Journal
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS
Volume 25, Issue 2, Pages 171-189Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/15257770500446915
Keywords
RNA secondary structure; free energy; cross linking entropy; Kuhn length; folding; renormalization theory
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We are developing a program to calculate optimal RNA secondary structures. The model uses di-nucleotide pairing energies as with most traditional approaches. However, for long-range entropy interactions, the approach uses an entropy-loss model based on the accumulated sum of the entropy of bonding between each base-pair weighted inversely by the correlation of the RNA sequence (the Kuhn length). Stiff RNA forms very different structures from flexible RNA. The results demonstrate that the long-range folding is largely governed by this entropy and the Kuhn length.
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