TY - JOUR
T1 - Statistical mechanics of RNA folding
T2 - Importance of alphabet size
AU - Mukhopadhyay, Ranjan
AU - Emberly, Eldon
AU - Tang, Chao
AU - Wingreen, Ned S.
PY - 2003
Y1 - 2003
N2 - We construct a base-stacking 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, most sequences have many alternative folding configurations and are consequently thermally unstable. Stable ground states are found 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.
AB - We construct a base-stacking 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, most sequences have many alternative folding configurations and are consequently thermally unstable. Stable ground states are found 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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U2 - 10.1103/PhysRevE.68.041904
DO - 10.1103/PhysRevE.68.041904
M3 - Article
C2 - 14682970
AN - SCOPUS:84990876639
SN - 1063-651X
VL - 68
JO - Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics
JF - Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics
IS - 4
ER -