CHARGE TRANSPORT IN DNA OLIGONUCLEOTIDES WITH VARIOUS BASE-PAIRING PATTERNS

Irena Kratochvílová^a, Tatiana Todorciuc^a, Karel Král^a, Hynek Němec^a, Martin Bunček^b, Jakub Šebera^c,d, Stanislav Záliš^d, Zuzana Vokáčová^e, Vladimír Sychrovský^e, Lucie Bednárová^e, Peter Mojzeš^f, Bohdan Schneider^g

^a Institute of Physics AS CR, v.v.i., Na Slovance 2, CZ-182 21 Prague 8, Czech Republic, email: krat@fzu.cz

^b GENERI BIOTECH s.r.o., Machkova 587, CZ-500 11 Hradec Králové, Czech Republic

^c Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic

^d J. Heyrovský Institute of Physical Chemistry AS CR, v.v.i., Dolejškova 3, CZ-182 23 Prague 8, Czech Republic

^e Institute of Organic Chemistry and Biochemistry AS CR, v.v.i, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic

^f Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic

^g Institute of Biotechnology AS CR, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic. email: bohdan@img.cas.cz

Keywords: DNA, charge transport, structure

Charge migration in DNA has attracted a considerable amount of interest for its relevance to the mechanism of damage in nucleic acid and for its possible applications in the area of nanotechnology. We have combined various experiments and theoretical models to elucidate further the DNA charge transfer process in terms of DNA base pairing patterns, base stacking interaction and the role of the sugar-phosphate backbone. Through an exploration of the relation between the physical and chemical statuses of a particular DNA modification and its charge transport properties, we intended to affect the extremely complex charge transport process and its biological and technical significance. Our experimental data as well as the results from the theoretical models and calculations indicate that DNA charge transport strongly depends on the presence of structural perturbations, in particular irregularities in base-pairing and base-stacking patterns. Even seemingly unimportant structural perturbations caused by the presence of mismatched base-pairs affect conductivity to a greater extent than expected from conformational changes and decreased thermal stability alone.