Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
Fig 3
The stability prediction for a sample RNA pseudoknot in the present model.
(a) The time-evolution of the number of base pairs for MMTV pseudoknot (shown in Fig 1A) at different temperatures (100°C, 80°C, 60°C, 40°C from top to bottom, respectively) in 50mM KCl solution. (b) The fractions of folded state (F, black), unfolded state (U, blue), and intermediate state (I, red) as a function of temperature for MMTV pseudoknot at 50mM [K+]. The dotted lines are fitted to the predicted data through Eqs. 2 and 3. (c) The fraction of denatured base pairs f as a function of temperature for MMTV pseudoknot at 50mM [K+]; symbols: from the present model; line: from Eq 4. Ball-stick: the typical 3D structures predicted at different temperatures shown with the PyMol (http://www.pymol.org).