Probe molecules binding properties

Experimental techniques based on the application of mechanical forces to single molecules in small assemblies have been applied to study the binding properties of biomolecules and their response to external mechanical manipulations. Among such techniques are atomic force microscopy (AFM), optical tweezers, biomembrane force probe, and surface force apparatus experiments (Binning et al., 1986 Block and Svoboda, 1994 Evans et ah, 1995 Israelachvili, 1992). These techniques have inspired us and others (see also the chapters by Eichinger et al. and by Hermans et al. in this volume) to adopt a similar approach for the study of biomolecules by means of computer simulations. 

In order to control the effect of Z1O2 on the electronic properties of Pd, an infrared study (using the CO probe molecule) and an XPS determination of the Pd binding energies have been performed... 

The surface and type of selected immobilization method will affect the bioactivity, the concentration, and the target-binding ability of bound probe molecules. Gold and glass substrates are good candidates for the immobilization of biomolecules. These substrates have a number of favorable characteristics (1) they are chemically homogeneous and stable, (2) surface properties like wettability can be fine-tuned,... 

The use of these labels for DNA detection typically requires covalent attachment because the probe molecules lack intrinsic DNA-binding capabilities. However, access to probes whose structural and electrochemical properties can be chosen for optimal efficiency amply justifies the added sample preparation time. In many of these cases, the electrochemical processes used for readout do not involve the DNA/electrode interface per se. Rather, the molecular-recognition properties of DNA are exploited to recruit the DNA-bound redox probes to the surface for analysis by more traditional electrochemical techniques, such as enzymatic catalysis or stripping voltammetry. 

Figure 4.20. Strategies for optical detection of intrinsic DNA bends and kinks. (Top) The FRET approach. The energy transfer donor dye (open circle) is covalently attached to the 5 end of a DNA strand. The complementary strand is labeled on its 5 end with an energy transfer acceptor dye (closed circle). The measured energy transfer is a function of the dye-to-dye distance R and should be different for the double helical straight DNA compared with the double helical bent DNA. (Bottom) The noncovalent probe approach. A probe molecule (shaded circle) is allowed to bind to either straight or bent duplex DNA. Equilibrium binding constants or kinetics of association may be monitored via the spectroscopic properties of the probe.

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