Secondary structures of influenza and Sendai Virus RNAs

The secondary structures of influenza and Sendai virus RNAs were investigated by thermal denaturation, circular dichroism and proflavine binding methods. In 0.1 M NaCl about 60% of the bases of both RNAs were involved in secondary structure. The melting temperatures (Tm) of both viral RNAs were linear functions of the logarithm of the sodium ion concentration in solution, but under all ionic conditions the melting temperatures of Sendai virus RNA were higher than those of influenza virus RNA. At all ionic strengths the melting range of Sendai virus RNA was less than influenza virus RNA, indicating that the helical regions in Sendai virus RNA were longer than those in influenza virus RNA. Although Sendai virus RNA had a higher thermal stability than influenza virus RNA, hyperchromicity and circular dichroism data showed that Sendai virus RNA had less G+C content (34%) within the double stranded regions than influenza virus RNA (48%). The binding isotherms of Sendai and influenza virus RNA-proflavine complexes were studied at different ionic strengths. The number of binding sites of proflavine with influenza virus RNA were significantly lower than those with Sendai virus RNA. These results demonstrate the essential difference between the secondary and tertiary structures of the RNAs under study.