The equilibrium partition function and base pair binding probabilities for RNA secondary structure

  title={The equilibrium partition function and base pair binding probabilities for RNA secondary structure},
  author={John S. McCaskill},
A novel application of dynamic programming to the folding problem for RNA enables one to calculate the full equilibrium partition function for secondary structure and the probabilities of various substructures. In particular, both the partition function and the probabilities of all base pairs are computed by a recursive scheme of polynomial order N3 in the sequence length N. The temperature dependence of the partition function gives information about melting behavior for the secondary structure… 

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Method for predicting RNA secondary structure.

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  • Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1975
In nearly all cases the cloverleaf is predicted to be the structure with the lowest free energy of formation.

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A new set of energy values to predict the secondary structures in RNA molecules has been derived through a multiple-step refinement procedure and achieves more than 80% success in predicting the cloverleaf pattern in tRNA and the consensus folding of 5S RNA.

Improved free-energy parameters for predictions of RNA duplex stability.

  • S. FreierR. Kierzek D. Turner
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1986
These parameters predict melting temperatures of most oligonucleotide duplexes within 5 degrees C, about as good as can be expected from the nearest-neighbor model.

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The theory leads to length dependent heats and entropies for short single strands in a natural way, and permits a more accurate assessment of the contribution of partially bonded states in thermal transitions than has previously been possible.

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Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA

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