Three overlapping RNA fragments containing the pseudoknot, as found in the tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA, have been isolated and purified. Site-directed cleavage of TYMV RNA by RNase H, followed by ammonium sulphate precipitation and ion-exchange HPLC, yielded a pure preparation of a 3'-terminal, 112-nucleotide TYMV RNA fragment. Transcription of TYMV cDNA by T7 RNA polymerase, resulted in the isolation of an 88-nucleotide fragment. Finally, a 44-nucleotide fragment containing the TY MV RNA pseudoknot and strongly resembling the aminoacyl acceptor arm of the viral RNA was also synthesised using T7 RNA polymerase. The three fragments were isolated in milligram amounts and used for biochemical structure mapping, ultraviolet melting studies and NMR spectroscopy.Chemical modification with diethyl pyrocarbonate and sodium bisulphite and enzymatic digestion with RNase TI confirmed the presence of the pseudoknot in the 44-nucleotide fragment. Also the analogue of the T-stem and T-loop of the tRNA-like structure of TYMV RNA was found. The results of modification at various temperatures in Mg2+-containing buffers were in general agreement with optical melting studies. Ultraviolet melting analysis of the longer fragments revealed their greater complexity and the results appear similar to those obtained for some tRNA species.To obtain direct biophysical evidence for base-pairing and stacking interactions in the pseudoknot, NMR studies were initiated. The first proton-NMR spectra ever obtained for plant viral RNA fragments are presented. NMR spectra were recorded at various buffer conditions and at various temperatures. The spectra for the 112-nucleotide and 88-nucleotide fragment are too complicated to be solved at present. In the case of the 44-nucleotide fragment, however, the imino proton resonances are well separated and this system turns out to be most promising for structural studies.tRNA-like structures are found at the 3' termini of a number of plant viral RNAs [l, 21. These structures are recognised not only by the viral replicase, but also by tRNA-specific enzymes. In recent years these tRNA-like structures were investigated in detail by biochemical methods. Structural models demonstrating the resemblance between canonical tRNA and the tRNA-like moieties were proposed [3 -61.A striking feature of these models is the presence of a new structural element called an RNA pseudoknot. Pseudoknots of the type found in the tRNA-like structures involve base pairing between nucleotides in a hairpin loop with nucleotides in a single-stranded region of the molecule. This type of interaction gives rise to quasi-continuous helical domains and has been discussed in detail by Pleij et al. [7]. Beside the pseudoknots found in the tRNA-like structures, tandemly arranged pseudoknots appear to be common elements in the 3' non-coding region of several non-polyadenylated plant viral RNAs [8, 91. Pseudoknots were also found in ribosomal RNAs and in a center of autocatalytic RNA splicing [7]. Recently, pseu...