Characterization of DNA Structures by Circular Dichroism

Circular dichroism (CD) of nucleic acids is commonly used to provide a signature for a given secondary structure. CD is particularly powerful for monitoring structural changes resulting from changes in environmental conditions such as temperature, ionic strength, and pH. A number of commercially available instruments are available for the measurement of CD spectra. Since the details of instrumental operation differ for each machine, this unit provides a descriptive guide, rather than a strict protocol. It describes considerations that the experimentalist will face when attempting to examine nucleic acid structures by CD spectropolarimetry. Specific details are also given for cell filling and cleaning, and for instrumental calibration. Finally, several examples of CD spectra are given to provide useful reference points for a variety of nucleic acid structures, ranging from single-stranded to triplex and quadruplex forms.