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

@article{McCaskill1990TheEP,
  title={The equilibrium partition function and base pair binding probabilities for RNA secondary structure},
  author={John S. McCaskill},
  journal={Biopolymers},
  year={1990},
  volume={29}
}
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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References

SHOWING 1-10 OF 39 REFERENCES
Improved free-energy parameters for predictions of RNA duplex stability.
  • S. Freier, R. Kierzek, D. Turner
  • Biology, Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1986
TLDR
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.
Computer-aided prediction of RNA secondary structures
TLDR
An argument is made for integrating the two approaches presented in this paper, enabling the user to generate proposed structures using thermodynamic criteria, allowing interactive refinement of these structures through the application of experimentally derived data.
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
TLDR
A new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature.
Improved parameters for prediction of RNA structure.
TLDR
Thermodynamic studies of oligoribonucleotides are providing parameters and insights for the fundamental interactions that determine RNA structure, and parameters for stacking and hydrogen bonding will likely be important for predicting the three-dimensional structures of RNAs and for interpreting RNA-RNA associations.
Theory of oligonucleotide stabilization. I. The effect of single‐strand stacking
TLDR
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.
Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA
TLDR
Tuncating the free energies of hairpin loops, bulges, internal loops and multibranched junctions to two significant digits yields structures nearly identical to those generated using three digit values, showing that one can safely use truncated values in RNA folding calculations.
Stability of ribonucleic acid double-stranded helices.
Solution conformations of B. subtilis ribosomal 5S RNA: A calorimetric study
TLDR
The conformational changes demonstrated here may facilitate the movement of the protein synthesis machinery during RNA translation and be interpreted according to hypothetical secondary and tertiary base‐pairing schemes.
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