Circular Dichroism of Protein-Nucleic Acid Interactions

Abstract

This chapter will treat the intrinsic ultraviolet CD spectra of interacting nucleic acids and proteins. The CD spectra to be discussed will be restricted to the ultraviolet wavelength region below 320 nm, where nucleic acids and proteins have optical activity as a result of their secondary structures. Since protein secondary structures generally dominate CD spectra at wavelengths below 250 nm, the region from about 250 to 320 nm provides a valuable spectral “window” for detecting the secondary structures of nucleic acids that are complexed with proteins. Of course, aromatic amino acid side chains contribute to the CD in the wavelength region from 250 to 320 nm, but this contribution is usually small relative to the CD of polymeric nucleic acids. Moreover, CD difference spectra (of complexes minus components) in this wavelength region do not generally exhibit the complex features that can be attributed to the transitions of the aromatic amino acids. Therefore, the CD effects observed above 250 nm on forming proteinnucleic acid complexes are usually considered to be reflective of changes in the nucleic acid secondary structure. Likewise, the CD contributions of individual amino acid side chains are often, but not always, less than those of peptide secondary structures at wavelengths below 250 nm. Exceptions to these generalities will be seen in the CD spectra of some filamentous phages, for which the DNA signal above 250 nm can be essentially absent, and in the CD spectra of the fd gene 5 protein, where tyrosines dominate the CD of a s-structure protein below 250 nm.