Helix-coil transitions in double-stranded viral RNA. Fine resolution melting and ionic strength dependence

Abstract

Helix-coil transitions of double-stranded RNA from reovirus and infectious bursal disease virus were measured optically in aqueous medium of different ionic strengths. In RNA from reovirus four transitions and in RNA from infectious bursal disease virus two transitions were resolved and evaluated quantitatively. The ionic strength dependence of their midpoint temperatures dT m dlog[Na +] were 13.5 ± 0.3°C for reovirus RNA and 14.9 ± 0.7°C for infectious bursal disease virus RNA. The midpoint temperatures extrapolated to 1 M ionic strength were 102.9, 104.3, 105.6, and 108.8 ± 0.3°C for reovirus RNA, and 108.8 ± 1.8 and 109.6 ± 1.0°C for infectious bursal disease virus RNA. The G + C content of the regions in reovirus RNA melting in the different transitions were determined from the spectrum of the hypochromicity. The quantitative interpretation of the data is carried out on the basis of the ion condensation theory. It is estimated for double-stranded RNA of 100% G + C, that dT m dlog[Na +] = 8.4° C . The two-dimensional dependence T m = T m (ionic strength, G + C content) is given. The ionic strength dependence in different double-stranded RNAs is correlated to the spacing of the phosphate backbone, secondary structure, and tertiary structure.