1996
DOI: 10.1006/jmbi.1996.0543
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Secondary Structure Probing of Potato Spindle Tuber Viroid (PSTVd) and Sequence Comparison with Other Small Pathogenic RNA Replicons Provides Evidence for Central Non-canonical Base-pairs, Large A-rich Loops, and a Terminal Branch

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Cited by 77 publications
(81 citation statements)
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References 67 publications
(174 reference statements)
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“…It is localized in the nucleus (Schumacher et al 1983), where it is thought to replicate via the DNA-dependent RNA polymerase II (Rackwitz et al 1981;Schindler & Muhlbach 1992) via the rolling circle mechanism (Branch and Robertson 1984). The partial self-complementarity that occurs along the 359 bases of the PSTVd genome gives rise to the secondary structure of an interrupted double helix with a branch at the left terminus (Gast et al 1996). The viroid molecule appears under the microscope shaped as a rod (Sanger et al 1976).…”
Section: Introductionmentioning
confidence: 99%
“…It is localized in the nucleus (Schumacher et al 1983), where it is thought to replicate via the DNA-dependent RNA polymerase II (Rackwitz et al 1981;Schindler & Muhlbach 1992) via the rolling circle mechanism (Branch and Robertson 1984). The partial self-complementarity that occurs along the 359 bases of the PSTVd genome gives rise to the secondary structure of an interrupted double helix with a branch at the left terminus (Gast et al 1996). The viroid molecule appears under the microscope shaped as a rod (Sanger et al 1976).…”
Section: Introductionmentioning
confidence: 99%
“…This conformation, however, differed significantly in the distribution and size of some loops and double-stranded segments when compared with others reported previously [11,17,20,21]. For the mc ASBVd (À) RNA the agreement was even better, with the three software programs predicting the same rod-shaped secondary structure.…”
Section: Discussionmentioning
confidence: 38%
“…The mc ASBVd (À) strand, although considerably less prevalent than its (+) counterpart, still reaches in planta a titre high enough to obtain the amount needed for dissection in vitro with several approaches. Previous thermodynamics-based predictions of the secondary structures of the mc ASBVd (+) and (À) RNAs, usually performed with the Mfold software program [30], have led to rod-like conformations that in some cases include a short bifurcation in one of the terminal domains [11,17,20,21,31]. Here we have reassessed this issue with recent versions of the same software program, and two others, considering that the high A+U content of the mc ASBVd (+) and (À) forms should result in secondary structures of minimal free energy less stable and more difficult to predict than those typical of other viroids.…”
Section: Resultsmentioning
confidence: 99%
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“…Uno de los más interesantes es el llamado bucle E, identificado inicialmente en el 5S rRNA y posteriormente detectado in vitro en el PSTVd mediante radiación UV (Branch et al, 1985) y modificación con dimetilsulfato (Gast et al, 1996). Es un motivo de RNA mantenido por interacciones no canónicas, al que podría unirse alguna proteína involucrada en la replicación o el transporte intranuclear .…”
Section: Tcr Ccrunclassified