Bioinformatics Molecular Biology

RNA Structure

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RNA is a single stranded structure and is made of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and a phosphate group. The fine structural difference between the sugars gives DNA added stability, making DNA more suitable for storage of genetic information, whereas the relative instability of RNA makes it more suitable for its more short-term functions. The RNA-specific pyrimidine  uracil forms a complementary base pair with adenine and is used instead of the thymine used in DNA. Even though RNA is single stranded, most types of RNA molecules show extensive intramolecular base pairing between complementary sequences within the RNA strand, creating a predictable three-dimensional structure essential for their function.

In 1961, French scientists François Jacob and Jacques Monod hypothesized the presence of an intermediary between DNA and its protein products, which they called messenger RNA. Evidence supporting their hypothesis was gathered soon afterwards showing that information from DNA is transmitted to the ribosome for protein synthesis using mRNA. 

Although RNA does not serve as the hereditary information in most cells, RNA does hold this function for many viruses that do not contain DNA. Thus, RNA clearly does have the additional capacity to serve as genetic information. 

RNA typically is a single-stranded biopolymer. However, the presence of self-complementary sequences in the RNA strand leads to intra-chain base-pairing and folding of the ribonucleotide chain into complex structural forms consisting of bulges and helices. The three-dimensional structure of RNA is critical to its stability and function, allowing the ribose sugar and the nitrogenous bases to be modified in certain different ways by cellular enzymes that attach chemical groups (e.g., methyl groups) to the chain. Such modifications enable the formation of chemical bonds between distant regions in the RNA strand, leading to complex contortions in the RNA chain, which further stabilizes the RNA structure. 

Like DNA, adjacent nucleotides in RNA are linked together through phosphodiester bonds. These bonds form between the phosphate group of one nucleotide and a hydroxyl (–OH) group on the ribose of the adjacent nucleotide.

This structure lends RNA its directionality that is the two ends of the chain of nucleotides are different. Carbon number five of ribose carries an unbound phosphate group which gives rise to the name 5’ end. The last ribose at the other end of the nucleotide chain has a free hydroxyl (–OH) group at carbon number 3; hence, this end of the RNA molecule is called 3’ end. As nucleotides are added to the chain during transcription, the 5’ phosphate group of the new nucleotide reacts with the 3’ hydroxyl group of the growing chain. Therefore, RNA is always assembled in the 5’ to 3’ direction.

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