Page - 68 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions accumulate, or passes to a barrel-like structure. Then, the double strand loses its helical character roughly at 6water molecules per phosphate group. Continued drying inducesa ruptureofhydrogenbondsandacollapseof thedouble-stranded structure toadisorderedcompact coil. The helical structure of microhydrated DNA can be supported by pulling at the 3’-ends. WhenmicrohydratedDNAispulledbyanexternal force, conformational changes require larger force than those in fully hydrated DNA. This may be ex- plained by the tendency of a molecular cluster in vacuo to maintain a compact shape, againstwhich thepulling force acts. When a part of the counterions is removed from themicrohydrated system (pro- vided this situation is real), the overstretched ladder structure occurs at aweaker externalpulling force. In conclusion, extensive investigationof the structural changesofDNAunder con- ditions resembling the experimentwas shown for homogeneousDNAsequences. Thedeveloped simulation strategies for the stretchingofDNAand the simulation ofmicrohydratedDNAconstitute thebasis for the investigationofchargetransport andcharge transferunder these conditions in thenext chapters. 68