Statistical mechanics of RNA folding: importance of alphabet size

Abstract

We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two kinds of bases, there are many alternate folding configurations, yielding thermodynamically stable ground-states only for a small set of structures of high designability, i.e., total number of associated sequences. In contrast, sequences made from four bases, as found in nature, or six bases have far fewer competing folding configurations, resulting in a much greater average stability of the ground state.

arXiv comment7 figures; uses revtex4

References in corpus (6)

• Why Do Proteins Look Like Proteins?
• Are Protein Folds Atypical?
• Statistical mechanics of secondary structures formed by random RNA sequences
• Designability, thermodynamic stability, and dynamics in protein folding: a lattice model study
• RNA secondary structure formation: a solvable model of heteropolymer folding
• An Analytical Approach to the Protein Designability Problem

Cited by in corpus (7)

• RNA secondary structure design
• Quantification of the differences between quenched and annealed averaging for RNA secondary structures
• Ground state and glass transition of the RNA secondary structure
• Dependence of RNA secondary structure on the energy model
• Model for Folding and Aggregation in RNA Secondary Structures
• New alphabet-dependent morphological transition in a random RNA alignment
• RNAlike polymer model: exact calculation on the Bethe lattice