DNA nanotechnology: steps towards automated synthesis.

The biosynthesis of proteins and other biomolecules is carried out with exquisite selectivity and efficiency, and with all building blocks present at the same time. In the laboratory, however, chemical synthesis is much less refined and is typically controlled by performing reactions with pure reactants, one step at a time and with purification steps in-between. Moreover, the formation of covalent bonds occurs through random collisions of reactants, so to proceed efficiently the reactant concentrations must in general be millimolar or higher. During the past decade an alternative approach has emerged that uses organic molecules linked to short DNA sequences1,2. The technique is known as DNA-templated synthesis and allows reactants to be supplied in nanomolar concentrations at which their chemical reactions can be controlled by the DNA sequences. This approach relies on hybridization events between complementary strands of DNA bringing the molecules into close proximity to each other and therefore increasing their local concentration so that they can react, even when the overall concentration of the molecules is low. (The hybridization events can be between two of the short DNA sequences, or between two short sequences and a DNA template.) The approach is possible because (non-covalent) DNA hybridization is several orders of magnitude faster than covalent chemical reactions. Numerous chemical reactions (including reactions that are otherwise non-compatible) have been controlled in the same reaction vessel with this approach2, and it has also been used in the synthesis of DNA-encoded combinatorial libraries of short peptides and other compounds3–5. However, these approaches require numerous interventions, such as the addition of chemical activators, the cleavage of linkers and protective groups, variations of temperature, or purification steps. Writing in Nature Nanotechnology, Yu He and David Liu of Harvard University now report carrying out the multistep synthesis of an oligamide without any kind of intervention by combining DNA-templated synthesis with a DNA walker6. In recent years, several dynamic DNA devices have been invented, including autonomously moving machines called DNA walkers7. In 2005, Chengde Mao and co-workers at Purdue University developed a DNA walker that autonomously and unidirectionally moves along an engineered DNA track8. The walker mechanism combines thermodynamically driven DNA hybridization interactions with an integrated DNAzyme that has the ability to specifically cleave a diribonucleotide built into the stations of the track. Once positioned on the track, the walker is driven to the first station, which is geometrically within range, to form a more stable DNA duplex. Once there, however, the DNAzyme cleaves the station strand at the diribonucleotide, decreasing the stability of the DNA duplex and driving the walker to the next station. DNA NANoTechNology