Equilibrium studies of ethidium-polynucleotide interactions

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Abstract
Equilibrium dialysis studies of the binding of ethidium to a variety of double-helical synthetic polynucleotides containing A.cntdot.U (or T) and I.cntdot.C base pairs are reported. The results are interpreted in terms of the neighbor exclusion model of drug binding, with allowance both for cooperativity of binding and for a structural switch of the helix to a different form which binds the drug more effectively. Both DNA and the alternating copolymers examined [poly[d(A-T)] and poly[d(I-C)]] showed high affinity (104-105 M-1) in 1 M salt. Homopolynucleotides showed a more complicated pattern of affinities: poly(rA).cntdot.poly(rU), poly(rA).cntdot.poly(dT), and poly(dA).cntdot.poly(rU) showed high affinity, whereas poly(dA).cntdot.poly(dT), poly(rI).cntdot.poly(rC), and poly(dI).cntdot.poly(dC) showed low affinity (.ltoreq. 103 M-1). Theneighbor exclusion range was inferred to be 2 base pairs for DNA or B family helices and 3 for RNA or A family helices. Generally, polynucleotides showed some cooperativity in their ethidium binding. The data reveal a switch of poly[d(I-C)] to a form able to bind ethidium more effectively.