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Comparative Study
. 2003 Jan;26(1):19-23.
doi: 10.1023/a:1022369803448.

A new structural motif in the left terminal domain of large viroids identified by covariation analysis

Frank-Ulrich Gast  1
Affiliations
Comparative Study

A new structural motif in the left terminal domain of large viroids identified by covariation analysis

Frank-Ulrich Gast. Virus Genes. 2003 Jan.

Abstract

Sequence alignment of non-hammerhead viroids (Pospiviroidae) reveals that they can be divided into large and small viroids. Covariation analysis of these groups provides evidence for a rod-like secondary structure, but also for two proposed suboptimal structures, namely hairpin I and a bifurcation in the left terminus of large viroids. The strongest covariation within the branched T1 domain of all large Pospiviroidae indicates a new tertiary interaction, resulting in a double-pseudoknot within the (+) strand or an additional hairpin in the (-) strand. The structural element is expected to play a role in the viroid's life cycle.

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