Thermodynamic characterization of ethidium bromide binding to a unique site on a yeast tRNA^Phe

Abstract

A self‐consistent thermodynamic characterization of the binding of ethidium to yeast phenylalanine‐specific tRNA at 25°C, pH 7.0, in 11 nM MgCl2, 375 nM NaCl, and 25 mM sodium phosphate has been obtained. Two ethidium molecules bind per tRNA under these conditions. The stronger site has a dissociation constant equal to 1.9 ± 0.5 μM and ΔHdis°′ = 12 ± 1 Kcal/mol, and the weaker sites has a dissociation constant equal to 24 ± 9 μM and ΔHdis°′ = 8.9 ± 1.5 Kcal/mol. The average calorimetric ΔHdis°′ for the to sites 10.6 ± 0.4 kcal/mol. The thermodynamics of binding to the stranger sites are most probably the thermodynamics of interaction between A·U (6) and A·U (7), the unique site identified by Jones and Kearns. The binding is enthalpically driven and classical hydrophobic interactions do not appear to be important in the binding reaction.

Energetic and structural aspects of ethidium cation intercalation into DNA minihelices

“…In other words, this latter value is probably more indicative of the more favorable EC intercalative binding reactions, whereas the former values may also include the less favored external or nonintercalative binding reactions as well. The above trends are in agreement with DNA melting studies53 and biphasic melting studieslOJ1 that suggest an increase in stability of ethidium-in- fG-C/C-GJ(II) and tA-T/T-AJ (14).…”

Phosphorus-31 nuclear magnetic resonance of ethidium complexes with ribonucleic acid model systems and phenylalanine-specific transfer ribonucleic acid

“…Effects of Eton tRNA. Fluorescence depolarization studies indicate that in the presence of Mg2+ there is one strong binding site for Et to tRNAph' (Tao et al, 1970;Wells & Cantor, 1977) and perhaps a weaker site (Sturgill, 1978). The binding constant for the stronger site is (4-5) X 105 M"1 and for the weaker site is ~4 X 104 M"1 at temperatures of 22-25 °C (Sakai & Cohen, 1976;Sturgill, 1978;Torgerson et al, 1980).…”

“…Fluorescence depolarization studies indicate that in the presence of Mg2+ there is one strong binding site for Et to tRNAph' (Tao et al, 1970;Wells & Cantor, 1977) and perhaps a weaker site (Sturgill, 1978). The binding constant for the stronger site is (4-5) X 105 M"1 and for the weaker site is ~4 X 104 M"1 at temperatures of 22-25 °C (Sakai & Cohen, 1976;Sturgill, 1978;Torgerson et al, 1980). Lifetime measurement studies indicate that at low Et:tRNA ratios, the fluorescence decays with a single lifetime of 28 ms and at higher ratios the decay contains shorter lived components as well (Jones et al, 1978).…”

Relaxation kinetics of DNA–ligand binding including direct transfer

“…(24)] and that the relative magnitudes of k-1 and k--2 are fixed by both Eqs. (25) and (27). Therefore, there is a limit to the size for K ( 0 ) that is compatible with a given set of kinetic data.…”