Abstract: The nucleic acids, RNA and DNA, play versatile and critically important roles in biology. The information storage capacity of DNA has long been recognized, and awareness of RNA’s prominence in biology continues to grow. Because both RNA and DNA carry large negative charge, interaction with oppositely charged partners is required for folding and function. Despite the important roles of these partners, little is known about how they structure, or interact with nucleic acids. We design experiments to reveal the role of partners, ranging from ions through proteins, in systems ranging from single stranded DNA or RNA through large assemblies, like viruses. Simulation and computation are important components of our work, and often offer surprising insight into our results.