Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions
Fig 4
The stability predictions for dsDNAs in the present model.
(A) The time-evolution of the number of base-pairs for a dsDNA (sequence: (GGACGTCC)2; strand concentration: 1mM) at different temperatures (90°C, 65°C, 40°C from top to bottom, respectively) in 1M NaCl solution. (B) The fractions of unfolded state f as functions of temperature for the dsDNA in (A). Green triangle: predictions at high strand concentration (1mM). Purple square: predictions at experimental strand concentration (0.1mM). Two dotted lines are the fitted melting curves to the corresponding predicted data. The solid line is calculated through Eq 7. Ball-stick: the typical 3D structures predicted at low and high temperatures shown with PyMol (http://www.pymol.org). (C) The melting temperatures (Tm’s) as functions of strand concentration for three dsDNAs: purple, (GGACGTCC)2, blue, (GTTGCAAC)2, and red, (CGATATCG)2 at 1M [Na+]. Symbols: experimental results [71]. Lines: predictions from the present model. (D) The predicted (solid lines) and experimental (dotted lines) melting curves [89] for the dsDNA harboring symmetric internal loops with sequences of CTCGTC(T)NCAGTGC/GCACTG(T)NGACGAG in 1M NaCl solution. Green: N = 0, i.e., the double helix without internal loop. Blue: N = 2. Purple: N = 6.