RNA molecules are crucial for all cellular processes, from control of gene expression to cellular differentiation. In addition, synthetic RNAs have found numerous applications in biomedicine and biomolecular engineering. RNA is an ideal molecule for nano-design, primarily due to its versatility in function and structure. RNA is the only biopolymer that can carry genetic information and posses catalytic properties. Moreover, RNA strands can naturally fold or can be programmed to self-assemble into complex structures. RNA has been demonstrated as an efficient nanoparticle. There are two major approaches that are used for the design of nanostructures: molecule-based and shape-based. The most frequently used one is the molecule-based approach, where the shape of RNA nanoparticle is dictated by the specific molecule. We are using a shape-based approach, where the RNA building blocks are chosen based on a desired shape of nanoparticle. For successful RNA nano-design we need to understand and control the hybridization kinetics, intermolecular associations, and various physical components affecting the building blocks. Computational modeling can provide such information and can assist and accelerate nano-design. One of the important RNA motifs that can guide nano-assembly is “kissing loops” motif. Using molecular dynamics simulations we have investigated a range of known RNA kissing-loops motifs. We found that the motif's stabilities strongly dependent on the water pockets and internal ions. Moreover, we have investigated mutations that can increase or decrease stability of such complexes. One of such motifs was used in computational design and optimization of RNA nanoring and RNA nanotube. In this presentation, I will discuss the result of our simulations and the computational approaches used for engineering RNA into nanoparticles and nanomaterials.