The tRNA-like structure of turnip yellow mosaic virus RNA: structural organization of the last 159 nucleotides from the 3′ OH terminus

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Abstract
The secondary structure of the isolated tRNA‐like sequence (n=159) present at the 3′ OH terminus of turnip yellow mosaic virus RNA has been established from partial nuclease digestion with S1 nuclease and T1, CL3, and Naja oxiana RNases. The fragment folds into a 6‐armed structure with two main domains. The first domain, of loose structure and nearest the 5′ OH terminus, is composed of one large arm which extends into the coat protein cistron. The second, more compact domain, is composed of the five other arms and most probably contains the structure recognized by valyl‐tRNA synthetase. In this domain three successive arms strikingly resemble the T[unk], anticodon, and D arms found in tRNA. Near the amino‐acid accepting terminus, however, there is a new stem and loop region not found in standard tRNA. This secondary structure is compatible with a L‐shaped three‐dimensional organization in which the corner of the L and the anticodon‐containing limb are similar to, and the amino‐acid accepting region different from, that in tRNA. Ethylnitrosourea accessibility studies have shown similar tertiary structure features in the T[unk] loop of tRNAVal and in the homologous region of the viral RNA.