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 nega tive-stained, carbon-coated replica and mica-adsorbed preparations of 200 mu M poly r(A - U) and 50 mu M ethidium bromide/200 mu M 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 foun d 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) combin ation appears as a heterogeneous population of condensed structures wh ose lengths and widths vary from 12 - 88 nm and 15 - 45 nm, respective ly. These conformational changes are due to a number of factors, inclu ding the displacement of ordered water surrounding the poly r(A - U) a nd charge shielding of the phosphate groups of the poly r(A - U) upon the binding of the ethidium.