RNA

Ribonucleotides, the building blocks of RNA, are molecules that consist of a nitrogen-containing base, a phosphate group, and ribose, a five-carbon sugar. The nitrogen-containing base may be adenine, cytosine, guanine, or uracil. These four bases are abbreviated as A, C, G, and U.

RNA is similar to deoxyribonucleic acid (DNA), another class of nucleic acid. However, DNA nucleotides contain deoxyribose, not ribose, and they use the nitrogen-containing base thymine (T), not uracil, along with ade-nine, cytosine, and guanine.

Nucleotides link to form RNA chains. Adenine is one of the four bases found in RNA. Adapted from Robinson, 2001.

The nucleotides in DNA and RNA molecules are linked together to form chains. The link between two nucleotides is between a phosphate group attached to the fifth (5′ or "five prime") carbon of the sugar on one nucleotide and a hydroxyl group on the third (3′ or "three prime") carbon of the sugar on the other. The link is called a 5′-3′ phosphodiester bond.

RNA, therefore, can be described as a chain of ribose sugars linked together by phosphodiester bonds, with a base protruding from each sugar, as shown in the figure below. The 5′-3′ linkage gives RNA directionality, or polarity, and results in its having two ends with different chemical structures. The 5′ end usually has one or three free phosphate groups, and the 3′ end usually has a free hydroxyl group.

Whereas DNA is usually double-stranded, with the bases on one strand pairing up with those on the other, RNA usually exists as single chains of nucleotides. The bases in RNA do, however, follow Watson-Crick base-pair rules: A and U can pair with each other, as can G and C. There is usually extensive pairing of bases within a single strand of RNA.

RNA strands fold, with the bases in one part of the strand pairing with the bases in another. Folding can create both "secondary" and "tertiary" structures. Secondary structures are those that can be described in two dimensions and that can be thought of as simple loops or helices. Tertiary structures are complex, three-dimensional shapes.

The most common secondary structures, "hairpins," "loops," and "pseudo-knots," are shown in the figure below. Such secondary structures are formed when hydrogen bonds form between bases in the nucleotides and by the stacking of bases to form helical structures.

Tertiary structures usually involve interactions between nucleotides that are distant from each other along an RNA strand. Such interactions may arise from hydrogen bonding between bases, as in regular Watson-Crick base pairing, or from interactions among other chemical groups in the nucleotides. Some RNA molecules, such as ribosomal RNA (rRNA) The molecular structures of the four RNA bases. Adapted from Robinson, 2001. and transfer RNA (tRNA), have structures that are very complex. In structure they resemble proteins more than they do DNA.

To understand the function of a given RNA molecule, scientists often need to know its structure. There are three general strategies for analyzing RNA structure. First, using the relatively simple base-pairing rules for RNA and the basic principles of thermodynamics, computers can be used to predict secondary RNA structure, although not always with complete success.

Second, researchers can analyze RNA molecules from various organisms and compare those molecules that have the same function. Even when the nucleotide sequences vary between species, important structures are usually preserved.

Third, the structure of an RNA molecule can be determined experimentally, using enzymes to cut it or chemicals to modify it. Some enzymes and chemicals cut or modify only nonpaired, single-stranded portions of the RNA molecule, allowing researchers to identify double-stranded regions by examining which ones remain uncut and unmodified.

Despite the usefulness of each of these methods, none can provide a complete and accurate three-dimensional structure. A more complete determination of structure can be achieved by the biophysical methods of X-ray crystallography and nuclear magnetic resonance.