMs) on gold and glass surfaces and functionalized magnetic nanoparticles have been characterized. Immobilization of 10,15 nm streptavidin-functionalized nanoparticles to biotinylated gold and glass surfaces was achieved by the strong interactions between biotin and streptavidin. Fluorescent streptavidin-functionalized nanoparticles, biotinylated surfaces, and combinations of the two were characterized by Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and electron and fluorescent microscopy to confirm that little or no functionalization occurred in nonbiotinylated regions of the gold and glass surfaces compared to the biotinylated sites. Together these techniques have potential use in studying the modification and behavior of functionalized nanoparticles on surfaces in biosensing and other applications. [source] Chemical Micropatterning of Polycarbonate for Site-Specific Peptide Immobilization and Biomolecular InteractionsCHEMBIOCHEM, Issue 3 2007Olivier Carion Dr. Abstract Polycarbonate (PC) is a useful substrate for the preparation of microfluidic devices. Recently, its utility in bioanalysis has attracted much attention owing to the possibility of using compact discs as platforms for the high-throughput analysis of biomolecular interactions. In this article we report a novel method for the chemical micropatterning of polycarbonate based on the printing of functionalized silica nanoparticles. The semicarbazide groups present on the surface of the nanoparticles were used for the site-specific semicarbazone ligation of unprotected peptides derivatized by an ,-oxoaldehyde group. The peptide micropatterns permitted the specific capture of antibodies. We report also the characterization of micropatterns on PC by using a wide-field optical imaging technique called Sarfus; this allows the detection of nm-thick films by using nonreflecting PC substrates and an optical microscope working with reflected differential interference contrast. The method described here is an easy way to modify polycarbonate surfaces for biomolecular interaction studies and should stimulate the use of PC for developing plastic biosensors. [source] Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interactionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2010Ling Wang Abstract Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Prussian Blue Dispersed Sphere Catalytic Labels for Amplified Electronic Detection of DNAELECTROANALYSIS, Issue 3 2008Siriwan Suwansa-ard Abstract A highly sensitive electrochemical DNA hybridization assay using Prussian blue (PB)-modified polymeric spheres as the oligonculeotide labeling tag is described. The sandwich assay relies on a secondary nucleic-acid probe functionalized with polystyrene beads loaded with numerous Prussian blue nanoparticles. The very strong catalytic activity of the captured PB ,artificial peroxidase' tag towards the reduction of hydrogen peroxide, along with the encapsulation of numerous catalytic particles onto polymeric beads, allows amperometric detection of the DNA target down to the 50,fM level (2.5,amol). Imaging and spectroscopic measurements are used to characterize the PB-tagged polystyrene beads. Such coupling of PB catalytic labels with polymeric carrier beads offers great promise for amplified transduction of different biomolecular interactions. [source] Tuning Specific Biomolecular Interactions Using Electro-Switchable Oligopeptide SurfacesADVANCED FUNCTIONAL MATERIALS, Issue 16 2010Chun L. Yeung Abstract The ability to regulate biomolecular interactions on surfaces driven by an external stimuli is of great theoretical interest and practical impact in the biomedical and biotechnology fields. Herein, a new class of responsive surfaces that rely on electro-switchable peptides to control biomolecular interactions on gold surfaces is presented. This system is based upon the conformational switching of positively charged oligolysine peptides that are tethered to a gold surface, such that bioactive molecular moieties (biotin) incorporated on the oligolysines can be reversibly exposed (bio-active state) or concealed (bio-inactive state) on demand, as a function of surface potential. The dynamics of switching the biological properties is studied by observing the binding events between biotin and fluorescently labeled NeutrAvidin. Fluorescence microscope images and surface plasmon resonance spectral data clearly reveal opposite binding behaviors when +0.3 V or ,0.4 V vs. SCE are applied to the surface. High fluorescence intensities are observed for an applied positive potential, while minimal fluorescence is detected for an applied negative potential. Surface plasmon resonance spectroscopy (SPR) results provided further evidence that NeutrAvidin binding to the surface is controlled by the applied potential. A large SPR response is observed when a positive potential is applied on the surface, while a negative applied potential induces over 90% reduction in NeutrAvidin binding. [source] Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognitionGENES TO CELLS, Issue 5 2000Masayuki Oda Thermodynamic and kinetic analyses of biomolecular interactions reveal details of the energetic and dynamic features of molecular recognition processes, and complement structural analyses of the free and complexed conformations. The recent improvements in both isothermal titration calorimetry and surface plasmon resonance sensoring provide powerful tools for analysing biomolecular interactions in thermodynamic and kinetic approaches. The thermodynamic and kinetic parameters obtained for binding between protein and DNA indicate the mechanism of specific DNA recognition, in the high-resolution structures of the protein,DNA complexes. The effects of temperature and ionic strength reflect the conformational changes of the protein and DNA molecules upon complex formation, including important contributions of water and solutes. When combined with mutational studies, the interactions can be reduced to several energetic contributions from individual contacts. These studies should be useful to determine general features of protein functions in genetic regulation. [source] Applications of Nanoparticles in Biology,ADVANCED MATERIALS, Issue 22 2008Mrinmoy De Abstract The wide variety of core materials available, coupled with tunable surface properties, make nanoparticles an excellent platform for a broad range of biological and biomedical applications. This Review provides an introduction to nanoparticle,biomolecular interactions as well as recent applications of nanoparticles in biological sensing, delivery, and imaging of live cells and tissues. [source] Complex molecular assemblies at hand via interactive simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2009Olivier Delalande Abstract Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N -ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid,protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactionsJOURNAL OF MOLECULAR RECOGNITION, Issue 3 2007Matthew A. Cooper Abstract