Predicting RNA pseudoknot folding thermodynamics

Song Cao, Shi Jie Chen

Research output: Contribution to journalArticlepeer-review

114 Scopus citations


Based on the experimentally determined atomic coordinates for RNA helices and the self-avoiding walks of the P (phosphate) and C4 (carbon) atoms in the diamond lattice for the polynucleotide loop conformations, we derive a set of conformational entropy parameters for RNA pseudoknots. Based on the entropy parameters, we develop a folding thermodynamics model that enables us to compute the sequence-specific RNA pseudoknot folding free energy landscape and thermodynamics. The model is validated through extensive experimental tests both for the native structures and for the folding thermodynamics. The model predicts strong sequence-dependent helix-loop competitions in the pseudoknot stability and the resultant conformational switches between different hairpin and pseudoknot structures. For instance, for the pseudoknot domain of human telomerase RNA, a native-like and a misfolded hairpin intermediates are found to coexist on the (equilibrium) folding pathways, and the interplay between the stabilities of these intermediates causes the conformational switch that may underlie a human telomerase disease.

Original languageEnglish
Pages (from-to)2634-2652
Number of pages19
JournalNucleic acids research
Issue number9
StatePublished - 2006


Dive into the research topics of 'Predicting RNA pseudoknot folding thermodynamics'. Together they form a unique fingerprint.

Cite this