Probe-analyte complex

Direct quantitative MS probe for complex analyte mixture (5)... 

The lifetime of the excited state of fluorophores may be altered by physical and biochemical properties of its environment. Fluorescence lifetime imaging microscopy (FLIM) is thus a powerful analytical tool for the quantitative mapping of fluorescent molecules that reports, for instance, on local ion concentration, pH, and viscosity, the fluorescence lifetime of a donor fluorophore, Forster resonance energy transfer can be also imaged by FLIM. This provides a robust method for mapping protein-protein interactions and for probing the complexity of molecular interaction networks. 

References. Because the detected fluorescence signal is a direct response of the dye-analyte complex formed, no reference measurement is required. Also no calibration of the probe is required, although the response function of the probe may be needed. 

Although previous applications of this technique in our laboratory had been concerned with aquatic animal metabolism of pesticides such as DDT, parathion, carbaryl, and trifluralin (14, 15), we also became interested in comparing metabolic routesljy means of a "metabolic probe". Such a compound ideally should be stable to nonbiological degradation, of low toxicity to maximize the dose, and subject to as many major routes of metabolism as possible without undue analytical complexity. 

Fluorescent Equilibrium Probes. Himel and co-workers (23, 24, 25) have synthesized active-site-directed fluorescent equihbrium probes which are competitive inhibitors of the active site of cholinesterase enzymes. The fluorescence intensity of the probe-enzyme complex is decreased by any foreign molecule (insecticide) which competes with the equilibrium fluorescent probe for the active site of the enzyme or which changes the equilibrium dynamics by exo area reaction with the enzyme. This highly specific and sensitive spectroscopic method is being developed as an analytical method for insecticides (26). 

The complex of the following destmctive and nondestmctive analytical methods was used for studying the composition of sponges inductively coupled plasma mass-spectrometry (ICP-MS), X-ray fluorescence (XRF), electron probe microanalysis (EPMA), and atomic absorption spectrometry (AAS). Techniques of sample preparation were developed for each method and their metrological characteristics were defined. Relative standard deviations for all the elements did not exceed 0.25 within detection limit. The accuracy of techniques elaborated was checked with the method of additions and control methods of analysis. 

It is particularly important to study process phenomena under dynamic (rather than static) conditions. Most current analytical techniques are designed to determine the initial and final states of a material or process. Instmments must be designed for the analysis of materials processing in real time, so that the cmcial chemical reactions in materials synthesis and processing can be monitored as they occur. Recent advances in nuclear magnetic resonance and laser probes indicate valuable lines of development for new techniques and comparable instmmentation for the study of interfaces, complex hquids, microstmctures, and hierarchical assemblies of materials. Instmmentation needs for the study of microstmctured materials are discussed in Chapter 9. 

As an analytical method becomes more complex, the number of factors is likely to increase and the likelihood is that the simple approach to experimental design described above will not be successful. In particular, the possibility of interaction between factors that will have an effect on the experimental outcome must be considered and factorial design [2] allows such interactions to be probed. 

The use of computer simulations to study internal motions and thermodynamic properties is receiving increased attention. One important use of the method is to provide a more fundamental understanding of the molecular information contained in various kinds of experiments on these complex systems. In the first part of this paper we review recent work in our laboratory concerned with the use of computer simulations for the interpretation of experimental probes of molecular structure and dynamics of proteins and nucleic acids. The interplay between computer simulations and three experimental techniques is emphasized (1) nuclear magnetic resonance relaxation spectroscopy, (2) refinement of macro-molecular x-ray structures, and (3) vibrational spectroscopy. The treatment of solvent effects in biopolymer simulations is a difficult problem. It is not possible to study systematically the effect of solvent conditions, e.g. added salt concentration, on biopolymer properties by means of simulations alone. In the last part of the paper we review a more analytical approach we have developed to study polyelectrolyte properties of solvated biopolymers. The results are compared with computer simulations. 

In an acetone extract from a neoprene/SBR hose compound, Lattimer et al. [92] distinguished dioctylph-thalate (m/z 390), di(r-octyl)diphenylamine (m/z 393), 1,3,5-tris(3,5-di-f-butyl-4-hydroxybenzyl)-isocyanurate m/z 783), hydrocarbon oil and a paraffin wax (numerous molecular ions in the m/z range of 200-500) by means of FD-MS. Since cross-linked rubbers are insoluble, more complex extraction procedures must be carried out (Chapter 2). The method of Dinsmore and Smith [257], or a modification thereof, is normally used. Mass spectrometry (and other analytical techniques) is then used to characterise the various rubber fractions. The mass-spectral identification of numerous antioxidants (hindered phenols and aromatic amines, e.g. phenyl-/ -naphthyl-amine, 6-dodecyl-2,2,4-trimethyl-l,2-dihydroquinoline, butylated bisphenol-A, HPPD, poly-TMDQ, di-(t-octyl)diphenylamine) in rubber extracts by means of direct probe EI-MS with programmed heating, has been reported [252]. The main problem reported consisted of the numerous ions arising from hydrocarbon oil in the recipe. In older work, mass spectrometry has been used to qualitatively identify volatile AOs in sheet samples of SBR and rubber-type vulcanisates after extraction of the polymer with acetone [51,246]. 

A similar type of biotin-dendritic multimer also was used to boost sensitivity in DNA microarray detection by 100-fold over that obtainable using traditional avidin-biotin reagent systems (Stears, 2000 Striebel et al., 2004). With this system, a polyvalent biotin dendrimer is able to bind many labeled avidin or streptavidin molecules, which may carry enzymes or fluorescent probes for assay detection. In addition, if the biotinylated dendrimer and the streptavidin detection agent is added at the same time, then at the site of a captured analyte, the biotin-dendrimer conjugates can form huge multi-dendrimer complexes wherein avidin or streptavidin detection reagents bridge between more than one dendrimer. Thus, the use of multivalent biotin-dendrimers can become universal enhancers of DNA hybridization assays or immunoassay procedures. 

Rarely will it be possible to draw conclusions directly from the raw data of analytical measurements and it is usual for some refinement of the data to be carried out. In its simplest form this could merely comprise background corrections, but it is often much more complex, requiring corrections for a number of factors as in mass spectrometry, X-ray fluorescence and electron probe microanalysis. More complex routines made available by computers include spectrum smoothing, stripping one component from a spectrum or making peak area measurements from chromatograms. 

The previous result is an important one. It indicates that there can be yet another fruitful route to describe lipid bilayers. The idea is to consider the conformational properties of a probe molecule, and then replace all the other molecules by an external potential field (see Figure 11). This external potential may be called the mean-field or self-consistent potential, as it represents the mean behaviour of all molecules self-consistently. There are mean-field theories in many branches of science, for example (quantum) physics, physical chemistry, etc. Very often mean-field theories simplify the system to such an extent that structural as well as thermodynamic properties can be found analytically. This means that there is no need to use a computer. However, the lipid membrane problem is so complicated that the help of the computer is still needed. The method has been refined over the years to a detailed and complex framework, whose results correspond closely with those of MD simulations. The computer time needed for these calculations is however an order of 105 times less (this estimate is certainly too small when SCF calculations are compared with massive MD simulations in which up to 1000 lipids are considered). Indeed, the calculations can be done on a desktop PC with typical... 

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