The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally ,bulk acoustic wave' (BAW), ,thickness shear mode' (TSM) sensors or ,quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed. Copyright © 2007 John Wiley & Sons, Ltd. [source] A survey of the year 2002 literature on applications of isothermal titration calorimetryJOURNAL OF MOLECULAR RECOGNITION, Issue 6 2003Matthew J. Cliff Abstract Isothermal titration calorimetry (ITC) is becoming widely accepted as a key instrument in any laboratory in which quantification of biomolecular interactions is a requisite. The method has matured with respect to general acceptance and application development over recent years. The number of publications on ITC has grown exponentially over the last 10 years, reflecting the general utility of the method. Here all the published works of the year 2002 in this area have been surveyed. We review the broad range of systems to which ITC is being directed and classify these into general areas highlighting key publications of interest. This provides an overview of what can be achieved using this method and what developments are likely to occur in the near future. Copyright © 2003 John Wiley & Sons, Ltd. [source] BIACORE J: a new platform for routine biomolecular interaction analysis,JOURNAL OF MOLECULAR RECOGNITION, Issue 4 2001Rebecca L. Rich Abstract SPR biosensor technology continues to evolve. The recently released platform from Biacore AB (Uppsala, Sweden), BIACORE J, is designed for the routine analysis of biomolecular interactions. Using an antibody,protein A and a ligand,receptor system, we demonstrate the utility of BIACORE J in determining active concentration and binding affinities. The results from these studies illustrate the high sensitivity of the instrument and its ability to generate reproducible binding responses. The BIACORE J is easy to operate and useful in diverse applications, making SPR technology widely accessible as a research tool. Copyright © 2001 John Wiley & Sons, Ltd. [source] Surface plasmon resonance label-free monitoring of antibody antigen interactions in real timeBIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 1 2007Asta Kausaite Abstract Detection of biologically active compounds is one of the most important topics in molecular biology and biochemistry. One of the most promising detection methods is based on the application of surface plasmon resonance for label-free detection of biologically active compounds. This method allows one to monitor binding events in real time without labeling. The system can therefore be used to determine both affinity and rate constants for interactions between various types of molecules. Here, we describe the application of a surface plasmon resonance biosensor for label-free investigation of the interaction between an immobilized antigen bovine serum albumin (BSA) and antibody rabbit anti-cow albumin IgG1 (anti-BSA). The formation of a self-assembled monolayer (SAM) over a gold surface is introduced into this laboratory training protocol as an effective immobilization method, which is very promising in biosensing systems based on detection of affinity interactions. In the next step, covalent attachment via artificially formed amide bonds is applied for the immobilization of proteins on the formed SAM surface. These experiments provide suitable experience for postgraduate students to help them understand immobilization of biologically active materials via SAMs, fundamentals of surface plasmon resonance biosensor applications, and determination of non-covalent biomolecular interactions. The experiment is designed for master and/or Ph.D. students. In some particular cases, this protocol might be adoptable for bachelor students that already have completed an extended biochemistry program that included a background in immunology. [source] Effects of 100 GHz radiation on alkaline phosphatase activity and antigen,antibody interaction,BIOELECTROMAGNETICS, Issue 3 2009A. Homenko Abstract Equipment that generates microwave radiation (MWR) spanning the frequency range of 300 MHz,100 GHz is becoming more common. While MWR lacks sufficient energy to break chemical bonds, the disagreement as to whether MWR exposure is detrimental to cellular dysfunction may be difficult to clarify using complex systems such as whole animals, cells, or cell extracts. Recently, the high frequency range of terahertz (THz) radiation has been explored and sources of radiation and its detectors have been developed. THz radiation is associated with the frequency interval from 100 GHz to 20 THz and constitutes the next frontier in imaging science and technology. In the present study, we investigated the effect of radiation in the low frequency THz range (100 GHz) on two defined molecular interactions. First, the interaction of soluble or immobilized calf alkaline phosphatase with the substrate p -nitrophenylphosphate and second, the interaction between an antibody (mouse monoclonal anti-DNP) and its antigen (DNP). Irradiation of enzyme either prior to addition of substrate or during the enzymatic reaction resulted in small but significant reductions in enzyme activity. These differences were not observed if the enzyme had previously been immobilized onto plastic microwells. Exposure of immobilized antigen to radiation did not influence the ability of the antigen to interact with antibody. However, irradiation appeared to decrease the stability of previously formed antigen,antibody complexes. Our data suggest that 100 GHz radiation can induce small but statistically significant alterations in the characteristics of these two types of biomolecular interactions. Bioelectromagnetics 30:167,175, 2009. © 2008 Wiley-Liss, Inc. [source] Chemical Micropatterning of Polycarbonate for Site-Specific Peptide Immobilization and Biomolecular InteractionsCHEMBIOCHEM, Issue 3 2007Olivier Carion Dr. Abstract Polycarbonate (PC) is a useful substrate for the preparation of microfluidic devices. Recently, its utility in bioanalysis has attracted much attention owing to the possibility of using compact discs as platforms for the high-throughput analysis of biomolecular interactions. In this article we report a novel method for the chemical micropatterning of polycarbonate based on the printing of functionalized silica nanoparticles. The semicarbazide groups present on the surface of the nanoparticles were used for the site-specific semicarbazone ligation of unprotected peptides derivatized by an ,-oxoaldehyde group. The peptide micropatterns permitted the specific capture of antibodies. We report also the characterization of micropatterns on PC by using a wide-field optical imaging technique called Sarfus; this allows the detection of nm-thick films by using nonreflecting PC substrates and an optical microscope working with reflected differential interference contrast. The method described here is an easy way to modify polycarbonate surfaces for biomolecular interaction studies and should stimulate the use of PC for developing plastic biosensors. [source] | ||||||||||||||||