Mapping the Binding Site of an Aptamer on ATP Using MicroScale Thermophoresis

The overall goal of this experiment is to characterize DNA aptamer small molecule interactions, including binding site mapping, using microscale thermophoresis. This method can help to answer key questions on basic binding parameters of molecular interactions. The main advantage of this technology is that it is independent of interaction partner size, allowing quality control data of challenging interactions between aptamers and small molecules to be obtained.

Though this method can provide insight into aptamer small molecule interactions, it can also be applied to other molecular interactions such as drug-target or antigen/antibody interactions. To begin the procedure, prepare a 100 micromolar stock solution of the Cy5 labeled DNA DH25.42 aptamer in distilled water. Then, dilute the aptamer stock solution to 200 nanomolar with binding buffer.