RecA protein mediated nano-scale patterning of DNA scaffolds

Molecular lock-and-key functionality inherent to a large number of biological molecules is arguably one of the most promising potential routes for building complex nanostructures and eventually nano-electronic devices by self-assembly. In particular DNA- and protein-based approaches with their intrinsic powerful self-assembly properties are promising candidates. Here, we investigate the use of the DNA-binding protein RecA as a tool for patterning DNA scaffolds site-specifically and in a programmable way at the nanometer-scale. RecA proteins bind to single-stranded DNA to form nucleoprotein filaments. When a double-stranded DNA, containing a region homologous to the single-stranded DNA of the nucleoprotein filament, is brought into contact with the nucleoprotein filament, a stable triple-strand DNA structure is formed. This mechanism can be exploited as a sequence-specific patterning tool and we demonstrate its use by patterning a double-stranded DNA scaffold at different locations with nanometer-sized nucleoprotein filaments. In addition, we demonstrate the simultaneous patterning of the scaffold at multiple locations. This is the first demonstration of a protein-based molecular patterning technique which is site-specific, programmable and scalable. This work offers a potential basis for molecular lithography applications, and opens previously inaccessible routes towards the fabrication of complex functional nano-electronic devices by self-assembly.