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RNA STRUCTURAL BIOINFORMATICS
INTRODUCTION
RNA molecules play a range of roles in cells, including key roles in both transcription and translation. Functional RNAs can have complex three-dimensional structures or simply rely on the properties of their primary sequence to perform their function. Among the highly structured RNAs are transfer RNAs (tRNA), ribosomal RNAs (rRNA), ribozymes and riboswitches. These classes of RNAs play catalytic or structural roles in the cell, facilitated by their complex three-dimensional structures. Other RNAs, such as micro-RNAs and sno-RNAs, perform their regulatory function by relying on simple base pairing to target RNAs.
Three levels of structure can exist in RNA, the primary sequence, secondary structure and tertiary structure, with each structural level serving an essential role in the function of RNA. The structure of RNA is covered extensively in Chapter 3; however, we will discuss briefly these different structural levels using tRNA to illustrate these principles. At the primary sequence level, four bases serve as the main components: adenine, guanine, cytosine, and uracil (a pyrimidine similar to the thymine found in DNA). In addition to this basic set, many modified bases such as pseudouridine and even the DNA base thymine are frequently present in RNA molecules. Figure 33.1a shows several primary sequences of molecules in the tRNA family in a multiple sequence alignment.
The ...
