Unit content
RNA strand structure, base pairing and folding
RNA is a nucleic-acid polymer built from ribonucleotide residues. Like DNA, an RNA strand has a sugar-phosphate backbone with directionality, but its sugar is ribose and its common pyrimidine base is uracil (U) rather than thymine.
Within an RNA strand, phosphodiester bonds connect the $3'$ hydroxyl of one ribose to the $5'$ phosphate side of the next residue. RNA sequences are therefore written $5'\rightarrow3'$.
The common RNA bases are adenine (A), guanine (G), cytosine (C) and uracil (U). Complementary Watson-Crick pairing is
A ↔ U
G ↔ C
RNA is often single-stranded, but single-stranded does not mean unstructured. Different regions of the same molecule can pair with one another. A complementary segment can form a stem, while unpaired residues can form a loop or bulge.
For example, a strand containing complementary regions
5' ... G C A A ... U U G C ... 3'
may fold so that part of the molecule pairs intramolecularly with another part. The exact fold depends on sequence, ions, temperature and interactions with other molecules.
This ability to fold gives RNA roles beyond carrying a linear message. Some RNAs serve as templates for protein synthesis, some recognize other nucleic-acid sequences, some form structural and catalytic parts of ribosomes, and others regulate cellular processes.
RNA therefore combines two properties: a directional nucleotide sequence that can store or transmit information, and a flexible single-stranded architecture that can fold into functional three-dimensional structures.