Structural and electrostatic effects on binding of trivalent cations to double‐stranded and single‐stranded poly[d (AT)]

Abstract

We have measured the thermal melting profile for poly[d(AT)] · poly[d(TA)] as a function of concentration of three trivalent cations: spermidine, me₈spermidine, and hexammine cobalt(III). Using McGhee's (1976) theory of DNA melting in the presence of ligands, we have estimated association constants K_h, K_c and binding site sizes n_h, n_c for binding to double-helical (h) and single-stranded (c) polynucleotide. The results are as follows: Cation K_h (M⁻¹) n_h (bp) K_c (M⁻¹) n_c (bases) Spermidine 9 × 10⁵ 2.2 1.3 × 10⁴ 4.5 Me₈spermidine 2 × 10⁵ 1.4 7 × 10³ 3 Hexammine cobalt(III) 1.1 × 10⁵ 1.5 6 × 10² 6 The binding parameters for spermidine and hexammine cobalt(III) to double helical molecules agree fairly well with direct equilibrium dialysis measurements, and are in reasonable accord with predictions of counterion condensation theory. However, despite their identical charges, the three ligands bind to single-stranded DNA with quite different affinities. Estimates of the charge spacing of single-stranded DNA suggest that poly[d(AT)] is less elongated in the presence of spermidine and hexammine cobalt (III) than it is when complexed with me₈spermidine.