Preferential binding of 3'-terminal fragments of alfalfa mosaic virus RNA 4 to virions

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Abstract
3''-Terminal fragments present in a partial RNase T1 digest of RNA 4 alfalfa mosaic virus were selectively bound to virions of the same virus by incubation in 10 mM sodium phosphate and 1 mM EDTA, pH 7.0. The virions with the associated fragments were separated from the remainder of the digest by velocity gradient centrifugation. When the incubation was performed in 27.7 mM Na2HPO4 and 6.2 mM citric acid, pH 6.8, plus 10% glycerol, much more, but less specific, binding was obtained. In this case the terminal fragments present in unbound material of the digest were almost exclusively 5'' termini. The 4 RNA species of alfalfa mosaic virus have an extensive 3''-terminal homology. It is expected that specific virion binding can be used to obtain 3''-terminal fragments of different lengths of the 3 genome RNA species (RNAs 1, 2 and 3) of alfalfa mosaic virus and, possibly, of related viruses. Such fragments are of great importance for the study of the specific 3''-terminal interaction with coat protein subunits which is thought to be responsible for the activation of the viral genome.