Charge transfer equilibria of aqueous single stranded DNA

Marco DAbramo*a, Massimiliano Aschib and Andrea Amadei*c 
aDepartament de Bioquímica i Biología Molecular, Facultat de Biología, Universitat de Barcelona, Av. Diagonal 645, Barcelona 08028, Spain. E-mail:marco.dabramo@irbbarcelona.org 
bDipartimento di Chimica, Ingegneria Chimica e Materiali, Università de lAquila, via Vetoio (Coppito 1), 67010 lAquila, Italia 
cDipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, via della Ricerca Scientifica 1, 00133 Roma, Italia. E-mail:andrea.amadei@uniroma2.it

Received 27th July 2009, Accepted 23rd October 2009

 

First published on the web 28th October 2009

FULL TEXT

 

The charge transfer thermodynamics of a simple model of DNA, a single stranded 10-mer poly-adenine oligonucleotide, in water is investigated by means of a computational/theoretical procedure, in which all the relevant environmental effects are considered. Our data indicate that water and counterions ultimately dominate the DNA reduction and oxidation free energies, which are also strongly influenced by the base position along the strand. In fact, we estimated that reduction free energies are large and negative, particularly for the bases close to the 5 and 3 positions, whereas the electron detachment is thermodynamically unfavoured all along the strand, but with a higher free energy cost in the central region of the molecule. Further investigation on double charging, i.e. one nucleobase is oxidized and one is reduced within the strand, predicts that charge-separated states are possible and thermodynamically largely stable when the ionic forms are separated by several nucleobases.