Structure and dynamics of peptide—polynucleotide complexes

Abstract

The mode and the dynamics of LysTrpLys-binding to double helical DNA and to single stranded poly(A) has been analyzed by measurements of the chemical relaxation detected by fluorescence and of the rotational diffusion using the electric dichroism. The chemical relaxation, induced by electric field pulses, requires two exponentials for a satisfactory representation, indicating a two step reaction mechanism. The data are consistent with a bimolecular reaction step followed by a relatively slow intramolecular transition, which is expected to reflect “insertion” of the Trp-indole residues between the nucleic acid bases. The experimental data are analyzed quantitatively by global fitting with exact correction of the convolution due to the experimental device. In this procedure a complete set of relaxation curves is fitted directly to the reaction model and, thus artifacts resulting from erroneous assignments of coupled modes are avoided. According to this analysis the bimolecular reaction step is controlled by diffusion. The intramolecular transition in adenylate chains is found to be dependent on the chain length and on the ionic strength I: at I = 2.5 m M the “insertion” rate constant is 3 × 10 4 s −1 for the polymer and 2 × 10 5 s −1 for A(pA) 19; the rate constant for poly(A) increases with increasing salt concentration. The corresponding “insertion” rate constant for DNA double helices with 30 kbp is 2.5 × 10 4 s −1. For DNA double helices we find again an increase of the “insertion” rate with increasing salt concentration and with decreasing chain length. The mode of LysTrpLys-binding to double helical DNA is compared with that of LysTyrLys, LysLeuLys and LysGlyLys by measurements of the rotational diffusion of complexes with restriction fragments of different chain lengths. The persistence lengths derived from these measurements do not reveal any special effects resulting from insertion of aromatic residues. Apparently “insertion” of indole rings into double helical DNA does not increase the length of the double helix, which may be attributed to a special form of insertion, e.g. partial insertion. According to these results the interaction of the indole residues of LysTrpLys with DNA double helices is not equivalent to e.g. intercalation of aromatic residues like ethidium-neither with respect to structure nor to dynamics.