Evidence of novel secondary structure in DNA-bound protamine is revealed by Raman spectroscopy

Raman spectroscopy studies of protamine-DNA complexes are reported for samples in the solid state at 98% relative humidity. Previous reports utilizing other physical techniques have indicated the presence of B-form DNA in protamine-DNA complexes. The present Raman data support the assignment of a modified B-form which is characterized by appreciable unstacking of the bases. The quality of the present spectra has made it possible, for the first time, to obtain the Raman spectrum of DNA-bound protamine by digital spectral subtraction. The difference spectrum indicates that protamine adopts an unusual secondary structure upon binding to DNA. A dominant amide I band is observed at 1683 cm-1 which is indicative of neither an alpha-helix or beta-sheet conformation. An amide I band at this position has been associated with the 1-->3 hydrogen bond that occurs within a gamma-turn [Bandekar, J., & Krimm, S. (1985) Int. J. Pept. Protein Res. 26, 158-165]. On the basis of this assignment, as well as preliminary results obtained by computer modeling, we propose a new model for the secondary structure of DNA-bound protamine that is rich in 1-->3 hydrogen bonding. Spectral data demonstrate that this structure is absent in protamine molecules in solution. Analyses of spectra of polyarginine-DNA complexes suggest that polyarginine, although similar to protamine in primary structure, assumes a conformation when bound to DNA that is distinct from that adopted by protamine.