When the Pseudoknot Folds

All seems stable before the fold
Observing RNA structures never gets old
Linkage stems form, fusing the loops
Somewhat akin to primordial soup
Embedded pseudoknots with thermodynamic equilibrium
Have multibranch hairpins exhibiting no structural delirium
Pleating process instigates hyperfunction,
Pseudoknots now resemble spaghetti junction

——

pseudoknot: a double-hairpin structure with an extended quasi-continuous double-helical stem region. Pseudoknots belong to an RNA structural motif that has significant roles in the biological function of RNA. An example is ribosomal frameshifting; in this mechanism, the formation of a local triplex changes the reading frame that allows for differences in the translation of mRNAs.

——

Image credit: Dawson WK, Fujiwara K, Kawai G (2007) Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding. PLoS ONE 2(9): e905. https://doi.org/10.1371/journal.pone.0000905 Figure 4: Some basic concepts of pseudoknot structure and folding that are considered in the vsfold5 algorithm:

• (a) Basic concept of folding for a core pseudoknot. The stable secondary structure is formed first, followed by addition of stem into the loop. The red region corresponds to the point where the linkage stem forms.
• (b) Basic concept of folding for an extended pseudoknot. An extended pseudoknot involves the fusing of two independent domains via a small segment of secondary structure. As in (a), this stable secondary structure is formed first, followed by joining the two independent domains into a single domain.
• (c) Basic concept of an embedded pseudoknot. Here, the secondary structure naturally permits a multibranch loop to form, and the extended pseudoknot that links two branches of the secondary structure is shown here in thermodynamic equilibrium with the standard secondary structure.
• (d) Basic concept of pleating. The secondary structure (shown above in d), appears to require a very long free strand region (green) to insure that the red segment of secondary structure is formed. However, when this is viewed more three dimensionally, the internal loop permits this structure to fold back on itself and requires a much shorter segment length.

——

Linked to dVerse Poets Pub — Quadrille #124 – Knot where Mish is hosting. She gave us the word knot, and then proclaimed, “I dare you to use pseudoknot.”

Quadrille Defined in a Quadrille

Quadrille: A poetic form introduced at dVerse Poets Pub circa 2011. The rules for Quadrille:

• not including the title, a poem of exactly 44 words, no more, no less
• use the prompt word or its variant. The word must be in the poem; not a description of or metaphor for.

See more quadrille poetry.