Neutral Networks of Interacting RNA Secondary Structures

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...

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 ...

RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties.

The secondary structures of nucleic acids form a particularly important class of contact structures. Many important RNA molecules, however, contain pseudo-knots, a structural feature that is excluded explicitly from the conventional definition of secondary structures. We propose here a generalization of secondary structures incorporating 'non-nested' pseudo-knots, which we call bi-secondary str...

Neutral Networks of Minimum Free Energy RNA Secondary Structures

Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks

The evolution and adaptation of molecular populations is constrained by the diversity accessible through mutational processes. RNA is a paradigmatic example of biopolymer where genotype (sequence) and phenotype (approximated by the secondary structure fold) are identified in a single molecule. The extreme redundancy of the genotype-phenotype map leads to large ensembles of RNA sequences that fo...