Page - 58 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions 4.4 EffectsofLowHydration Tomodel the lowhydration ofDNA,most of thewatermoleculeswere removed from the simulationbox. Since the exact amount ofwater remaining in the cluster isnotknown in the single-molecule experiments, fourdifferent levels ofhydration were probed in this work. Four sets of DNA–water clusters were prepared for everyDNAsequence, containing 1/10 (Dry1), 1/20 (Dry2), 1/40 (Dry3) and 1/80 (Dry4) of the original number ofwatermolecules, respectively, see table 3.3. Free MD simulation was then commenced for 10 ns, and the structure of the DNA oligomerswasmonitored. Table4.4: Appearance of themicrohydrated systems after anMDsimulation of 10ns withno external force. Helical – structure close to thatwith full hydration, withnoorminimal curvature; bent–structure that lost the linear shapeyet with preserved helical character; distorted – structure that lost the helical character but with observable hydrogen-bonding pattern; coiled – severely deformed structurewith corruptedhydrogenbondingofnucleobases. sequence Dry1 Dry2 Dry3 Dry4 A5 helical bent bent coiled A9 helical bent distorted coiled A13 bent bent distorted coiled G5 helical bent distorted coiled G9 helical bent distorted coiled G13 helical bent distorted coiled The structures of all the studied systems are summarized in table 4.4. The helical structure of DNA in the Dry1 systems is generally retained, howeverwith some defects. The A-like favoring oligomer G13 forms a structure with an even larger diameter thanA-DNAbut shorter, a sort of abarrel structure, seefigure4.9. The species A13, on the other hand, bends toward the major groove so that the endsof thedouble strandcomecloser toeachother. Themajorgroove isextremely narrowin thebend, and thereare severalNa+ ions in thegroove,preventingunfa- vorable contacts of thephosphates in thebackbones, seefigure4.10. 58