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Nucleic Acids Research, 1978, Vol. 5, No. 4 1221-1236
© 1978

Articles

Studies on the primary and secondary structure of potato spindle tuber viroid: products of digestion with ribonuclease A and ribonuclease T1, and modification with bisulfite

Horst Domdey, Peter Jank, Heinz L. Sänger* and Hans J. Gross

Max-Planck-Institut für Biochemie D-8033 Martinsried bei München *Arbeitsgruppe Pflanzenvirologie, Justus Liebig-Universität Frankfurterstr. 107, D-6300 Giessen, GFR

Received March 13, 1978. Potato spindle tuber viroid (PSTV), a small infectious RNA, has been completely digested with RNase T1 and RNase A, and the resulting oligonucleotides have been sequenced using 5'-terminal 32P-labelling with {gamma}-32P ATP and T4 polynucleotide kinase, fingerprinting and controlled nuclease P1 digestion. Modified nucleotides have not been detected in 5'-positions of these oligonucleotides. PSTV consists of about 359 nucleotides and contains a remarkable stretch of 18 purines, mainly adenosines; there is no AUG initiation triplet present. The established oligonucleotide sequences preclude a perfect intramolecular base complementarity within the covalently closed viroid circle. Therefore, the rigid, rod-like native secondary structure of PSTV, as seen in the electron microscope, must be based on a defective rather than on a homogeneous RNA helix. The detailed analysis of the bisulfite-catalized modification of cytidine to uridine in PSTV revealed a higher reactivity for the majority of the cytidines than would be expected for a perfect helix. Since only cytidines in single-stranded regions are known to be fully reactive, this finding provides additional evidence for defects in the helical secondary structure of PSTV.


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