Marco Pretti, CNR-ISC @ Politecnico di Torino #
Chemically-controlled denaturation of a RNA-like polymer model #
We consider a lattice polymer model of the 2-tolerant type (i.e., a random 
walk allowed to visit lattice bonds at most twice), in which 
doubly-visited bonds yield an attractive energy term (pairing energy). 
Such a model has been previously proposed as a rough, non-specific 
description of the RNA folding mechanism. In fact, the model predicts, 
besides the usual theta-collapse, an extra transition to a low-temperature 
fully-paired state.
In the current work, we propose an extension of the model, in which an 
additional (micromolecular) chemical species can bind the polymer and 
locally forbid base-pairing. This special kind of interaction is meant to 
mimic a generic mechanism by which micro-RNA molecules could hamper 
messenger RNA folding, and ultimately
exert their down-regulating effect within a gene-expression network. We 
investigate equilibrium thermodynamics in the grand-canonical picture, at 
the level of a Bethe approximation, which is, a refined mean-field 
technique, equivalent to the exact solution on a random-regular graph.
The general trend we observe is that expected from the mechanism 
implemented in the model (increasing micro-RNA concentration favors 
denaturation and lowers the folding temperature), but the resulting phase 
diagram turns out to be unexpectedly interesting and rich.