Thermodynamic Aspects of DNA Nanoconstruct Stability and Design

In the present study, we use the fluorescent DNA base analog tC° to investigate the thermal stability of a small DNA hexagon and the thermodynamic factors that govern the formation of such a structure. The DNA molecule is becoming increasingly popular as a material for bottom-up construction of nanostructures; however, relatively little attention has been given to the thermodynamics of such biomacromolecule-based constructs. With the goal of increasing information density and structural complexity, the size of the nanoarchitectures decreases and, more importantly, the fine structure is becoming more detailed. In this process the thermal stability and formation of unwanted byproducts will become critical features to consider in the design and assembly of such structures. Using tC° as a fluorescent probe in fluorescence monitored DNA melting allows for individually observing the denaturing of each of the six 10-mer sides in the pseudohexagonal multicomponent system. Experimental results demonstrate that the ring-opening of the cyclized hexamer is virtually exclusive to one side and that the stability of this side is increased as a result of the cyclization. Moreover, a theoretical model describing the formation and melting of the nanostructure is presented. The results show that the cyclized structure is thermodynamically favored over linear polymeric structures under the conditions and concentrations used for the self-assembly.