Page - 59 - in Charge Transport in DNA - Insights from Simulations

4.4EffectsofLowHydration Figure4.9: ThemicrohydratedDNAspeciesG13 (Dry1)adoptsamorecompact(barrel- like) structure in an MD simulation with no stabilizing external force. (Side aswell as topview; surroundingwatermoleculesnot shown for clar- ity.) The difference between polyA and polyG can be explained by the larger hydra- tion of polyA and its known inability to assume anA-like structure. Indications of these effects are generally visible in the shorterDNAoligomers, too. TheDNA oligomers lose thehelical character in theDry3 systems,andtheycollapse todisor- deredcompactstructure inDry4,whereeventhehydrogenbondingofnucleobases disappears. All of these quite different conformational transitionsmaybe seen as apursuit to assumeamore compact conformation,undergivenconditions. Theobserved irregularitiesmaybeovercomeby the applicationof amoderate ex- ternalpulling forceactingagainst the tendencyof the insufficientlyhydratedDNA double strand to bend. For this reason aswell as to emulate the setupof conduc- tivityexperiments, furthersimulationswereperformedwithanadditionalexternal force applied to theO3’ atomson the3’-endsof eachDNAstrand. Themagnitude of this forcewas chosen in such away that theDNAwould retain straight helical double-strandedstructure,which turnedout tobe50kJ/mol·nm=83pNforDry1 and100kJ/mol·nm=166pNforDry2. Selectedhelicalparameterswereevaluated along these simulations, see table 4.5. In the Dry3 andDry4 systems, no helical 59