Page - 65 - in Charge Transport in DNA - Insights from Simulations

4.6Effect ofWater and Ionson theStretchingProfileofDNA Figure4.13: Stretching profiles of DNA A13 in a microhydrated environment with a smallernumber of ions. It canbe interpreted in twoquite independentways: 1. thehelicalstructureofmicrohydrateddouble-strandedDNAisprovidedsup- port by the external stretching force ofmoderatemagnitude, acting against thebendingof theoligomer, as conceivedbefore. 2. this structurecanresista largermechanical stress thantheDNAinwatercan. However, the situation is not quite unambiguous, as can be seen on the example of the short oligomer A5, see figure 4.12 (left). Here, the double-stranded struc- ture is stillmore stable in theDry1hydration shell than in bulk solution, but the Dry2hydration is already insufficient to support anykindofhelical pattern. Con- sequently, no clear conformational transition can be seen in the stretchingprofile, and the length of the double strand increases gradually up to a point where the strands separate. This kind of behavior was observed for this quite short DNA oligomer only. Another anomaly could be thought of in case of longer oligomers, where someparts of the double strandwould remain in the helical conformation longer (i.e. up to a larger external force) than others thatwould pass to a ladder structuremore readily. An example of a stretching profile that correspondswith such a hypothesis is that of the A9 specieswith hydration shell Dry2 (see figure 4.12 (right)): The increase of distance vs force consists of several steps thatwould represent the successive transitions of different parts of the double strand to the ladder conformation. 65