Nucleotide Structure and Nomenclature

Nucleic acids (DNA and RNA) are assembled from nucleotides, which consist of three components: a nitrogenous base, a five-carbon sugar (pentose), and phosphate.

Five-Carbon Sugar

Nucleic acids (as well as nucleosides and nucleotides) are classified according to the pentose they contain. If the pentose is ribose, the nucleic acid is RNA (ribonucleic acid); if the pentose is deoxyribose, the nucleic acid is DNA (deoxyribonucleic acid).


There are two types of nitrogen-containing bases commonly found in nucleotides:
purines and pyrimidines.

  • Purines contain two rings in their structure. The two purines commonly found in nucleic acids are adenine (A) and guanine (G); both are found in DNA and RNA. Other purine metabolites, not usually found in nucleic acids, include xanthine, hypoxanthine, and uric acid.
  • Pyrimidines have only one ring. Cytosine (C) is present in both DNA and RNA. Thymine (T) is usually found only in DNA, whereas uracil (U) is found only in RNA.

Nucleosides and Nucleotides

Nucleosides are formed by covalently linking a base to the number 1 carbon of a sugar (Figure I-1-4). The numbers identifying the carbons of the sugar are labeled with “primes” in nucleosides and nucleotides to distinguish them from the carbons, of the purine or pyrimidine base.

Nucleotides are formed when one or more phosphate groups are attached to the 5′ carbon of a nucleoside (Figure I-1-5). Nucleoside di- and triphosphates are high-energy compounds because of the hydrolytic energy associated with the acid anhydride bonds (Figure I-1-6).

The nomenclature for the commonly found bases, nucleosides, and nucleotides is shown in Table I-1-2. Note that the “deoxy” part of the names deoxythymidine, dTMP, etc., is sometimes understood, and not expressly stated, because thymine is almost always found attached to deoxyribose.

Nucleic Acids

Nucleic acids are polymers of nucleotides joined by 3′, 5′-phosphodiester bonds; that is, a phosphate group links the 3′ carbon of sugar to the 5′ carbon of the next sugar in the chain. Each strand has a distinct 5′ end and 3′ ends and thus has polarity. A phosphate group is often found at the 5′ ends, and a hydroxyl group is often found at the 3′ ends.

The base sequence of a nucleic acid strand is written by convention, in the 5′→3′ direction (left to right). According to this convention, the sequence of the strand on the left in Figure I-1-7 must be written 5′-TCAG-3′ or TCAG: ● If written backward, the ends must be labeled: 3′-GACT-5′ ● The positions of phosphates may be shown: pTpCpApG ● In DNA, a “d” (deoxy) may be included: dTdCdAdG.

In eukaryotes, DNA is generally double-stranded (dsDNA) and RNA is generally single-stranded (ssRNA). Exceptions occur in certain viruses, some of which have ssDNA genomes and some of which have dsRNA genomes.

DNA Structure

Figure I-1-8 shows an example of a double-stranded DNA molecule. Some of the features of double-stranded DNA include:

● The two strands are antiparallel (opposite in direction).

● The two strands are complementary. A always pairs with T (two hydrogen bonds), and G always pairs with C (three hydrogen bonds). Thus, the base sequence on one strand defines the base sequence on the other strand.

● Because of the specific base pairing, the amount of A equals the amount of T, and the amount of G equals the amount of C. Thus, total purines equal total pyrimidines. These properties are known as Chargaff’s rules.

With minor modifications (substitution of U for T) these rules also apply to dsRNA.Most DNA occurs in nature as a right-handed double-helical molecule known as Watson-Crick DNA or B-DNA (Figure I-1-8). The hydrophilic sugar-phosphate backbone of each strand is on the outside of the double helix.

The hydrogen-bonded base pairs are stacked in the center of the molecule. There are about 10 base pairs per complete turn of the helix. A rare left-handed double-helical form of DNA that occurs in G-C–rich sequences are known as Z-DNA. The biological function of Z-DNA is unknown but may be related to gene regulation.

Denaturation and Renaturation of DNA

Double-helical DNA can be denatured by conditions that disrupt hydrogen bonding and base stacking, resulting in the “melting” of the double helix into two single strands that separate from each other. No covalent bonds are broken in this process.

Heat, alkaline pH, and chemicals such as formamide and urea are commonly used to denature DNA. Denatured single-stranded DNA can be renatured (annealed) if the denaturing condition is slowly removed. For example, if a solution containing heat-denatured DNA is slowly cooled, the two complementary strands can become base-paired again (Figure I-1-9).

Such renaturation or annealing of complementary DNA strands is an important step in probing a Southern blot and in performing the polymerase chain reaction. In these techniques, a well-characterized probe DNA is added to a mixture of target DNA molecules.

The mixed sample is denatured and then renatured. When probe DNA binds to target DNA sequences of sufficient complementarity, the process is called hybridization.

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