DNA Parallelograms as Addressable Vessels for Functional Chemical Moieties

Complex function arises in biology from the proximity and relations amongst different functional units. Often, separate containers are employed in order to segregate specialized function within a cell, or in order to control reactions by facilitated substrates and products diffusion. Self-assembled nucleic-acids nanostructures can serve as templates for the designed assembly of different functional units that can be stably attached at locations defined with nanometer accuracy. In this poster, a few examples are presented where the self-assembled DNA parallelogram, originally designed by Ned Seeman (Sha, Liu et al. 2000), can be used as a relatively rigid template for the assembly of different functional elements, such as oligonucleotides, fluorophores, proteins. Depending on its structure, the functional units can be included in the assembly of the parallelogram, or added later after the assembly is completed. This yields the possibility of building nanostructures with a number of different hierarchical levels of complexity, for instance allowing recycling of the functional units without need of breaking down the more complex parallelogram structure. DNA parallelograms can also be polymerized, yielding the possibility of preparing 1D or 2D multi-functionalized templates with controlled distance between multiple functional units (Brucale, Zuccheri et al. 2006). As in the case of fluorophores, it can be shown that the rigidity and addressability of the parallelogram tile enables a high degree of control of the relation among the functional units: the measured FRET between two organic dyes is greater than in other less flexible structures where the dyes could in principle be located at the same distance one from the other. As these templates can bind multiple different elements, controlling their location and interaction, it is in principle possible to design functional nano-objects such as smart toxins (by assembling lytic enzymes with homing peptides or antibodies), small enzyme nanofactories (keeping multiple enzymes close in space) or smart-binders (multifunctional rigid binders that can bind and select particular conformational states of macromoleculas).