Prediction and design of DNA and RNA structures

Computational tools for prediction and design of DNA and RNA structures are used for different approaches in nucleic acid research. The prediction tools are used for the identification and modeling of biologically important nucleic acid structures, whereas the design tools aim at constructing novel molecular architectures and devices for nanotechnology and synthetic biology. The recent successes in predicting RNA three-dimensional structure directly from sequence and in designing sequences that self-assemble into predefined DNA and RNA nanostructures show that nucleic acid structure is predictable and controllable. The prediction and design approaches deal with reverse problems of relating sequence and structure, but share the main computational principles, visual representations and modeling approaches. The prediction and design tools are introduced together here to provide an overview of their current capabilities and deficiencies. The tools are listed by input and output to provide a user perspective and an extended tool table is made available at http://www.cdna.dk/tools/.