Page - 62 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions Figure4.11: Watson–Crickhydrogen-bondingpatternof themicrohydratedspeciesA13 in simulationwith stabilizing external force –Dry1 (top) andDry2 (bot- tom). Red–hydrogenbondpresent,white –nohydrogenbond. and there are several defects in theDry2 case. The hydrogen-bonding pattern in the shorter DNA oligomers is more vulnerable and is destroyed almost entirely within a fewnanoseconds in theDry2 systems. SeefigureA.2 in the appendix for a completeoverviewof thehydrogenpatternof thedifferent sequences. 4.5 EffectsofDecreased IonContent Another important component of themolecular system is the counterions,Na+ in thiscase. InanextremecaseofcompletelydehydratedDNAwithnoions, thehelix wouldunwind, and the strandswould separate readily due to the repulsive elec- trostatic interactionof thenegatively-chargedbackbones. Note that thephosphate groups in thebackbones retain theirnegative charges throughout thiswork.While a partial protonation of phosphates was considered in a previous study, where DNAunder harsh conditions (electrospray)wasmodeled,[122], thiswork aims at thedescriptionofDNAin themilder setupof single-molecule experimentswhere the solvent is removed partially with a stream of gas. Themost straightforward assumptionis thatofunchangedchargestateofphosphates,whichmaybeneutral- izedbycounterionsremaininginthehydrationshell. Then, thequestioniswhether thenumberofcounterionsnecessary forneutralizationwouldremain in thecluster or rather be carried awayby the streamof gas togetherwith the solvent. It is not possible toprovide ananswerbasedon the simulations in thiswork, yetwhat can bedone is to investigate if andhow the stability ofDNAstructure changeswhen the counterions are (partially) removed, at a givendegree of hydration. Todo so, the systemsDry1 andDry2 from theprevious section (with 1/10 and 1/20 of the 62