Binding behavior of lysine-containing helical peptides to DNA duplexes immobilized on a 27 MHz quartz-crystal microbalance

Binding behavior of alanine-based oligopeptides containing four or six cationic lysine residues (K4 and K6) to a dA₃₀-dT₃₀ or dG₃₀-dC₃₀ duplex-immobilized on a 27 MHz quartz-crystal microbalance (QCM) were studied in an aqueous buffer solution. Eight kinds of alanine-based oligopeptides were prepared systematically, in which positions of K residues were changed in the helical structure according to common features in DNA recognition helices of the DNA binding protein. The binding amount (Δm) on a nanogram scale and binding constant (K_a) could be obtained from frequency decreases (mass increases) of the DNA-immobilized QCM. Cationic oligopeptides were confirmed, from circular dichroism (CD) spectra, to form α-helical conformations as a result of the binding to DNA strands with random conformations. Δm and K_a values were greatly affected by ionic strength and the position of cationic K residues of peptides. At the low ionic strength, all peptides can bind with the almost same affinity to DNA strands by electrostatic interactions. At the high ionic strength of 40mM NaCl, oligopeptides with cationic K groups at the one side of the α helix showed larger Δm_max (35 ± 5 ngcm^-2) and K_a values (10⁴M^-1) than those of oligopeptides having K groups in random positions (Δm = 10 ± 5 ng cm^-2 and K_a = 10³M^-1).