Lecturer Wing-Kin Sung Scribe Ngo Thanh Son.pdfVIP

CS5238 Combinatorial Methods in Bioinformatics 2006/2007 Semester 1 Lecture 11: RNA Secondary structure Prediction - November 3, 2006 Lecturer: Wing-Kin Sung Scribe: Ngo Thanh Son 11.1 Introduction A RNA (Ribonucleic acid) molecule is a single-stranded chain of the nucleotides A, C, G, U. RNA has the properties of both DNA and protein. Like the DNA, RNA can store and transfer information. An example of RNA being used as information storage can be seen in viruses such as the infamous HIV. In fact, most of the known viruses are RNA based. Unlike double-stranded DNA, RNA is a single stranded molecule. It has an extra OH attaching to the 2’ carbon which allows it to form extra hydrogen bond and enables it to have 3D structure. This difference is shown in Figures 11.1(a)and 11.1(b) below. Due to the ability to have 3D structure, RNA is able to function as a catalyst and perform functions such as tRNA which associates amino acid with codon. 11.1.1 RNA Structure Secondary structure of a RNA is a list of base pairs that are close together in its three dimensional structure. According to the theory of thermodynamics the optimal foldings of an RNA sequence are those of minimum free energy, and thus the native foldings i.e. the foldings encountered in the real world should correspond to the optimal foldings. Information on the secondary structure of a RNA molecule can be used as a stepping stone to model the full structure of a RNA molecule which in turn relates to the biological function. Therefore, it is important to study the structure of the RNA as well as ways to predict it[8]. In fact, due to the higher degree of freedom, the number of structures the RNA can produce is more than the number of structures the protein can pro- duce. The RNA structure can be described in three levels: primary structure, secondary structure and tertiary structure. 1 Primary structure The primary structure of a RNA is just a sequence of nucleotides describing the RNA. An example of the primary