Examples of supramolecular dynamics studies

The application of the techniques discussed above to the binding of guests to DNA or cyclodextrins (CDs) is described below. The intent of this section is not to provide an exhaustive review and analysis of the available data, but the objective is to use examples to show how the different techniques were employed in studies of supramolecular dynamics. The values for rate and equilibrium constants stated below 

The dynamics of intercalation of small molecules with DNA, groove binding and binding to specific sites, such as base pair mismatches have been studied by stopped-flow,23,80 108 temperature jump experiments,26,27,94 109 120 surface plasmon resonance,121 129 NMR,86,130 135 flash photolysis,136 138 and fluorescence correlation spectroscopy.64 The application of the various techniques to study the binding dynamics of small molecules will be analyzed for specific examples of each type of binding. 

A stopped-flow methodology using deuterium exchange was employed to study the binding dynamics of 1 with ct-DNA.93 This method relies on the fact that the absorption spectrum of 1 changed upon deuteration, and the rate for deuteration was slowed down when 1 was bound to DNA when compared to the rate in aqueous solution. This method was validated by comparing the rate constant values with 

Temperature jump studies were performed in combination with stopped-flow experiments94 in response to criticism as to the reliability of temperature jump experiments26,142 and divergent interpretation of the kinetics. In particular, the suggestion from pressure jump experiments that the association step is diffusive in nature 

The values for k+ and k were compared for temperature jump and stopped-flow conditions for DNA concentrations where the decay followed a mono-exponential function and no migration between DNA molecules occurred (see below).94 This report shows the importance of detecting fluorescence signals at the magic angle, which eliminated the fast components in the kinetics due to artifacts. The values for the association and dissociation rate constants obtained by both techniques are similar. 

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