Structural modification of DNA by a DNA-binding motif SPKK: detection of changes in base-pair hydrogen bonding and base stacking by UV resonance Raman spectroscopy.

Interactions of a DNA-binding motif SPKK with polynucleotides have been investigated by uv resonance Raman spectroscopy. Analysis of the Raman spectra has shown that the tetrapeptide SPKK weakens the adenine-thymine base-pair hydrogen bonding in poly(dA-dT).poly(dA-dT) and reduces the adenine-adenine base stacking interactions in poly(dA).poly(dT), both effects being indicative of destabilization of the DNA double helical structure. On the other hand, poly(dG-dC).poly(dG-dC) and poly(dG).poly(dC) do not show any structural change in the presence of SPKK. The present observations confirm that the SPKK motif, which is frequently found in histone H1 proteins, specifically binds to A/T-rich regions of DNA and loosens the DNA double-helical structure. One of the roles of the SPKK motifs in histones may be to increase DNA flexibility so that DNA can wrap around core histones and be assembled into chromosomes more easily.