virusoid - PMC

Battur Magvan, Anne Alina Kloeble, Johannes Ptok, Daniel Hoffmann, Daniel Habermann, Anuujin Gantumur, Martha Paluschinski, Gerelmaa Enebish, Vera Balz, Johannes C. Fischer, Battogtokh Chimeddorj, Andreas Walker, Jörg Timm

Front Med (Lausanne) 2023; 10: 1108543. Published online 2023 Mar 13. doi: 10.3389/fmed.2023.1108543

PMCID:: PMC10077969

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Less isn’t always more

OLKE C. UHLENBECK

RNA. 2003 Dec; 9(12): 1415–1417. doi: 10.1261/rna.5155903

PMCID:: PMC1370494

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Specific RNA self-cleavage in coconut cadang cadang viroid: potential for a role in rolling circle replication.

Y H Liu, R H Symons

RNA. 1998 Apr; 4(4): 418–429.

PMCID:: PMC1369628

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Grapevine Virology in the Third-Generation Sequencing Era: From Virus Detection to Viral Epitranscriptomics

Vahid Jalali Javaran, Peter Moffett, Pierre Lemoyne, Dong Xu, Charith Raj Adkar-Purushothama, Mamadou Lamine Fall

Plants (Basel) 2021 Nov; 10(11): 2355. Published online 2021 Oct 31. doi: 10.3390/plants10112355

PMCID:: PMC8623739

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Translation schematic for the genome of a protein-coding virusoid.

In This Issue

Proc Natl Acad Sci U S A. 2014 Oct 7;111(40):14309-14310.
Figure 8

Delta virusoid. The predicted most significant mutation for the virusoid sequence from Hepatitis delta virus. (A) Wild-type folded structure along with its representing dot plot matrix. The computed RNAfold global minimum energy is dG = -68.6. (B) The mutated folded structure with the largest distance grade from DoPloCompare (DP) = 0.023. The RNAdistance grade for this structure (Rdist) = 60. The computed RNAfold global minimum energy is dG = -67.5. (C) The mutated folded structure with the largest RNAdistance grade (Rdist) = 62. The DoPloCompare grade (DP) = 0.022. The computed RNAfold global minimum energy is dG = -63.7 kcals/mole.

An image processing approach to computing distances between RNA secondary structures dot plots

Algorithms Mol Biol. 2009;4:4-4.
Figure 2.

RNA secondary structure and coarser levels of representation. ((A) Secondary structure of an HDV virusoid sequence taken from []. (B) Tree-graph representation of the secondary structure. (C) Laplacian matrix corresponding to the tree-graph representation. (D) Spectrum of the Laplacian matrix. (E) Second-smallest eigenvalue of the Laplacian matrix.

A Mathematical Analysis of HDV Genotypes: From Molecules to Cells

Mathematics (Basel). ;9(17):2063.
FIGURE 1.

Secondary structures of hammerheads arranged to resemble the crystal structure. The catalytic core residues are indicated by open letters. (A) The rapidly cleaving sequence derived from the satellite RNA of tobacco ringspot virus studied by . The proposed tertiary interaction occurs between the loops at the ends of Stems 1 and 2. (B) The 55-nucleotide minimal hammerhead derived from the virusoid of leucerne transient streak virus identified by Forster and Symons. Hammerheads formed from two oligonucleotides described by (C) and (D) .

Less isn’t always more

RNA. 2003 Dec;9(12):1415-1417.