Nonspecific interactions probes

To overcome the nonspecific interactions between ssDNA-C and CCP, Fan et al. introduced a magnetic microparticle assisted assay [54], which allows DNA detection in human serum with 0.1 nM sensitivity. In addition, DNA intercalating dyes were introduced for DNA detection as shown in Scheme 5. These special dyes have much higher fluorescence quantum yields upon intercalation with dsDNA relative to those in the presence of ssDNA or in their free states. As a result, when complementary ssDNA strands (target and probe) are present, the intercalating dye... 

The kinetics of the immobibzation of a NA onto a polymeric gel depends in part upon the diffusion of the probe through the gel structure. The rate of this process is determined by the viscosity of the gel and the possible nonspecific interactions that occur between the NA and the polymeric matrix. On the contrary, considering planar substrates, NAs have direct access to the surface active groups for their attachment and the immobibzation process proceeds more rapidly. The same principles are relevant when considering the hybridization and washing processes involved in using these materials in applications. These are generally slower when diffusion of the reactants comes into play in gel systems. 

The phosphate backbone of DNA molecules often results in undesirable electrostatic interactions with the substrate. Although the electrostatic interactions of DNA can be utilized for physical adsorption of DNA to the surface, this process can also lead to the nonspecific physical adsorption of target DNA on the surface. Rather than sample DNA hybridizing to the probe, it can adsorb to the surface and lead to interferences with the final detection call. Nonspecific adsorption effects have primarily been examined by the microarray community. Blocking strategies have been developed to prevent these nonspecific interactions. Succinic anhydride (SA) and bovine serum albumin (BSA) are two common methods to prevent nonspecific adsorption on amine modified surfaces. Blocking strategies are desired to react with or pas-... 

With conventional chips, it is well known that thiolated-DNA can be easily immobilized on gold but does not interact by ordered self-assembly, due to nonspecific interactions between the DNA bases and the gold. Different alkanethiols have been used to improve the hybridization efficiency and the selectivity, followed by immobilization of thiolated-DNA on the substrate [59,61,69]. Hence, this method requires two steps and needs consideration concerning the experimental conditions. However, DNA-conjugated polymer does not only prevent desorption of probe DNA from the surface, because the DNA is covalently bound to the self-assembly polymer, but it also... 

The concentration of bulk carrier DNA and of BSA that needs to be added in the binding reaction, in order to prevent nonspecific interactions with the probe, greatly depends on the purity of the retmoid-receptor preparation. Titrations of these components need to be carried out to determine the optimal conditions for complex formation. 

A variety of methods have been explored to increase the surface area, and thereby the number of probe molecules available for target capture. Polymeric gel-pad matrices of polyacrylamide, for example, have been reported to have a significantly higher capacity for DNA immobilization compared to the two-dimensional arrays on glass (Proudnikov, 1998 Yershov, 1996 Dubiley, 1997). However, these polymeric gels suffer from some specific problems including low mobility of the target DNA molecules in the gel network, and nonspecific interactions which adversely affect the reaction kinetics, and increase the hybridization times. 

Bolis et al. [46] recendy summarized their data concerning calorimetry of CO adsorption on oxides. They concluded that, CO adsorption calorimetry is not a good technique for the characterization of the surface Lewis acidity at least for aluminas because the adsorption exothermic signal is in part combined by an endothermic signal due to surface reconstruction phenomena. Due to the nonspecific interaction of CO2 with basic sites, Rossi et al. [47,48] proposed the use of hexa-fluoro isopropanol as an alternative for the characterization of basic sites. The use of sulfur dioxide as a probe is also successful [49]. 

An important factor in all these experiments is the choice of bead used to immobilize the probe. Biochemists have considered cross-linked agarose beads to be exceptionally hydrophilic with a low tendency to bind proteins nonspecifically, and these beads have the further attraction of being commercially available in activated forms (succinimidyl esters, epoxides, and maleimides, for example). However, early trials of bead-based chemical proteomics have shown that many proteins in mammalian cell lysates bind tenaciously to agarose beads. This was unimportant in many studies in which protein-protein interactions were detected by coimmunoprecipitation with immunochemical... 

Basic molecules such as pyridine and NH3 have been the popular choice as the basic probe molecules since they are stable and one can differentiate and quantify the Bronsted and Lewis sites. Their main drawback is that they are very strong bases and hence adsorb nonspecifically even on the weakest acid sites. Therefore, weaker bases such as CO, NO, and acetonitrile have been used as probe molecules for solid acid catalysts. Adsorption of CO at low temperatures (77 K) is commonly used because CO is a weak base, has a small molecular size, a very intense vc=0 band that is quite sensitive to perturbations, is unreactive at low temperature, and interacts specifically with hydroxyl groups and metal cationic Lewis acid sites.26... 

From a practical viewpoint, Ej values are quickly and easily obtained, giving a very useful and convenient scale. However, a general polarity scale based on a single probe molecule has its limitations because a single compound cannot experience the diversity of interactions that the whole range of solvents can offer. The Kamlet-Taft parameters a, /3 and n tackle this problem by using a series of seven dyes to produce a scale for specific and nonspecific polarity of liquids [23], Whilst it undoubtedly gives a more detailed description of the solvents properties,... 

Sonicated and denatured salmon sperm DNA (or other anionic maCTomolecules) may be used to reduce nonspecific probe interaction and electrostatic forces. The latter also may be reduced with dextran sulfate. High-stringency (low-sodium) hybridization ensures that complete complementarity will characterize the probe-target hybrid. 

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