Page - 82 - in Charge Transport in DNA - Insights from Simulations

ChargeTransport inMicrohydratedDNA The energetics of hole transport in DNA is determined by the IP of the nucle- obases. Apart from themean value of the IP, the hole transport is determined by thefluctuationsof the IP in time. The std. deviation of the IP was found to be 0.3–0.4 eV in previous studies of fully solvated DNA.[124, 125] An important observation for the microhydrated systems is that themagnitude of these IP fluctuations is identical to that in fully solvatedDNA.Thestd.deviationof the IP is0.29–0.30eVfor thesystemsDry1and Dry2, as compared to 0.31 eVobtained for the fully hydrated system in thiswork. See appendix B.3 for an complete overviewof the IP of the single nucleobases in the investigated sequences. Clearly, the fluctuations of the IP in fully hydrated DNAare caused by the nearest hydration shell(s) of the nucleobases – thewater molecules in contact orvery close to thenucleobases. Table6.2: ESP (inV) induced at a nucleobase in theGToligo by the various parts of themolecular environment. Environment ESP inducedby DNA water Na+ Full −25.25 +6.91 +18.85 Dry1 −26.91 +0.76 +26.25 Dry2 −28.19 +0.84 +27.45 The IPofnucleobases aredrivenby the electricfield inducedby themolecular en- vironment [124,125]. Therefore, theelectrostaticpotential (ESP) inducedbytheen- vironmentonanucleobase in thevariouslyhydratedGToligowascalculated.[124] Muchthesameasthefluctuationsof theIP, thefluctuationsofESPremainthesame evenupondehydration. Amounting to0.30,0.29and0.29Vfor the fullyhydrated, Dry1 andDry2 systems, respectively. This is an evidence that thedecisiveportion of electric effect comes fromthenearest hydration shell of thenucleobases. Further, theESPonanucleobasewasdecomposed tocontributions inducedby the components of themolecular environment,which areDNAbackboneswith all of theothernucleobases,watermolecules, andNa+ ions. SeeTab.6.2 foranoverview of the ESP of these groups. Interestingly, the magnitude of ESP induced by the ions increases, as does theESP inducedby theDNAbackbones (so that it ismore negative). 82