An RNA Structure Primer

1. What is RNA?

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 identified.

2. What does RNA do in cells?

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.

3. The Structure of RNA

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).

Figure 1

The structure of the RNA backbone is an alternating polymer of ribose and phosphate groups. (Source: IUPAC-IUB Joint Commission on Biochemical Nomenclature Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains)

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.

Figure 2

Each nucleotide unit is usually coupled to one of four side chains: adenine, cytosine, guanine or uracil. Occasionally, thymine or other side chains are also used. (Source: IUPAC-IUB Joint Commission on Biochemical Nomenclature Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains)

4. The Three-Dimensional Structure of RNA

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.

Three-Dimensional Structure of Group I Intron P4-P6

Figure 3

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 entry 1GID)

5. Describing The Three-Dimensional Structure of RNA

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 1.

Figure 4

There are five dihedral angles around the ribose ring: ν₀, ν₁, ν₂, ν₃, ν₄. However, because the ring cannot easily be broken, there are limited combinations for the five dihedrals. Consequenty, the ring system can accurately be described in terms of a ring puckering phase (P) and amplitude (ν₀). (Source: IUPAC-IUB Joint Commission on Biochemical Nomenclature Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains)

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: θ_n = ν_n+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).

Figure 5

The five-membered ring of the ribose moiety of ribonucleotides can adopt various puckering forms, several of which are shown here in Newman projections. The conformations can be classified into envelope (E) forms, in which one atom lies out of the plane of the other four, and twist (T) forms, in which two consecutive atoms lie on opposite faces of plane of the other three. (Source: IUPAC-IUB Joint Commission on Biochemical Nomenclature Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains)

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).

Figure 6

The ribose pucker can be described in terms of a puckering phase (P) which ranges between 0 and 360 degrees. The ranges of values available to RNA and DNA are indicated with arrows labeled r and d, respectively. (Source: IUPAC-IUB Joint Commission on Biochemical Nomenclature Abbreviations and Symbols for the Description of Conformations of Polynucleotide Chains)