Nucleic Acid Chemistry:- Nucleotides and Nucleic Acids Undergo Nonenzymatic Transformations
Purines and pyrimidines, along with the nucleotides of which they are a part, undergo a number of spontaneous alterations in their covalent structure. The rate of these reactions is generally very slow, but they are physio logically significant because of the cell’s very low tolerance for alterations in its genetic information. Alterations in DNA structure that produce permanent changes in the genetic information encoded therein are called mutations, and much evidence suggests an inti mate link between the accumulation of mutations in an individual organism and the processes of aging and carcinogenesis.
Several nucleotide bases undergo spontaneous loss of their exocyclic amino groups (deamination) (Fig. 8–33a). For example, under typical cellular conditions, deamination of cytosine (in DNA) to uracil occurs in about one of every 107 cytidine residues in 24 hours. This corresponds to about 100 spontaneous events per day, on average, in a mammalian cell. Deamination of adenine and guanine occurs at about 1/100th this rate.
The slow cytosine deamination reaction seems in nocuous enough, but is almost certainly the reason why DNA contains thymine rather than uracil. The product of cytosine deamination (uracil) is readily recognized as foreign in DNA and is removed by a repair system (Chapter 25). If DNA normally contained uracil, recognition of uracils resulting from cytosine deamination would be more difficult, and unrepaired uracils would lead to permanent sequence changes as they were paired with adenines during replication. Cytosine deamination would gradually lead to a decrease in G≡C base pairs and an increase in A=U base pairs in the DNA of all cells. Over the millennia, cytosine deamination could eliminate G≡C base pairs and the genetic code that de pends on them. Establishing thymine as one of the four bases in DNA may well have been one of the crucial turning points in evolution, making the long-term storage of genetic information possible.
Another important reaction in deoxyribonucleotides is the hydrolysis of the N-β-glycosyl bond between the base and the pentose (Fig. 8–33b). This occurs at a higher rate for purines than for pyrimidines. As many as one in 105 purines (10,000 per mammalian cell) are lost from DNA every 24 hours under typical
FIGURE 8–33 Some well-characterized nonenzymatic reactions of nucleotides. (a) Deamination reactions. Only the base is shown. (b) Depurination, in which a purine is lost by hydrolysis of the N-β- glycosyl bond. The deoxyribose remaining after depurination is readily converted from the β -furanose to the aldehyde form (see Fig. 8–3). Fur ther nonenzymatic reactions are illustrated in Figures 8–34 and 8–35.
cellular conditions. Depurination of ribonucleotides and RNA is much slower and generally is not considered physiologically significant. In the test tube, loss of purines can be accelerated by dilute acid. Incubation of DNA at pH3 causes selective removal of the purine bases, resulting in a derivative called apurinic acid.
Other reactions are promoted by radiation. UV light induces the condensation of two ethylene groups to form a cyclobutane ring. In the cell, the same reaction between adjacent pyrimidine bases in nucleic acids forms cyclobutane pyrimidine dimers. This happens most frequently between adjacent thymidine residues on the same DNA strand (Fig. 8–34). A second type of pyrimidine dimer, called a 6-4 photoproduct, is also formed during UV irradiation. Ionizing radiation (x rays and gamma rays) can cause ring opening and fragmentation of bases as well as breaks in the covalent back bone of nucleic acids.
Virtually all forms of life are exposed to energy-rich radiation capable of causing chemical changes in DNA. Near-UV radiation (with wavelengths of 200 to 400 nm), which makes up a significant portion of the solar spec trum, is known to cause pyrimidine dimer formation and other chemical changes in the DNA of bacteria and of human skin cells. We are subject to a constant field of ionizing radiation in the form of cosmic rays, which can penetrate deep into the earth, as well as radiation emit ted from radioactive elements, such as radium, plutonium, uranium, radon, 14C, and 3H. X rays used in medical and dental examinations and in radiation therapy of cancer and other diseases are another form of ionizing radiation. It is estimated that UV and ionizing radiations are responsible for about 10% of all DNA damage caused by environmental agents.
DNA also may be damaged by reactive chemicals introduced into the environment as products of industrial activity. Such products may not be injurious per se but may be metabolized by cells into forms that are. Two prominent classes of such agents (Fig. 8–35) are (1) deaminating agents, particularly nitrous acid (HNO2) or compounds that can be metabolized to nitrous acid or nitrites, and (2) alkylating agents.
Nitrous acid, formed from organic precursors such as nitrosamines and from nitrite and nitrate salts, is a potent accelerator of the deamination of bases. Bisulfite has similar effects. Both agents are used as preservatives in processed foods to prevent the growth of toxic bacteria. They do not appear to increase cancer risks
FIGURE 8–34 Formation of pyrimidine dimers induced by UV light. (a) One type of reaction (on the left) results in the formation of a cyclobutyl ring involving C-5 and C-6 of adjacent pyrimidine residues. An alternative reaction (on the right) results in a 6-4 photoproduct, with a linkage between C-6 of one pyrimidine and C-4 of its neighbor. (b) Formation of a cyclobutane pyrimidine dimer introduces a bend or kink into the DNA.
significantly when used in this way, perhaps because they are used in small amounts and make only a minor contribution to the overall levels of DNA damage. (The potential health risk from food spoilage if these preservatives were not used is much greater.) Alkylating agents can alter certain bases of DNA. For example, the highly reactive chemical dimethylsul fate (Fig. 8–35b) can methylate a guanine to yield O6 methylguanine, which cannot base-pair with cytosine.
Many similar reactions are brought about by alkylating agents normally present in cells, such as S-adenosyl methionine.
Possibly the most important source of mutagenic al terations in DNA is oxidative damage. Excited-oxygen species such as hydrogen peroxide, hydroxyl radicals, and superoxide radicals arise during irradiation or as a byproduct of aerobic metabolism. Of these species, the hydroxyl radicals are responsible for most oxidative DNA damage. Cells have an elaborate defense system to destroy reactive oxygen species, including enzymes such as catalase and superoxide dismutase that convert reactive oxygen species to harmless products. A fraction of these oxidants inevitably escape cellular defenses, however, and damage to DNA occurs through any of a large, complex group of reactions ranging from oxidation of deoxyribose and base moieties to strand breaks. Accurate estimates for the extent of this dam age are not yet available, but every day the DNA of each human cell is subjected to thousands of damaging oxidative reactions.
This is merely a sampling of the best-understood reactions that damage DNA. Many carcinogenic com pounds in food, water, or air exert their cancer-causing effects by modifying bases in DNA. Nevertheless, the in tegrity of DNA as a polymer is better maintained than that of either RNA or protein, because DNA is the only macromolecule that has the benefit of biochemical repair systems. These repair processes (described in Chapter 25) greatly lessen the impact of damage to DNA.
