Binding of ligands to a one‐dimensional heterogeneous lattice. II. Intercalation of tilorone with DNA and polynucleotides

Abstract

SynopsisThe interaction of tilorone with DNA and five synthetic polydeoxyribonucleotides [(I): poly[d(G-C)]; (IV): poly(dG).poly(dC); and (V): poly(dA)-poly(dT)] has been investigated. Binding isotherms for the homopolymers were obtained by microdialysis equilibria using ''CC-labeled tilorone and interpreted with different models: exclusion effect, associated or not associated with cooperativity, or variable exclusion. Affinity appears to be related more to local structure than to base composition and decreases in the following order: (I) > (11) > (111) > (IV) > (V). Intercalation in circular DNA was demonstrated by electrophoresis migration and electron microscopy, which yielded an average unwinding angle of 7 O per bound dye. The behavior observed in CD and UV spectroscopy shows a sequence similar to the affinities. Tilorone seems to be less intercalated in (IV) and not a t all in (V). The experimental binding isotherm of tilorone to DNA was well fitted on the basis of a model where DNA acts as a heterogeneous lattice built with the six different possible couples of adjacent base pairs, each potential site behaving as if it were in the corresponding homopolymer. The results are discussed in terms of specificity of alternating Pyr-Pur sequences and related to theoretical calculations on intercalation energies of DNA.

Footprinting Studies on the Sequence-Selective Binding of Tilorone to DNA

“…Long-range structural distortions of DNA remote from the site of intercalation are also frequently observed (Neidle and Abraham, 1984;Neidle et al, 1987). Tilorone almost certainly produces such effects since it was found to remove and reverse the supercoiling of PM2 DNA and to decrease the sedimentation coefficient of nicked circular PM2 DNA in the fashion characteristic of intercalating agents (Wright et al, 1980).Although the apparent association constant for tilorone binding to calf thymus DNA is similar to that of ethidium (Chandraand Woltersdorf, 1976) the helix unwinding angle for tilorone is much lower than that of ethidium (Wright et al, 1980;Sturm et al, 1981). Clearly explanation (1) for the enhancement of DNAase I cutting must be carefully considered.…”

“…Theoretical (Chen et sl., 1988) and experimental (Chandra et al, 1972b;Chandra and Woltersdorf, 1976) studies have both suggested that tilorone binds predominantly to AT-rich DNA sequences. Further investigations of the binding of tilorone to various synthetic polynucleotides have revealed a preference for alternating pyrimidine-purine sequences, not restricted to the poly(dA-d1) polymer (Sturm et al, 1981;Sturm, 1982). But caution must be exercised in using synthetic polynucleotides as models for base sequence specificity.…”

Binding of ligands to a one‐dimensional heterogeneous lattice. I. General model for the calculation of binding isotherms by a Monte Carlo approach

“…2 Again, in the computer program, minor modifications and additions in the tests of step 2 of the basic model are sufficient to solve the problem.…”

Binding of ligands to a one‐dimensional heterogeneous lattice. III. Kinetic model and relaxation study of the interaction of tilorone with DNA and polynucleotides

“…refers to the concentrations of free dye calculated from the binding isotherms reported previous1y.l The concentration of available binding sites, s, is calculated from the extent of binding r , the concentration of nucleotides P , and the exclusion number n'. 12 The concentration dependence of the relaxation times were obtained by using a series of solutions having different DNA concentrations but the same degree of binding r . This was done by diluting a concentrated stock solution of the complex with various amounts of a tilorone solution at a concentration B.…”