An RNA Structure Primer
RNA is ribonucleic acid, a close cousin of deoxyribonucleic
acid or DNA. RNA is a polymer of ribonucleoside-phosphates.
It's backbone is comprised of alternating ribose and phosphate
groups. Ribose is a five carbon sugar that is found in a
puranose, or five-membered ring, form in RNA. The phosphate
groups link consecutive ribose groups and each bear one negative
charge. Each monomer also has a nitrogenous base for a side
chain. The four commonly found side chains in RNA are adenine,
cytosine, guanine and uracil. Several other bases are
occasionaly found in RNAs including: thymine, pseudouridine and
methylated cytosine and guanine.
Inside of cells, there are three major types of RNA:
messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA
(rRNA). There are a number of other types of RNA present in
smaller quanitites as well, including small nuclear RNA (snRNA),
small nucleolar RNA (snoRNA) and the 4.5S signal recognition
particle (SRP) RNA. Novel species of RNA continue to be
RNA serves a multitude of roles in living cells. These
include: serving as a temporary copy of genes that is used as a
template for protein synthesis (mRNA), functioning as adaptor
molecules that decode the genetic code (tRNA) and catalyzing the
synthesis of proteins (rRNA). There is much evidence
implicating RNA structure in biological regulation and
catalysis. Interestingly, RNA is the only biological polymer
that serves as both a catalyst (like proteins) and as
information storage (like DNA). For this reason, it has be
postulated RNA, or an RNA-like molecule, was the basis of life
early in evolution.
RNA molecules are built from three basic components: ribose,
a five-carbon suger, phosphate, and a family of four
heterocyclic bases. The backbone of RNA is an alternating
polymer of ribose and phosphate wherein phosphodiester moeities
bridge the O3' and O5' atoms from consecutive riboses (Figure 1).
Typically, one of four heterocyclic bases is attached to
the C1' atom of each ribose via a glycosidic linkage
(Figure 2). These heterocycles are either
purine derivatives (guanine and andenine) or pyrimidine
derivatives (cytidine and uracil). Thymine, a pyrimidine
normally found in DNA, is also occasionally used in RNAs.
Furthermore, a large variety of base modifications are also
observed in naturally occuring RNA molecules.
Although RNA molecules are linear polymers, they fold back on
themselves to make intricate secondary and tertiary structures
that are essential for them to perform their biological roles.
The three-dimensional structure of tRNA as determined
by x-ray crystallography (left) and the P4-P6 domain of
the group I intron (right). Bases form both Watson-Crick
pairs and non-Watson-Crick pairs which stack together to
form sstems. In tRNA, four stems stack together pairwise
to make the two arms of the L-shaped tRNA. (Source:
coordinates from PDB
entry 1QTQ and PDB
The three dimensional structure of molecules is usually
described in Cartesian coordinates. This is the format stored
in both the PDB and NDB. An equivalent
description can also be given in internal coordinates. This
description can be provided by given values for all the dihedral
angles in a molecule. For nucleic acids, a further
simplification can be made by describing the ribose ring in
terms of pseudrotation. This method allows the conformation of
each residue to be completely specified by five backbone
dihedral angles (α, β, γ, ε and ζ)
a sidechain dihedral angle (χ) and two ribose pucking
paramters (P and ν0). For a definition of the
backbone and sidechain dihedrals see Figure
In RNABase, we use a slightly different nomenclature for the
dihedral angles around the ring. We use the dihedral angles
θ0, θ1, θ2,
θ3, θ4. There is a simple
relationship between the θ notation and the ν notation:
θn = νn+2.
Essentially, θ0 = ν2,
θ1 = ν3,
θ2 = ν4,
θ3 = ν0 and
θ4 = ν1. Because all
of these torsion angles described rotation about bonds that are
in a five-membered ring, there are relatively few combinations.
Indeed, the only conformations available to ribose rings are
various puckers (Figure 5).
The puckering mode can be described in terms of an amplitude
(ν0), which describes the extent to which one or
two atom(s) lie out of the plane of the others, and a phase (P)
which describes which atom(s) lies out of the plane of the
others and on which side (Figure 6).