Binding of ethidium ion to left-handed Z-RNA induces a cooperative transition to right-handed RNA at the intercalation site

Abstract

The equilibrium binding of the ethidium cation (Etd+) to the right-handed A-form of poly-[r(C-G)], the B-form of poly[d(C-G)], and the left-handed Z-forms of Br-poly[r(C-G)] and Br-poly[d(C-G)] was investigated in 0.22 M NaCl by optical methods. Scatchard analysis indicates that Etd+ intercalates into right-handed forms of poly[r(C-G)] and poly[d(C-G)] in a noncooperative manner. Correlation of Etd+ absorbance binding isotherms and polynucleotide circular dichroism data indicates that drug binding to Br-poly[r(C-G) and Br-poly[d(C-G)] results in cooperative conversion from left-handed Z-forms to right-handed intercalated conformations. Approximate stoichiometries necessary to induce the left- to right-handed transitions are 1 Etd+/9 base pairs (bp) for Z-RNA and 1 Etd+/6 bp for Z-DNA. The apparent limiting binding stoichiometries are approximately 1 Etd+/3 bp for RNA and 1 Etd+/2 bp for DNA. The equilibrium binding constants for binding to the right-handed forms decrease in the order Br-poly[d(C-G)], Br-poly[r(C-G)], poly[d(C-G)], and poly[r(C-G)]. Thermodynamic parameters are obtained by van't Hoff analysis of Etd+ absorbance thermal dissociation data. Enthalpy values for all four polynucleotides are negative and of similar magnitude. Negative entropy values indicate that the binding processes are primarily enthalpically driven.(ABSTRACT TRUNCATED AT 250 WORDS)

Modeling of Nucleic Acid Complexes with Cationic Ligands: A Specialized Molecular Mechanics Force Field and Its Application

“…Table XI. The energy calculations reflect a preference for intercalative binding at the CpG step of the DNA oligomer over the CpG step of the RNA oligomer, consistent with experimental results (9). The modeling results support several primary conclusions.…”

“…The similar nonalternating sequence in DNA, dA · dT, is one of the least preferred binding sites for ethidium (6)(7)(8). A generally stronger binding of ethidium to RNA over DNA cannot be concluded at present because the compound binds better to an alternating GC sequence in a DNA polymer than in the similar RNA polymer (9). To our knowledge, however, ethidium is the only small molecule that at present has been shown to exhibit significant RNA duplex binding specificity.…”

“…Ethidium, for example, is known to intercalate and bind strongly to both RNA and DNA duplex conformations (1,(6)(7)(8)(9). Although ethidium binding shows no significant base pair composition dependence with natural DNA (10), experimental evidence with synthetic polymers and oligomers indicates that the intercalator has a strong binding preference for nonalternating rA · U sequences (6)(7)(8).…”

Synthesis, characterization, and DNA-binding studies of ruthenium complexes [Ru(tpy)(ptn)]2+ and Ru(dmtpy)(ptn)]2+

“…EB is well known to convert Z DNA to an intercalated right-handed B form under solution condition [62]. The effects of EB on the B→Z transition induced by Ru(II) complexes were exhibited in Fig.…”

Interaction of Isoquinoline Alkaloids with Polymorphic DNA Structures

“…For example, several intercalating molecules have now been characterized to convert the left-handed Z-form conformation to the bound B form. Ethidium [32] [33], actinomycin D [39], daunomycin [34], sanguinarine [26] [36], aristololactam b-d-glucoside [40], and several others cooperatively convert the Z-form structure back to bound B-form conformation. The binding of small molecules, however, to other polymorphic forms of DNA is still poorly studied [37] [41].…”