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Statistical mechanics of RNA folding: importance of alphabet size

Ranjan Mukhopadhyay·Eldon Emberly·Chao Tang·Ned S. Wingreen
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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.

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Ranjan Mukhopadhyay, Eldon Emberly, Chao Tang, Ned S. Wingreen. 2003-08-04. Statistical mechanics of RNA folding: importance of alphabet size. https://doi.org/10.1103/physreve.68.041904

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