Charge Transport in DNA Oligonucleotides with Various Base-Pairing Patterns

Irena Kratochvílová¹, Tatiana Todorciuc¹, Martin Bunček², Jakub Šebera^3,4, Stanislav Záliš⁴, Zuzana Vokáčová⁵, Vladimír Sychrovský⁵, Lucie Bednárová⁵, Peter Mojzeš⁶, Bohdan Schneider⁷

¹Institute of Physics, AS CR, v.v.i., Na Slovance 2, CZ-182 21 Prague 8, Czech Republic, email: krat@fzu.cz

²GENERI BIOTECH s.r.o., Machkova 587, CZ-500 11 Hradec Králové, Czech Republic

³Institute of Macromolecular Chemistry, AS CR, v.v.i., Heyrovského nám. 2, CZ-162 06 Prague 6, Czech Republic

⁴J. Heyrovský Institute of Physical Chemistry, AS CR, v.v.i., Dolejškova 3, CZ-182 23 Prague 8, Czech Republic

⁵Institute of Organic Chemistry and Biochemistry, AS CR, v.v.i, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic

⁶Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic

⁷Institute of Biotechnology, AS CR, v.v.i., Vídeňská 1083, CZ-142 20 Prague 4, Czech Republic. email: bohdan@img.cas.cz

Charge migration along DNA double-helical molecules may be of biological importance as the extended electronic states of DNA could play a role in the processes of sensing and/or repair of DNA damage. 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 various perturbations, in particular irregularities in base-pairing, base-stacking patterns and various metals/metal groups presence/interactions. 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.