Incorporating Ligands Binding to Specific Sequence/Structure Motifs

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

Typedefs

typedef struct vrna_sc_motif_s vrna_sc_motif_t

#include <ViennaRNA/constraints/ligand.h>

Type definition for soft constraint motif.

Functions

int vrna_sc_add_hi_motif(vrna_fold_compound_t *fc, const char *seq, const char *structure, FLT_OR_DBL energy, unsigned int options)

#include <ViennaRNA/constraints/ligand.h>

Add soft constraints for hairpin or interior loop binding motif.

Here is an example that adds a theophylline binding motif. Free energy contribution is derived from \(k_d = 0.1 \mu M\), taken from Jenison et al. 1994. At \(1M\) concentration the corresponding binding free energy amounts to \(-9.93~kcal/mol\).

theo_aptamer.svg

vrna_sc_add_hi_motif(fc,
                     "GAUACCAG&CCCUUGGCAGC",
                     "(...((((&)...)))...)",
                     -9.93, VRNA_OPTION_DEFAULT);

SWIG Wrapper Notes:

This function is attached as method sc_add_hi_motif() to objects of type fold_compound. The last parameter is optional an defaults to options = VRNA_OPTION_DEFAULT. See, e.g. RNA.fold_compound.sc_add_hi_motif() in the Python API .

Parameters

• fc – The vrna_fold_compound_t the motif is applied to

• seq – The sequence motif (may be interspaced by ‘&’ character

• structure – The structure motif (may be interspaced by ‘&’ character

• energy – The free energy of the motif (e.g. binding free energy)

• options – Options

Returns

non-zero value if application of the motif using soft constraints was successful

vrna_sc_motif_t *vrna_sc_ligand_detect_motifs(vrna_fold_compound_t *fc, const char *structure)

#include <ViennaRNA/constraints/ligand.h>

vrna_sc_motif_t *vrna_sc_ligand_get_all_motifs(vrna_fold_compound_t *fc)

#include <ViennaRNA/constraints/ligand.h>

struct vrna_sc_motif_s

Public Members

int i

int j

int k

int l

int number