RNA is a single stranded molecule containing a ribose sugar. It has a distinctive structure and, unlike DNA, there are variations and various types of RNA structures.
The basic structure of RNA
The basic structure of RNA, however, can be outlined as a ribose sugar, which is numbered from 1’ through 5’, with:
- a base attached to the 1’ position
- a hydroxyl group at the 2' position
- a phosphate attached to the 3’ position of one ribose and the 5' position of the next
Ribonucleic acid (RNA) has the bases adenine (A), cytosine (C), guanine (G), and uracil (U). Image Credit: National Institute of General Medical Sciences
A base is attached to the 1' position, generally adenine (A), cytosine (C), guanine (G) or uracil (U).
Adenine and guanine are purines; cytosine and uracil are pyrimidines. The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.
Unlike DNA that contains only four bases A, T, G and C, mature RNA can contain modified bases and sugars.
Pseudouridine (Ψ), in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine (T), are found in various places. Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine (I).
RNA hydroxyl group
There is presence of a hydroxyl group at the 2' position of the ribose sugar. This makes RNA different from DNA and makes the RNA adopt a A-form geometry rather than the B-form most commonly observed in DNA. This means there is a very deep and narrow major groove and a shallow and wide minor groove.
The hydroxyl group at 2’ means that in the flexible regions of an RNA molecule chemicals may attack the adjacent phosphodiester bond to cleave the backbone.
RNA phosphate group
A phosphate group is attached to the 3' position of one ribose and the 5' position of the next.
The phosphate groups have a negative charge. This makes the RNA a charged molecule (polyanion).
RNA tertiary structure
Once the RNA is formed, like proteins it requires to undergo changes to form a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements which are hydrogen bonds within the molecule. The strand forms hairpin loops, bulges and internal loops. Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary and tertiary structures.
RNA tertiary structures are determined using chemical probing and modification interference mapping, nuclear magnetic resonance (NMR), X-ray crystallography and cryo-electron microscopy.