Transmission electron microscopy and scanning force microscopy of poly r(A-U) and poly r(A-U)-ethidium bromide

Transmission electron microscopy and scanning force microscopy of negative-stained, carbon-coated replica and mica-adsorbed preparations of 200 microM poly r(A-U) and 50 microM ethidium bromide/200 microM poly r(A-U) have been employed to evaluate ethidium-induced changes in poly r(A-U) topology. Poly r(A-U) alone exhibits elongated conformations 85-115 nm in length that possess a number of hairpin loops as well as single-stranded domains. While the double-stranded domains are found predominately at the base of the hairpin loops (diameter = 5-30 nm), other rod-like (presumably double-stranded) regions ranging from 25-80 nm in length are present in other portions of the poly r(A-U). In contrast with the poly r(A-U) alone, the EB/poly r(A-U) combination appears as a heterogeneous population of condensed structures whose lengths and widths vary from 12-88 nm and 15-45 nm, respectively. These conformational changes are due to a number of factors, including the displacement of ordered water surrounding the poly r(A-U) and charge shielding of the phosphate groups of the poly r(A-U) upon the binding of the ethidium.