Relation between genomic and capsid structures in RNA viruses.

Yamamoto, K; Yoshikura, H

We described a new computer program for calculation of RNA secondary structure. Calculation of 20 viral RNAs with this program showed that genomes of the icosahedral capsid viruses had higher folding probabilities than those of the helical capsid viruses. As this explains virus assembly quite well, the information of capsid structure must be imprinted not only in the capsid protein structures but also in the base sequence of the whole genome. We compared folding probability of the original sequence with that of the random sequence in which base composition was the same as the original. All the actual genomes of RNA viruses were more folded than the corresponding random sequences, even though most transcripts of chromosomal genes tended to be less folded. The data can be related to encapsidation of viral genomes. It was thus suggested that there exists a relation between actual sequences and random sequences with the same base ratios, and that the base ratio itself has some evolutional meaning.