Journal
PHYSICAL REVIEW E
Volume 94, Issue 4, Pages -Publisher
AMER PHYSICAL SOC
DOI: 10.1103/PhysRevE.94.042410
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Funding
- NSF [PHY13-16748]
- Division Of Physics
- Direct For Mathematical & Physical Scien [1316748] Funding Source: National Science Foundation
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We propose a new topological characterization of ribonucleic acid (RNA) secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc representation of RNA secondary structures, we consider a model that couples both (i) the topological genus of the graph and (ii) the number of crossing arcs of the corresponding primitive graph. We add a term proportional to these topological invariants to the standard free energy of the RNA molecule, thus obtaining a novel free-energy parametrization that takes into account the abundance of topologies of RNA pseudoknots observed in RNA databases.
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