Page - 6 - in Charge Transport in DNA - Insights from Simulations

Introduction acterofDNAunderambient conditions. ThedependenceofDNAconductanceon the distance of the electrodeswas proposed by Tao et al.,[8] however in amacro- scopic fashion. Stepwise decrease of conductancewas reported, as the individual DNAmoleculesbetween theelectrodeswerebreaking. The fundamental features of CT in DNA have been described as well. First, the exponentialdependenceofCTefficiencyon the lengthof theDNAoligomers. Sec- ond, the role of experimental setup that is both crucial and challenging to charac- terize. In conclusion, carefully preparedDNAdevices exhibitedmeasurable con- ductance, and this fact together with the practicable synthesis of even very long DNAmoleculeswere the initial impulses for the contemplations on the potential useofDNA-baseddevices innano-electronics.[14,15] Albeit, thestructureof theDNAspecies in theseexperimentscouldnotberesolved unambiguously. While it was concluded that the structure played a key role in determining the conductance, it could only be guessed on the basis of observed electricpropertieswhat the structural contourswere. Allmentionedexperimental studies share thegeneral featuresof the experimental setup.ADNAoligomerof several tensofbasepairs is linkedtometallic electrodes viaathioalkylgroupattachedusuallytothe3’-endofeachoftheDNAstrands. The distance of electrodes is or can be varied in the experiments, stretching theDNA molecule, and theCTefficiency is affectedby the alteredDNAstructure. This fact directs the focusof the intendedresearchtoaconsiderableextent to themechanical properties of theDNAspeciesunder thegiven conditions. Thepotential ability of DNA to stretch in biological processeswasmentioned already in 1953,[16] in an article thatdirectly followedtheproposalofDNAstructurebyWatson&Crick.[17] The responseofdsDNAstructure to stretching stresshasbeen studiedextensively since the 1990s. First considerations on entropic elasticity of DNA [18] were fol- lowedby studies on theDNA ‘overstretching’,[19, 20] and earlymodeling studies revealed that dsDNAwoulddeformdifferently if the strands are pulled indiffer- ent ways.[21, 22] Also, a structurewas proposed that DNAwould assume upon stretching of the 3’-ends of each strand – so-called S-DNAwithmaintained inter- strand base pairing but unwound, in a sort of a ladder structure. On the other hand, when dsDNA was stretched and supercoiled, another new structure was observed.[23] 6