Characterization of hairpin DNA-binding properties of the N terminal domain of yeast Dna2

Abstract

Large unstructured segments are often found in proteins that carry out multiple functions. Yeast Dna2 is an essential enzyme with multiple biochemical activities such as DNA helicase, endonuclease, and DNA binding activities, and is implicated in various DNA transactions including Okazaki fragment maturation, homologous recombination repair, and cell cycle checkpoint activation. The largely unstructured N terminal domain of Dna2 undergoes multiple post-translational modifications and acts as a platform for interaction with various partner proteins. It was also found to direct the enzyme to secondary structure flaps that arise during Okazaki fragment maturation. In this study, we have determined that the minimal region of the N terminal domain of yeast Dna2 necessary to bind hairpin DNA lies within the first 101 amino acids. The results obtained suggest that the N-terminal segment of Dna2 recognizes and binds DNA through the formation of transient heat-stable short $\alpha$-helix. The ability of the segment to bind DNA is dependent on electrostatic interactions. The high-degree of flexibility and the open conformation of the disordered N-terminal region are critical in vivo, since substitution of lysine with $\alpha$-helix promoting alanine residues at positions 41-45 of the N-terminal domain of Dna2 renders mutant cells mildly temperature-sensitive and increases their sensitivity to DNA damaging agents.