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. 2023 Jul 24;51(16):8850–8863. doi: 10.1093/nar/gkad618

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© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 1. — Enterovirus cloverleaf RNA forms an H-type four-way junction. (A) Schematic representation of an enterovirus genome. The genome contains one open reading frame (ORF), flanked by a highly structured 5′ untranslated region (UTR) and a 3′ UTR with a poly(A) tail. The 5′ UTR contains the cloverleaf and internal ribosome entry site (IRES) structures and is covalently linked to VPg (viral protein genome-linked). The cloverleaf structure is located at the 5′ terminus of the 5′ UTR immediately followed by the 3′ poly-rC region (hatched box). (B) Design of tRNA-fused coxsackievirus B3 (CVB3) cloverleaf. CVB3 cloverleaf (nucleotides 2–87) is inserted into the anticodon loop of human tRNA^Lys scaffold sequence to create tRNA-CL^CVB3. The nucleotide numbers in cloverleaf are also shown on the secondary structure in parenthesis in blue. Cloverleaf consists of stem A and stem–loops B, C and D. The PCBP2 binding site in stem–loop B is colored in yellow, and the 3CD^pro binding site is colored in green. The pyrimidine mismatch region in stem–loop D is boxed. (C) Crystal structure of CVB3 cloverleaf fused with a tRNA-scaffold. Cloverleaf RNA is colored by domain: stem A, orange; stem–loop B, blue; stem–loop C, cyan; and stem–loop D, green. The tRNA scaffold is colored purple. The missing nucleotides in stem–loop B are indicated by a dotted line. The secondary structure of CVB3 cloverleaf derived from the crystal structure is shown on the right. The PCBP2 binding site, the 3CD^pro binding site and the pyrimidine mismatch region are highlighted as in (B). The nucleotides involved in the A•C-U base triple are indicated by an arrow. (D) Design of tRNA-fused poliovirus (PV) cloverleaf. The PV cloverleaf sequence (nucleotides 2–88) is inserted into the anticodon loop of human tRNA^Lys. Additional G-C base pair was introduced between the tRNA scaffold and PV cloverleaf sequence to facilitate crystallization (colored in red). Functional regions in tRNA-CL^PV are indicated as in (B). (E) Crystal structure of PV cloverleaf fused with a tRNA-scaffold. The tRNA-CL^PV construct is colored by domain as in (C). The secondary structure derived from the crystal structure is shown on the right. PV cloverleaf has two base triples A•C-U and G•G-C, and their locations are indicated with arrows.