The dimerization domain of potato spindle tuber viroid, a possible hallmark for infectious RNA.
Covalently closed circular (+) RNA of the potato spindle tuber viroid (PSTVd) can efficiently dimerize noncovalently upon heating and slow cooling in the presence of monovalent cations or Mg2+. In vitro transcription of subgenomic fragments reveals that the ability to dimerize resides in the "upper strand" of its self-complementary rod-like structure. Nuclease probing of these fragments, namely, molecules spanning either the upper or the lower strand of PSTVd, confirms the existence of the previously proposed hairpins I-III, of which hairpin I might contain noncanonical G.A and A.A base pairs. In addition, the upper and lower (+) strands contain large hairpin loops consisting of stretches rich in either adenosine or uridine. Dimerization of the upper (+) strand results in a nuclease-resistant core encompassing hairpin I and is inhibited by an antisense oligonucleotide spanning the entire hairpin; this palindromic domain thus represents the dimerization site. When upper and lower strands were heated and cooled together, no annealing to a viroid-like duplex of both molecules occurs, only dimerization of the upper strand. Therefore, the dimerization hairpin of viroid RNA represents a unique conformational signal that is homologous to similar regions in the human immunodeficiency virus and other retroviruses.
Gast
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FU
Institut für Biochemie, Justus-Liebig-Universität Giessen, Germany. Frank-Ulrich.Gast@chemie.bio.uni-giessen.de
Kempe
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Sänger
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D001483:Base Sequence; D001665:Binding Sites; D019281:Dimerization; D016679:Genome, Viral; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry; D016376:Oligonucleotides, Antisense / Q000378:metabolism; D010935:Plant Diseases / Q000235:genetics / Q000821:virology; D010942:Plant Viruses / Q000737:chemistry* / Q000378:metabolism / Q000472:pathogenicity; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism; D006163:Ribonuclease T1 / Q000378:metabolism; D011198:Solanum tuberosum / Q000821:virology*; D014158:Transcription, Genetic; D014772:Viroids / Q000737:chemistry* / Q000378:metabolism / Q000472:pathogenicity
D009692:Nucleic Acid Heteroduplexes; D016376:Oligonucleotides, Antisense; D012367:RNA, Viral; D006163:Ribonuclease T1