Page - 43 - in Charge Transport in DNA - Insights from Simulations

3.1TheDNAMolecule Table3.1: The studied DNA fragments of the first part of this work. Shown are the descriptors used throughout this work and the nucleobase sequence of the well-matcheddsDNAoligomers. Homogeneous sequences A5 5’-AAAAA-3’ 3’-TTTTT-5’ A9 5’-AAAAAAAAA-3’ 3’-TTTTTTTTT-5’ A13 5’-AAAAAAAAAAAAA-3’ 3’-TTTTTTTTTTTTT-5’ G5 5’-GGGGG-3’ 3’-CCCCC-5’ G9 5’-GGGGGGGGG-3’ 3’-CCCCCCCCC-5’ G13 5’-GGGGGGGGGGGGG-3’ 3’-CCCCCCCCCCCCC-5’ strongly. BothpolyAandpolyGDNAprobablyexhibitsomespecialproperties that are not foundwith other (irregular) sequences though. Yet, they are undoubtedly very different, and this provides a chance to see qualitativelywhat the sequence- relatedeffects in such short oligonucleotides are. Therefore, subject of thefirst study (chapter4) arepoly-adenine andpoly-guanine double-strandedhelicalDNAspecies, containingfive,nineand13basepairs; every specieswas cappedwith twoGCbase pairs on each end. Note that 13 base pairs correspond to slightlymore than one complete helical turn in the B-DNAconfor- mation. So, there are six dsDNAspecies in the first part, see table 3.1. Note that thepolyADNAspeciesareunlikely tobe thermodynamically stableundernormal conditions. However, suchA-tractsmayoccuras fragmentswithin longerdsDNA, and the cappingGCbase pairs act as stabilizers of the double-stranded structure here. In theproceedingchapters, anewsetofDNAsequenceswillbe introduced.As the general featuresof theDNAstructureundermechanical stressandmicrohydration 43