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A two length scale polymer theory for RNA loop free energies and helix stacking Daniel P. Aalberts and Nagarajan Nandagopal
 

Summary: A two length scale polymer theory for RNA loop free energies and helix stacking
Daniel P. Aalberts and Nagarajan Nandagopal
Physics Department, Williams College,
Williamstown, MA 01267
RNA, in press (2010).
The reliability of RNA secondary structure predictions is subject to the accuracy of the underly-
ing free energy model. mfold and other RNA folding algorithms are based on the Turner model,
whose weakest part is its formulation of loop free energies, particularly for multibranch loops. RNA
loops contain single-strand and helix-crossing segments, so we develop an enhanced two-length freely
jointed chain theory and revise it for self-avoidance. Our resulting universal formula for RNA loop
entropy has fewer parameters than the Turner/mfold model, and yet simulations show that the
standard errors for multibranch loop free energies are reduced by an order of magnitude. We further
note that coaxial stacking decreases the effective length of multibranch loops and provides, surpris-
ingly, an entropic stabilization of the ordered configuration in addition to the enthalpic contribution
of helix stacking. Our formula is in good agreement with measured hairpin free energies. We find
that it also improves the accuracy of folding predictions.
I. INTRODUCTION
Accurate prediction of macromolecular structure from
primary sequence is one of the grand challenges of com-
putational biology. The secondary structure of RNA, de-

  

Source: Aalberts, Daniel P. - Department of Physics, Williams College

 

Collections: Physics