Page - 67 - in Charge Transport in DNA - Insights from Simulations

4.7Conclusion cursatasmallerexternal force than in thecorrespondingsimulationwith thesame amount of water and the original number of counterions (passing from the red curve to theblue, and from thegreenone to theyellow). This effectwasobserved for allDNAspecies studied. The observations in stretching simulations are summarized in table 4.7. Certain trends are visible even thoughonly one simulationwasperformed for eachDNA species and considered conditions. So, larger force is needed to induce the over- stretching transition aswell as the separationof strands in themicrohydrated sys- temsDry1andDry2, comparedtothefullyhydratedDNA.Theeffectof thecontent of counterions ismoreblurred, yet still theonset of theoverstretched ladder struc- ture seems to occur at a smaller force if some counterions are removed from the microhydratedDNAcomplex. 4.7 Conclusion In this chapter, the structural features of microhydrated DNA and their changes upon stretching stress were investigated with classical MD simulation. The pre- liminarynatureof this studydoesnot allow todrawanyquantitative conclusions. Still, there are severalpoints tobemade. Both water and counterions are structure-stabilizing factors. The amount of wa- ter and the content of counterions necessary to support a helical double-stranded structure in the simulationswas characterized. The removal of a certain number of counterionsmaystabilize the structureof amicrohydratedDNAoligomer, even thoughsucha systembears anon-zero electric charge. Conformational transitions were observed at smaller forces when the DNA was stretchedmore slowly. This illustrates the irreversibility of the stretching process in the simulations,when the pulling is several orders ofmagnitude faster than in experiments. For this reason, further interpretationof the stretching simulations is limitedtothecomparisonoftheresponseofmicrohydratedDNAwiththeresponse ofDNAinsolution,pulledwith the same loading rates. The helical structure of DNAundergoesmarked changes upon removal ofwater fromthe cluster. First, thehelixbends toward themajorgroovewhere counterions 67