ABSTRACT
In this chapter, we quantify ligand-DNA interactions and characterize various DNA-binding modes. Optical tweezers measurements are used as a DNA-binding assay for drugs and potential drug candidates. Changes in the measured DNA force
6.1 Introduction .................................................................................................. 136 6.2 Background and Basics ................................................................................. 136
6.2.1 Trapping and Stretching Single Molecules Using Optical Tweezers ................................................................................. 136 6.2.2 Polymer Models and Melting Free Energy ....................................... 140 6.2.3 Small-Molecule Interactions with DNA ........................................... 141
6.3 Case Studies .................................................................................................. 141 6.3.1 Intercalators ...................................................................................... 141
6.3.1.1 Qualitative Effects with Stretching Experiments .............. 142 6.3.1.2 Measuring Persistence and Contour Lengths .................... 143 6.3.1.3 Estimation of Melting Free Energy Change ...................... 144 6.3.1.4 Fitting to McGhee-von Hippel Isotherm to Obtain
Binding Parameters ............................................................ 145 6.3.1.5 Quantifying the Force Dependence to Obtain Zero
Force Intercalation ............................................................. 146 6.3.2 Single-Stranded DNA Binding ......................................................... 147 6.3.3 Groove Binders ................................................................................. 149 6.3.4 Multiple-Binding Modes ................................................................... 150 6.3.5 Complex-Binding Modes .................................................................. 151
6.4 Conclusions ................................................................................................... 154 Acknowledgments .................................................................................................. 155 References .............................................................................................................. 155
versus extension reveal the DNA-binding mode and af•nity of these molecules as they bind to the DNA.
