Determination of Aptamer Structure Using Circular Dichroism Spectroscopy

G-quadruplexes can be important as three-dimensional structures for aptamers as they improve the properties of the nucleic acids like higher nuclease degradation resistance. For the characterization of the quadruplex type and its formation, circular dichroism (CD) spectroscopy is one of the most common used identification methods. It is possible to differentiate the parallel and antiparallel G-quadruplex forms as well as the different number of nucleic acid strands by very specific CD spectral patterns at distinct absorption wavelengths. In this chapter, the protocol describes the model characterization of the anthracycline aptamer DRN-10 by CD spectroscopy, in order to show the usefulness and simple handling of this method for analyzing three-dimensional nucleic acid structures.