Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme.

@article{Isambert2000ModelingRF,
  title={Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme.},
  author={H. Isambert and Eric D. Siggia},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={2000},
  volume={97 12},
  pages={6515-20}
}
A quantitative understanding of nucleic acid hybridization is essential to many aspects of biotechnology, such as DNA microarrays, as well as to the structure and folding kinetics of RNA. However, predictions of nucleic acid secondary structures have long been impeded by the presence of helices interior to loops, so-called pseudoknots, which impose complex three-dimensional conformational constraints. In this paper we compute the pseudoknot free energies analytically in terms of known standard… CONTINUE READING

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