Crossover regions in foot-and-mouth disease virus (FMDV) recombinants correspond to regions of high local secondary structure

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Abstract
The RNA genome of foot-and-mouth disease virus (FMDV) was analysed for the degree of inverted complementarity and thus potential secondary structure using the procedure of Pustell and Kafatos [Nucleic Acids Res (1982) 10: 4765–4782]. Regions of crossover in 42 FMDV recombinants [King et al. (1985) Virus Res 3: 373–384; Saunders et al. (1985) J Virol 56: 921–929] and regions lacking crossovers were assigned an average secondary structure score against which the number of observed recombinants was plotted. In general it was found that the mean value of potential secondary structure is significantly higher in crossover zones than in recombination-free zones. Recombination increased much more steeply with increasing secondary structure in the part of the genome coding for non-structural proteins than in the 5′ third of the genome coding for structural proteins.