Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions
Fig 5
The stability predictions for ssDNA hairpins in the present model.
(A) The time-evolution of the number of base-pairs for a simple hairpin (GCGC(T)5GCGC) at different temperatures (90°C, 70°C, 50°C from top to bottom, respectively) in 0.1M NaCl solution. (B) The fraction of unfolded state f as a function of temperature for the hairpin in (A). Symbols: predictions from the present model. Line: fitted melting curve to the predicted data through Eqs 4–6. Ball-stick: the typical 3D structures predicted at low and high temperatures shown with PyMol (http://www.pymol.org). (C) The comparisons between predictions (solid lines) and experiments (dotted lines) for four DNA hairpins (GCGC(T)NGCGC) with different loop lengths at 0.1M [Na+]. Red: N = 3. Green: N = 5. Blue: N = 7. Black: N = 9. df/dT: the first derivative of predicted f with the temperature. Cp: the heat capacity from experiment [90].