DNA-Ligand Flow Linear Dichroism
Linear dichroism (LD) is the difference in the absorption of light polarized parallel and perpendicular to an orientation direction. A signal therefore implies that a sample is oriented. DNA is a semirigid polymer which can be shear flow-oriented if it is more than ~450 base pairs in length. Anything bound to it is also oriented. If we know how the transition moments are oriented within a molecular coordinate framework, we can, from an observed linear dichroism (LD) spectrum, deduce something about how the molecules are aligned within the sample. Since small molecules cannot be flow-oriented, a simple and sometimes very useful application of LD is for detecting interactions between a small molecule and a biological macromolecule such as DNA that can be flow-oriented. Complete absence of a flow LD at the ligand transition wavelengths is generally a safe indication that the dye does not interact with DNA,...