Page - 66 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions Table4.7: Force at which the overstretching transition as well as strand separation (melting) occurred. Data from simulations of fully hydrated systems (with two different loading rates) as well as for the systems Dry1, Dry2 and Dry1 with a decreased number of sodium ions. All figures in pN; ‘—’ denotes cases where no clear transition was observed. a The loading rate was 50 pN/ns for A5, A9, G5 and G9 while it was 83 pN/ns for A13 and G13. transition fullyhydrated Dry1 Dry2 Dry1with1/2 ions 50/83pN/nsa 10pN/ns A5 overstretchingat 187 142 288 — 184 separationat 508 458 901 941 860 A9 overstretchingat 199 154 361 — — separationat 746 678 1229 1109 946 A13 overstretchingat 293 173 395 580 335 separationat 1014 708 1365 1331 1674 G5 overstretchingat 172 171 301 309 121 separationat 713 704 932 1112 864 G9 overstretchingat 421 231 432 788 — separationat — 1001 1444 1451 895 G13 overstretchingat 397 314 412 551 298 separationat 1431 1332 1958 1164 1761 The significance of counterions present in the solvent formaintaining thedouble- strandedstructureofDNAwasseen in the freesimulationsalready. Following this line, the stretchingofmicrohydrateddouble-strandedDNAwas investigatedwith a smallernumberof counterions thanrequired toneutralize thenegative chargeof DNAbackbone (see the abovediscussionof such anoccurrence). Performedwere two further simulations for eachDNAoligomer studied: 1. with1/10of thebulknumberofwatermolecules (Dry1) and1/2of thenum- berof counterions required forneutralization, and 2. with1/20oforiginalwater (Dry2) and3/4of theoriginal counterions. The stretching profiles for A13 are presented in figure 4.13. The influence of the decreasednumber of counterions is visible here. The overstretching transition oc- 66