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() Rod-like secondary structure that the nucleotides involved in both hammerheads adopt in the predicted most stable conformation of the reference variant of ELVd (+) RNA (accession number AJ536613)

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posted on 2011-12-31, 02:55 authored by Alberto Carbonell, Marcos De la Peña, Ricardo Flores, Selma Gago

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Taken from "Effects of the trinucleotide preceding the self-cleavage site on eggplant latent viroid hammerheads: differences in co- and post-transcriptional self-cleavage may explain the lack of trinucleotide AUC in most natural hammerheads"

Nucleic Acids Research 2006;34(19):5613-5622.

Published online 05 Oct 2006

PMCID:PMC1636495.

© 2006 The Author(s)

Sequences forming the hammerheads are delimited by flags, motifs conserved in most natural hammerheads are within boxes, and self-cleavage sites are marked by arrows. Black and white backgrounds refer to (+) and (−) polarities, respectively. () Structure of the ELVd (+) and (−) hammerheads according to crystallographic data obtained for the hammerhead (). Open square next to open triangle denotes Hoogsteen/sugar edge. Numbering of nucleotides and nomenclature of helices and loops is consistent with the standard criterion. Motifs conserved in most natural hammerheads are within boxes, and self-cleavage sites are marked by arrows. Black and white backgrounds refer to (+) and (−) polarities, respectively. The ovals represent the proposed tertiary interactions between loops 1 and 2 that increase the self-cleavage rates. The inset at the right displays the mutants derived from the ELVd (+) hammerhead used in the present work, with the changes introduced within boxes. () Structure of the (+) hammerheads of PLMVd, CChMVd and sTRSV.

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