Necklace-Cloverleaf Transition in Associating RNA-like Diblock Copolymers

TL;DR

This paper investigates how the structure of RNA-like diblock copolymers transitions between cloverleaf and necklace forms depending on bond strengths, revealing a second-order phase transition between these states.

Contribution

It introduces a model for RNA-like diblock copolymers and analyzes the phase transition between cloverleaf and necklace structures based on bond strength ratios.

Findings

Polymer can be in cloverleaf or necklace state depending on bond strengths.

Transition between states is a second-order phase transition.

Structural properties depend on relative A--A, A--B, B--B bond strengths.

Abstract

We consider a ${\rm A}_m{\rm B}_n$ diblock copolymer, whose links are capable of forming local reversible bonds with each other. We assume that the resulting structure of the bonds is RNA--like, i.e. topologically isomorphic to a tree. We show that, depending on the relative strengths of A--A, A--B and B--B contacts, such a polymer can be in one of two different states. Namely, if a self--association is preferable (i.e., A--A and B--B bonds are comparatively stronger than A--B contacts) then the polymer forms a typical randomly branched cloverleaf structure. On the contrary, if alternating association is preferable (i.e. A--B bonds are stronger than A--A and B--B contacts) then the polymer tends to form a generally linear necklace structure (with, probably, some rear side branches and loops, which do not influence the overall characteristics of the chain). The transition between cloverleaf and necklace states is studied in details and it is shown that it is a 2nd order phase transition.