Bases, in nucleic acids

The sugars are typically ribose (ribonucleic acids, RNA), or 2-deoxyribose (deoxyribonucleic acids, DNA). There are five common bases in nucleic acids adenine (A) thymine (T) uracil (U) cytosine (C) and guanine (G). DNA polymers incorporate the four bases. A, T, C, and G, and RNA, the set A, U, C, and G. 

Amine bases in nucleic acids can react with alkylating agents in typical Sjsj2 reactions. Look at the following electrostatic potential maps, and tell which is the better nucleophile, guanine or adenine. The reactive positions in each are indicated. 

Figure 11.18 The diazonium group of p-diazobenzoylbiocytin can couple to the C-8 position of guanidine bases in nucleic acids, forming diazo bonds.

Thymine and other bases in nucleic acids undergo dimerisation when irradiated with ultraviolet light, and this can result in DNA mutation or even cell death. 

The presence of small quantities of methylated purine and pyrimidine bases in nucleic acid of micro-organisms and animals has been widely documented. The methyl group is transferred from N-adenosylmethionine to these bases, and methylation occurs at the polynucleotide level rather than by transfer to the acid-... 

NUCLEOTIDES AND NUCLEIC ACIDS Abbreviations and symbols for nucleic acids, polynucleotides and their constituents /. Biol. Chem. (1970) 245, 5171-5176 Corrections, J. Biol Chem. (1971) 246, 4894 Abbreviations and symbols for the description of conformations of polynucleotide chains Eur. J. Biochem. (1983) 131, 9-15 Nomenclature for incompletely specified bases in nucleic acid sequences... 

Closely related to solvent effect, and governed by the same or similar factors, are the phenomena of dimerization via self-association, and association with other species present in solution, such as cations or anions, in definite stoichiometric proportions. Studies of such associations lead to further knowledge of such interactions involving the more complex bases in nucleic acid structures. One of the earliest workers to study dimerization systematically was Shindo (59CPB407), who examined the broad N—H stretch region 3300-2400 cm-1 in the IR spectra of a variety of substituted pyridin-2-ones and quinolin-2-ones in perfluorocarbon mulls and CC14 solution. 

Alkaloids that contain a purine skeleton (see Section 4.7) are commonly known as purine alklaoids, e.g. caffeine and theobromine. We have already learnt that two of the bases in nucleic acids, adenine and guanine, are purines. 

The purine and pyrimidine bases are hydrophobic and relatively insoluble in water at the near-neutral pH of the cell. At acidic or alkaline pH the bases become charged and their solubility in water increases. Hydrophobic stacking interactions in which two or more bases are positioned with the planes of their rings parallel (like a stack of coins) are one of two important modes of interaction between bases in nucleic acids. The stacking also involves a combination of van der Waals and dipole-dipole interactions between the bases. Base stacking helps to minimize contact of the bases with water, and base-stacking interactions are very important in stabilizing the three-dimensional structure of nucleic acids, as described later. 

Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences http //www.chem.qmul.ac.uk/iubmb/misc/naseq.html Nomenclature of Peptide Hormones http //www.cliem.qimil.ac.uk/iubmb/misc/ phorm.html... 

The diazines (pyridazine, pyrimidine, and pyrazine) are six-membered aromatic heterocycles that have two nitrogens in the ring. Cytosine, thymine, and uracil are derivatives of pyrimidine that are important bases in nucleic acids (DNA and RNA). Heterocyclic analogs of the aromatic hydrocarbon naphthalene include pteridines, which have four nitrogens in the rings. Naturally occurring pteridine derivatives include xanthopterin (a pigment) and folic acid (a vitamin). Methotrexate is a pteridine used in cancer chemotherapy. 

The imidazole nucleus appears in a number of naturally occurring products, among which the most important are the amino acid histidine (203) and the purines, which comprise many of the important bases in nucleic acids. These purines, of which adenosine (204) is an example, are fused imidazopyrimidines. Their chemistry is discussed in Chapter 4.09. 

Stacked bases in nucleic acids absorb less ultraviolet light than do unstacked bases, an effect called hypochromism. Thus, the melting of nucleic acids is easily followed by monitoring their absorption of light, which peaks at a wavelength of 260 nm (Figure 517). 

FIGURE 10-9 H bonding of purine and pyrimidine bases in nucleic acids. Left, cytosine and guanine. Right, thymine and adenine. [From Pauling and Corey, Arch. Biochem. and Biopkys. 65, 164-81 (1956).]... 

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