The binding of Arg- and Lys-peptides to single stranded polyribonucleotides and its effect on the polymer...

The interactions between basic oligopeptides (Lys2, Lys3, Arg2 and Arg3) and single stranded polynucleotides (poly(A), poly(C), poly(I) and poly(U) were investigated at low ion concentration by UV spectroscopy, circular dichroism and field jump relaxation. Various domains of binding were detected: 1) High concentrations (up to 1 mM) of some peptides induce opalescence followed by coacervation. Arg3 causes coacervation in all polynucleotides used, yet Lys3 only in poly(I). In the case of poly(I) the threshold concentration for coacervation is much lower for Arg3 (150 muM) than for Lys3 (500 muM). 2) Medium concentrations (greater than 10 muM) of Arg3 and Lys3 induce helix formation in poly(U). In the case of poly(I) cooperative helix formation is only induced by Lys3, but not by Arg3. 3) The onset of peptide association is observed at very low peptide concentrations (greater than or equal to 1muM) already by using the field jump method. The association is reflected by a relaxation process, that can be described by a single exponential within experimental accuracy. Measurements of relaxation time constants as a function of the peptide concentration provide information on the association constants K, the number of nucleotide residues per binding place n and the rate constants kR and kD. Using a simple model with independent and "separate" binding sites, K for Arg3 and Lys3 is found to be in the range of 10(6) to 10(7) M-1. In the case of Arg2 and Lys2 K is lower by a factor of about 10. For various polynucleotides KArg3 is only slightly higher than KLys3, except in the case of poly(I), where KArg3/KLys3 approximately 5. Similar data are obtained by application of a "sphere model" (see below). These results provide quantitative evidence for specific hydrogen bonding between the guanidino group of Arg and inosine. They also explain the absence of helix formation for poly(I) + Arg3: Arg blocks the hydrogen bonding sites of inosine. Thus cooperative coupling leads in this case to a considerable amplification of specificity in the peptide-polynucleotide interation. Both field jump and stopped flow data demonstrate a high mobility of the peptide ligands along the polymer, resulting in a redistribution being fast compared with the overall binding step. Based on this result the relaxation data are analysed by a "sphere" model, which considers a) excluded binding under the condition of fast ligand distribtuion along the lattice and b) the connection of sites into a polymer sphere. The rate constants obtained by this model are in the range of 4 X 10(11) M-1 s-1. These high values reflect the large reaction distance for polymers of chain lengths around 1000. A comparison with rate constants obtained previously for oligomer complexes indicates that the recombination rate is approximately a function of the square root of the nucleotide chain length, which is directly related to the mean radius of coiled polymers.