The ends of La Crosse virus genome and antigenome RNAs within nucleocapsids are base paired.

The three La Crosse virus genomes are found as circular structures in the electron microscope, and the RNA ends of at least the small (S) and medium (M) segments are highly complementary. When examined for psoralen cross-linking, about half of the S, at most 1 to 2% of the M, and none of the large (L) nucleocapsid RNAs could be cross-linked in virions or at late times intracellularly, under conditions in which each free RNA reacted completely. For the S segment, genomes and antigenomes first detected intracellularly could not be cross-linked at all, and their cross-linkability increased gradually with time. Antigenomes behaved similarly to genomes in all respects. It appears that the majority of all three segments are base paired at their ends and that the limited cross-linkability reflects the accessability of the RNA within nucleocapsids to psoralen. The gradual increase in cross-linkability may be important in persistent mosquito cell infection, in which it correlates with decreased S mRNA synthesis rates, and may be part of the mechanism which this infection becomes self-limiting. The implications of double-stranded RNA panhandles within nucleocapsids are discussed.