NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY STRUCTURES

Neutral Networks of Interacting RNA Secondary Structures

RNA molecules interact by forming inter-molecular base pairs that compete with the intramolecular base pairs of their secondary structures. Here we investigate the patterns of neutral mutations in RNAs whose function is the interaction with other RNAs, i.e., of co-folding RNAs. We find that (1) the degree of neutrality is much smaller in interacting RNAs compared to RNAs that just have to cofor...

Neutral Networks of Minimum Free Energy RNA Secondary Structures

Generic properties of combinatory maps: neutral networks of RNA secondary structures.

Random graph theory is used to model and analyse the relationships between sequences and secondary structures of RNA molecules, which are understood as mappings from sequence space into shape space. These maps are non-invertible since there are always many orders of magnitude more sequences than structures. Sequences folding into identical structures form neutral networks. A neutral network is ...

Relation Between RNA Sequences, Structures, and Shapes via Variation Networks

Background: RNA plays key role in many aspects of biological processes and its tertiary structure is critical for its biological function. RNA secondary structure represents various significant portions of RNA tertiary structure. Since the biological function of RNA is concluded indirectly from its primary structure, it would be important to analyze the relations between the RNA sequences and t...

RNA Secondary Structures

The central dogma of molecular biology states that the flow of information is from DNA, through RNA, to proteins. What this means is that DNA is the storage medium of genomic information, while proteins are the molecules with functional and structural rôles. In this view, RNA is mostly considered a ‘supporting actor’, being the medium used for transporting information from storage to where it i...