Page - 63 - in Charge Transport in DNA - Insights from Simulations

4.5EffectsofDecreased IonContent original amount ofwater, respectively)were stripped further of 1/4, 1/2 and 3/4 of the original number of sodium ions aswell as of all of them. MD simulations were thenperformedwith no external force. The observed structural changes are described in table4.6. Table4.6: Appearance of the Dry1 complexes after MD with a decreased number of sodium ions. B-like – long helical structure with a small diameter, A-like – shorter helical structure with a large diameter, ladder – parallel linear double-stranded structure. 3/4 ions 1/2 ions 1/4 ions 0 ions A5 B-like B-like ladder separation A9 B-like B-like ladder separation A13 B-like B-like ladder separation G5 A-like B-like ladder ladder G9 A-like B-like ladder separation G13 A-like B-like ladder separation In the complexeswithmorewater (Dry1), thehelical double-stranded structureof DNAwas preserved even upon the removal of half of the ions. Interestingly, the helical structure of the studiedDNAspecies ismore stablewith a slightly smaller number of ions thannecessary for neutralization. The transition to a ladder struc- ture occurredonly after the removal of further 1/4of theoriginal numberof ions. These structures resemble those reported in previous simulations of DNA with similar charge state[122] closely. Even though the simulated systems were very different otherwise (no water whatsoever, no counterions and phosphate groups neutralizedpartially). Eventually, theDNAstrands separatedwhenall of the ions were removed. The structure ofmorepoorlyhydratedDNAoligomers (Dry2)wasmoreprone to perturbations causedby the removal of ions, as the ladder structurewasobserved already with 1/2 of the amount of ions necessary for neutralization. Neverthe- less, the separationofDNAstrands tookplace only after the complete removal of counterions. Another interesting effect is that the polyGoligomers passed to aB- like conformationwhen1/2of the ionswere removed. Thismaybe interpreted in termsof the significanceof counterions tomaintain theA-likeDNAconformation. 63