This method involves the determination of finite elements that represent a physical property of a nucleotide strand. Using the values based on one of the physical properties of the nucleotide strand (i.e., nucleotide length, stretching spring constant, bending spring constant, twisting spring constant, electrostatic charge, steric repulsion, rupture criteria, etc.,), properties such as bending, twisting, stretching, vibrational modes, internal strain energy, relaxed shape, can be determined. More specifically, the method allows modification of base pair crossover spacing of nucleotide strands to generate under/over twist, as well as strain and compression for design control.
This strategy can be used in an iterative manner to optimize a desired property of a target DNA nanostructure. This method includes on-lattice (I.e., square or honeycomb lattices) modeling of DNA structures. However, this technology is not limited to the design of nucleic acid nanostructures having an antiparallel structure. By employing a junction-centric structure prediction framework, this technology enables lattice free design of DNA assemblies.