The formation of specific interaction between poly(3,4- ethylenedioxythiophene) (PEDOT) and adenine (A), cytosine (C) and thymine (T) single stranded homonucleotides has been investigated, complementing our previous investigation on complexes formed by PEDOT and guanine (G) homonucleotide (B. Teixeira-Dias et al, Soft Matter, 2011, 7, 9922-9932). Results derived from UV-vis and FTIR spectroscopy suggest that A and, especially, C homonucleotides form adducts dominated by non-specific electrostatic interactions, while complexes with T homonucleotides show a behavior that differ from those found for A-, C- and G-containing systems. Results provided by molecular dynamics simulations were consistent with these experimental observations. Thus, specific interactions are much less abundant in A- and C-containing complexes than in those involving G. Moreover, simulations allowed us to detect a structural re-organization in the T-containing complexes, which occurs after their initial formation. This has been attributed to the optimization of electrostatic interactions rather than to the formation of new specific interactions, as was previously found in complexes with G. From the analysis of the interaction of the different nucleotides with an EDOT molecule it is concluded that the most stabilizing specific interaction corresponds to the formation of N-H⋯O<inf>EDOT</inf> hydrogen bonds. Stabilization comes from electrostatic interactions, although the covalent contribution is non negligible. © 2013 The Royal Society of Chemistry.