Ligands Binding to RNA Structures

In our library, we provide two different ways to incorporate binding of small molecules and proteins to specific RNA structures. The first approach is implemented as an actual extension of the folding grammar. It adds auxiliary derivation rules for each case when consecutive unpaired nucleotides are evaluated. Therefore, this model is applicable to ligand binding to any loop context.

The second approach, on the other hand, uses the soft-constraints feature to change the energy evaluation of hairpin- or internal-loops. Hence, it can only be appleid when a ligand binds to a hairpin-like, or internal-loop like motif.

Unstructured Domains

Sometime, certain ligands, like single strand binding (SSB) proteins, compete with intramolecular base pairing of the RNA. In situations, where the dissociation constant of the ligand is known and the ligand binds to a consecutive stretch of single-stranded nucleotides we can use the Unstructured Domains functionality to extend the RNA folding grammar. This module provides a convenience default implementation that covers most of the application scenarios.

The function vrna_ud_add_motif() attaches a ligands sequence motif and corresponding binding free energy to the list of known ligand motifs within the domains_up attribute of vrna_fold_compound_t. The first call to this function initializes the /grammar/domains_up feature with our default implementation. Subsequent calls of secondary structure prediction algorithms with the modified vrna_fold_compound_t then directly include the competition of the ligand with regules base pairing. Since we utilize the unstructured domain extension, The ligand binding model can be removed again using the vrna_ud_remove() function.

Hairpin-/Internal Loop Motifs

Ligand binding to specific hairpin/internal loop like motifs using the Soft Constraints feature.