Topoisomerases relax supercoiled DNA What is the significance of supercoiling in vivo?
Disease box 2.2 Topoisomerase-targeted anticancer drugs
Chapter summary Analytical questions
Suggestions for further reading
DNA is often perceived as simply a very long sequence of base pairs organized into an invariant, ladder-like, double-helical structure. However, at the 1988 European Molecular Biology Organization (EMBO) Workshop on DNA curvature and bending, two sessions were scheduled to establish a common nomenclature for parameters used to describe the geometry of nucleic acid chains and helices. As a result, DNA can tip, propeller twist, buckle, roll, tilt, stagger, stretch, shear, rise, slide, and shift! Before considering the flexibility of nucleic acids, the more familiar primary structure will be reviewed.
2.2 Primary structure: the components of nucleic acids
While the acronyms DNA and RNA are considered standard nomenclature these days, their names underwent a long evolution, from nuclein to thymus nucleic acid to nucleic acid to deoxyribonucleic acid and ribonucleic acid. DNA was first called thymus nucleic acid because it was isolated from the thymus gland of cattle, while RNA was first identified as yeast nucleic acid. Nucleic acids are a long chain or polymer of repeating subunits, called nucleotides. Each nucleotide subunit is composed of three parts: a five-carbon sugar, a phosphate group, and a base. The chemical structures of these basic components are shown in Fig. 2.1.
Five-carbon sugars
Nucleotide subunits of RNA contain a pentose (five-carbon) sugar called ribose. Nucleotide subunits of DNA contain the sugar deoxyribose. The five carbon atoms in each pentose sugar are assigned numbers 1′ through 5′. Primes are used in the numbering of the ring positions in the sugars to differentiate them from the ring positions of the bases. Both sugars have an oxygen as a member of the five-member ring;
Purines Bases
Adenine (A) Guanine (G)
Cytosine (C)
Also represented as P O Figure 2.1 Components of nucleic
acids: bases, sugars, and phosphate.
Primes are used in the numbering of the ring positions in the sugars to differentiate them from the ring positions of the bases. Hydrogen and carbon atoms are usually omitted for clarity.
Figure 2.2 Chargaff’s data showing the base composition of DNA. (Reproduced from Chargaff, E. 1951.
Structure and function of nucleic acids as cell constituents. Federation Proceedings 10:654 –659 by copyright permission of Blackwell Publishing Ltd.)
the 5′-carbon is outside the ring. The sugars differ only in the presence or absence (“deoxy”) of an oxygen in the 2′ position. This minor distinction between RNA and DNA dramatically influences their function.
The remarkable versatility of RNA is critically dependent on this 2′-hydroxyl group (see Chapter 4).
Nitrogenous bases
As their name suggests, the bases are nitrogen-containing molecules having the chemical properties of a base (a substance that accepts an H+ion or proton in solution). Two of the bases, adenine (A) and guanine (G) have a double carbon–nitrogen ring structure; these are called purines. The other three bases, thymine (T), cytosine (C), and uracil (U) have a single ring structure; these are called pyrimidines. Thymine is found in DNA only, while uridine is specific for RNA.
A few years before Watson and Crick proposed the three-dimensional structure of DNA, Erwin Chargaff developed a paper chromatography method to analyze the amount of each base present in DNA. Chargaff observed certain regular relationships among the molar concentrations of the different bases (Fig. 2.2). These relationships are now called Chargaff ’s rules. He showed that the number of A residues in all DNA samples was equal to the number of T residues; i.e. [A]= [T], where the molar concentration of the base is denoted by the symbol for the base enclosed in square brackets. Accordingly, the number of G residues equals that of C: [G]= [C]. Finally, the amount of the purine bases equals that of the pyrimidine bases: [A] + [G] = [T] + [C]. Chargaff also found that the base composition of DNA, defined as the “percent G+ C,” differs among species but is constant in all cells of an organism within a species. The G+ C content can vary from 22 to 73%, depending on the organism.
The phosphate functional group
The phosphate functional group (PO4) gives DNA and RNA the property of an acid (a substance that releases an H+ion or proton in solution) at physiological pH, hence the name “nucleic acid.” The linking bonds that are formed from phosphates are esters that have the additional property of being stable, yet are
easily broken by enzymatic hydrolysis. When a nucleotide is removed from a DNA or RNA chain, the nucleotide is not destroyed in the process. Further, after the phosphodiester bond is formed (see below), one oxygen atom of the phosphate group is still negatively ionized. The negatively charged phosphates are extremely insoluble in lipids, which ensures the retention of nucleic acids within the cell or nuclear membrane.
Nucleosides and nucleotides
A DNA or RNA chain is formed in a series of three steps (Fig. 2.3). In the first reaction, each base is chemically linked to one molecule of sugar at the 1′-carbon of the sugar, forming a compound called a nucleoside. When a phosphate group is also attached to the 5′-carbon of the same sugar, the nucleoside
CH2 N
DNA chain – nucleotide + nucleotide + nucleotide + ...
+
Figure 2.3 Formation of nucleic acid chains. DNA and RNA chains are formed through a series of three steps:
(1) a base attached to a sugar is a nucleoside, (2) a nucleoside with one or more phosphates attached is a nucleotide, and (3) nucleotides are linked by 5′ to 3′ phosphodiester bonds between adjacent nucleotides to form a DNA or RNA chain. Bond formation occurs by a condensation reaction involving the removal of H2O and pyrophosphate. The structure of a nucleoside and three nucleotides with differing numbers of phosphates is shown for DNA.
becomes a nucleotide. Finally, nucleotides are joined (polymerized) by condensation reactions to form a chain. The hydroxyl group on the 3′-carbon of a sugar of one nucleotide forms an ester bond to the phosphate of another nucleotide, eliminating a molecule of water. This chemical bond linking the sugar components of adjacent nucleotides is called a phosphodiester bond, or 5′ → 3′ phosphodiester bond, indicating the polarity of the strand.