This study explores the use of N-substituted polypyrroles as a route for localizing DNA molecules onto conducting surfaces. N-substituted pyrrole monomers containing N-hydroxysuccinimidyl groups for DNA binding reactions were synthesized. These monomers were electro-copolymerized under different conditions on platinum or gold working electrodes in a three-electrode/single compartment cell. Subsequent DNA reactions were performed by incubating the resulting polymer conductive films with amino-substituted DNA sequences. In addition, the electro-copolymerization reactions of pyrrole monomers were conducted on preselected. electrode positions of the Molecular Nanosystems (MNS) wafers and the formation of conductive films was demonstrated. In these experiments, it was determined also that by controlling the electro-copolymerization reactions, the conductive films can be restricted to grow on specific locations of the MNS wafer. This was achieved by electrically passivating the chosen electrodes with self-assembled multilayers (SAM)s of alkane thiols. Hexadecane thiol (HDT) was found the most efficient in forming SAMS and in preventing the pyrrole electropolymerization. Various analytical techniques including AFM, IR, and cyclic voltammetry (CV) were used to characterize the monomers, the electropolymerized polymers, and the attachment of amine-terminated DNA to polypyrrole copolymers. (C) 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 6014-6024, 2009