ENERGETICS OF THE HAIRPIN TO MISMATCHED DUPLEX TRANSITION OF D(GCCGCAGC) ON NACL SOLUTION

We report Potential of Mean Force studies to describe the relative thermodynamic stabilities of d(GCCGCAGC) in a mismatched duplex and a hairpin monomer conformations in NaCl solution. The PMF calculations are combined with previous molecular mechanics and normal mode analysis in order to estimate the role of different components of the free energy in determining the relative stability of the duplex and hairpin structures. The high entropy associated with the loop region and the lack of minor groove phosphate-phosphate interactions in the hairpin compete against the gain in enthalpic contribution to the free energy due to base pairing in the mismatched duplex. The combined free energy calculations show that the hairpin is the most stable conformation at low salt and that a hairpin to duplex transition takes place at 0.47 M NaCl. In addition, we studied the hairpin to partially stacked single helical conformation equilibrium at low salt. We found a small variation in transition temperature in salt concentration. 2-3° K/decade, in contrast to the duplex to hairpin or duplex to partially stacked single helix transition where the transition temperature exhibited marked dependence on salt concentration. This is in qualitative agreement with experimental data. Based on the Potential of Mean Force free energy calculation, the order of relative stability of the three-conformations studied varies with salt concentration. We observe the following orders of stability: stacked single helix > hairpin > duplex for cs < 0.77 M NaCl; single helix > duplex > hairpin for0.77 < cs < 2.1 M; and duplex > hairpin > single strand fore, > 2.1M. From the calculated PMF free energy curves in the NaCl concentration range, 0.01 < c, < 5.0 M, we can assign upper and lower bounds for the non-ionic differences in free energy between the duplex, hairpin, and stacked single helical states (at standard conditions: cs = 1.0M.T = 25°C, and 1 M oligomer concentration). We found that for ^GduplexsingieheUx = Gduplex 2 X Gsingieheljx < -7.38 Kcal/mol, the single helix is the least stable state. For the duplex-to-hairpin free energy difference in the range, -1.87 < AGduplex.hairpin < 0.03 Kcal/mol, there will always be a salt- induced hairpin-to-duplex transition for 0.01 <cs< 1.6MNaCl.IfbxGdup]ex.hairpin < -1.87, the duplex is always more stable than the hairpin; and for AGduplex.hairpin > 0.23 Kcal/mol, the hairpin state is always more stable than the duplex, for all salt concentrations. © Taylor & Francis Group, LLC.