A kinetic model of RNA folding

• Published in: BioSystems Vol. 30; no. 1-3; p. 49
• Main Authors: Mironov, A A, Lebedev, V F
• Format: Journal Article
• Language: English
• Published: Ireland 1993
• Subjects: Algorithms; Kinetics; Markov Chains; Models, Chemical; Molecular Structure; Nucleic Acid Conformation; RNA - chemistry; Thermodynamics
• ISSN: 0303-2647
• DOI: 10.1016/0303-2647(93)90061-G

The RNA folding process is represented as a Markov process with states corresponding to RNA secondary structures and transition probabilities corresponding to transformations of a secondary structure caused by formation or disintegration of a helix. Transition probabilities (kinetic constants) are determined. A notion of a group of structures is introduced, and it allows to reduce the state space. Energetic and kinetic parameters of pseudoknots are estimated. Algorithms for computation of a kinetic ensemble for structures and groups of structures are presented, as well as their modifications that take into account pseudoknots. The described algorithms are implemented as a procedure for prediction of RNA secondary structure that is included in the package DNA-SUN.