Pyrimidines bases, in nucleic acids

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-... 

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).]... 

The coloured parts of the molecules below emphasize the characteristic features of the bases, purine bases in nucleic acids pyrimidine bases in nucleic acids... 

Many natural products contain the coumarin structure [42], Aesculetin (28) is isolated from horsechestnuts and psoralen (29) from the Indian plant Psoralea corylifolia. Furocoumarins such as 29 are photochemicaUy active on UV irradiation, they induce processes in the cell which lead to an increase in skin pigmentation and inhibition of cell division. This is due to (2 + 2)-cycloaddition (cyclobutane formation) of the pyrimidine bases in nucleic acids. Psoralens are used in the treatment of psoriasis. 

Even though the model is primitive, it gives insight into the origin of the quantized 7i-electron energy levels in cyclic conjugated systems, such as the aromatic side chains of phenylalanine, tryptophan, and tyrosine, the purine and pyrimidine bases in nucleic acids, the heme group, and the chlorophylls. 

Draw the structures of the three pyrimidine bases in nucleic acids. 

It is well known that pyrimidine bases convert to photodimers upon irradiation to UV light near the X max( > 270 nm). This photochemical reaction has a lethal effect in biological systems due to the photochemical transformation of pyrimidine bases of nucleic acids. However the photodimerization is a reversible reaction and the photodimers split to afford the original monomers very efficiently upon irradiation at a shorter wavelengths as shown in Scheme 1(1). 

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. 

Figure 5-6 Outlines of the purine and pyrimidine bases of nucleic acids showing van der Waals contact surfaces and some of the possible directions in which hydrogen bonds may be formed. Large arrows indicate the hydrogen bonds present in the Watson-Crick base pairs. Smaller arrows indicate other hydrogen bonding possibilities. The directions of the green arrows are from a suitable hydrogen atom in the base toward an electron pair that serves as a hydrogen acceptor. This direction is opposite to that in the first edition of this book to reflect current usage.

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. 

Conformational Flexibility of Pyrimidine Ring in Nucleic Acid Bases... 

An analysis of character and frequencies of normal vibrations and scan of relaxed potential energy surface represents two complementary approaches to investigation of conformational flexibility of pyrimidine rings in nucleic acid bases. A combined application of these approaches allows estimating population of conformations with nonplanar rings for each molecule. 

The most complete picture of conformational flexibility of pyrimidine rings in nucleic acid bases has been provided by molecular dynamics study of isolated molecules using ab initio Carr-Parinello method [45]. According to these studies, the population of planar conformation of heterocycle does not exceed 20% for thymine, cytosine, and guanine and amounts to about 30% for adenine (Table 21.4). These values are considerably smaller as compared to estimations based on vibrational frequencies mentioned above. Such difference is quite natural because in the case of vibrational analysis, only the lowest ring out-of-plane normal mode is considered. However, there are also smaller contributions of the other ring out-of-plane vibrations not included in this analysis. Therefore, such estimation should be considered as an upper limit for assessment of population of planar conformation of ring. 

Pyrimidine bases of nucleic acids, synthesis and reactivity of 78CLY591. Pyrimidines in analytical chemistry 82MI2. 

In the fields of molecular associations, G. Port and A. Pullman have determined the location of the main hydration sites in the purinic and pyrimidinic bases of nucleic acids 77>. An expansion of the electrostatic potential somewhat different from those reported in Chap. VIII was employed 78>. The results show that association with a water molecule is preferred in every case on the ring plane, with well evidenced minima. 

A FIGURE 2-15 Chemical structures of the principal bases in nucleic acids. In nucleic acids and nucleotides, nitrogen 9 of purines and nitrogen 1 of pyrimidines (red) are bonded to the 1 carbon of ribose or deoxyrlbose. U is only in RNA, andT is only in DNA. Both RNA and DNA contain A, G, and C. 

The observations of Hart et al. (17, 18) and Scholes et al. (23) have shown that both the purine and pyrimidine bases of nucleic acids react rapidly with both e aq and OH. In this paper, the reaction rates of these primary species with a variety of nucleic acid derivatives have been measured under different chemical conditions in an attempt to understand the factors responsible for variations in their reactivities. 

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