Massively parallel, bottom-up controlled incorporation of DNA molecules into microfabricated interdigital gold contact arrays is reported. The specific attachment of the ends of the DNA molecules to the metal contacts is provided via thiol functional groups obtained by conjugation of the sticky ends of the DNA duplexes with thiol modified nucleotides. Directed flow in an open flow cell has been used to accomplish stretching of single-tethered, coiled duplexes into a linear "wirelike" conformation. Simultaneously, the free molecule end is forced to move towards the adjacent contact and can anchor there resulting into DNA-based interconnects between neighboring contact fingers. The used experimental setup allows the application of hydrodynamic flow in user-defined areas of the integrated electrode structure with a maximum degree of flexibility concerning both flow profile and direction. The developed method for the formation of interconnects is robust, shows a high yield, and is highly specific. (C) 2009 American Vacuum Society. [DOI: 10.1116/1.3002385]