RNA (Ribonucleic acid) as a molecule has been posited as being the origin of life. Though it was long considered nothing more than an intermediary between the code in the DNA and the functional proteins, RNA has been shown to serve many different functions, spanning the entire realm of genomics. Part of the cause for its versatility is the many possible conformations that RNA can be found in. Being made up of a more flexible backbone than DNA, RNA exhibits interesting and varied structures that can inform us on its many purposes. Certain structures of RNA, for example, lend themselves to catalytic activities while others serve as the tRNA, and mRNA that are so important during the process of converting the DNA’s code into proteins The aim for this chapter is to learn methods that can explain, or even predict the secondary structure of RNA in the hope that they will shed light on the many properties of this versatile molecule.
To accomplish this, we first look at RNA from a biological perspective and explain the known biological roles of RNA. Then, we study the different methods that exist to predict RNA structure. There are two main approaches to the RNA folding problem: 1) predicting the RNA structure based on thermodynamic stability of the molecule, and looking for a thermodynamic optimum 2) probabilistic models which try to find the states of the RNA molecule in a probabilistic optimum.
Finally, we can use evolutionary data in order to increase the confidence of our predictions by these methods.