Pyrimidines, in DNA

Amino groups of purine basesin RNA and DNA Oygen of purines and pyrimidines in DNA and... 

Chromones and Coumarins Anwii species (Umbettiferae) Corfandrum sativum DNA, RNA viruses and Bacteriophages HIV Cross linking viral DNA Adds to viral pyrimidines (in DNA) and uridines (in RNA), forming cycloadduct [11] [21]... 

Base Chemically, an alkali. Also used as a general term for the purines and pyrimidines in DNA and RNA. 

It has been shown that purine-pyrimidine dinucleotides are considerably more add-labile than pyrimidine-pyrimidine dinudeotides and that the cytosine deox3uibose bond is more labile than the thymine deoxyribose bond. Thus, when thymidylic-uridylic add dinucleotide is hydrolyzed more thymidine 3, 5 -diphosphate is formed lhan uridine 3, 5 -diphos-phate [Eq. 56]. On the basis of these data an attempt was made to gain information on the distribution of pyrimidine deoxynucleotides in different preparations of DNA (255). Differences were detected in the rate of appearance of the pyrimidine deoxynucleoside dipho hates, i.e., early appearance from isolated pyrimidine deoxynucleotides and later appearance from adjoining pjuimidine deoxynucleotide sequences. This indicates that the distribution of pyrimidines in DNA is not random and differs from one preparation to another, even in samples of DNA with the same base composition. 

Light has profound effect, both beneficial and harmful, on all of life. In this chapter, we consider a beneficial effect of visible light on repairing harmful changes induced by UV light in DNA. The harm is the dimerization of pyrimidines in DNA from UV radiation, the repair is the photoreactivation of the dimers by visible light. In particular we focus on the molecular level characterization of the photoreactivation process. Our discussion is based on the application of ab initio molecular orbital and density functional methods to this molecular process. 

These relationships are general. Hydroxyl-substituted purines and pyrimidines exist in their keto forms fflnino-substituted ones retain structures with an anino group on the ring. The pyrimidine and purine bases in DNA and RNA listed in Table 28.1 follow this general rule. Beginning in Section 28.7 we ll see how critical it is that we know the correct tautomeric forms of the nucleic acid bases. 

The most important derivatives of pyrimidines and purines are nucleosides. Nucleosides are N-glycosides in which a pyrimidine or purine nitrogen is bonded to the anomeric carbon of a carbohydrate. The nucleosides listed in Table 28.2 are the main building blocks of nucleic acids. In RNA the carbohydrate component is D-ribofuranose in DNA it is 2-deoxy-D-ribofuranose. 

The common naturally occurring pyrimidines are cytosine, uracil, and thymine (5-methyluracil) (Figure 11.3). Cytosine and thymine are the pyrimidines typically found in DNA, whereas cytosine and uracil are common in RNA. To view this generality another way, the uracil component of DNA occurs as the 5-methyl variety, thymine. Various pyrimidine derivatives, such as dihydrouracil, are present as minor constituents in certain RNA molecules. 

As indicated in Chapter 11, the base pairing in DNA is very specific the purine adenine pairs with the pyrimidine thymine the purine guanine pairs with the pyrimidine cytosine. Further, the A T pair and G C pair have virtually identical dimensions (Figure 12.10). Watson and Crick realized that units of such similarity could serve as spatially invariant substructures to build a polymer whose exterior dimensions would be uniform along its length, regardless of the sequence of bases. 

The sugar component in RNA is ribose, and the sugar in DNA is 2 -deoxy-ribose. (The prefix 2 -deoxv indicates that oxygen is missing from the 2 position of ribose.) DNA contains four different amine bases, two substituted purines (adenine and guanine) and two substituted pyrimidines (cytosine and thymine). Adenine, guanine, and cytosine also occur in RNA, but thymine is replaced in RNA by a closely related pyrimidine base called uracil. 

The nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are biological polymers that act as chemical carriers of an organism s genetic information. Enzyme-catalyzed hydrolysis of nucleic acids yields nucleotides, the monomer units from which RNA and DNA are constructed. Further enzyme-catalyzed hydrolysis of the nucleotides yields nucleosides plus phosphate. Nucleosides, in turn, consist of a purine or pyrimidine base linked to Cl of an aldopentose sugar—ribose in RNA and 2-deoxyribose in DNA. The nucleotides are joined by phosphate links between the 5 phosphate of one nucleotide and the 3 hydroxyl on the sugar of another nucleotide. 

Lyamichev, V., Frank-Kamenetskii, M., Soyfer, V. Protection against UV-induced pyrimidine dimerization in DNA by triplex formation. Nature, Vol.344, No. 6266, (1990), pp. 568-570, ISSN 1476-4687... 

Small quantities of additional purines and pyrimidines occur in DNA and RNAs. Examples include 5-methyl-cytosine of bacterial and human DNA, 5-hydroxy-methylcytosine of bacterial and viral nucleic acids, and mono- and di-N-methylated adenine and guanine of... 

Ribonucleic acid (RNA) is a polymer of purine and pyrimidine ribonucleotides finked together by 3, 5 -phosphodiester bridges analogous to those in DNA (Figure 35—6). Although sharing many features with DNA, RNA possesses several specific differences ... 

KATIYAR s K, PEREZ A and MUKHTAR H (2000b) Green tea polyphenol treatment to hiunan skin prevents formation of ultraviolet light B-induced pyrimidine dimers in DNA , Clin Cancer Res, 6 (10), 3864-9. 

Malins, D.C. and Haimanot, R. (1990). 4,6,-Diamino-5-formamido-pyrimidine, 8-hydroxyguanine and 8-hydroxyadenine in DNA from neoplastic liver of English sole exposed to carcinogens. Biochem. Biophys. Res. Commun. 173, 614-619. 

GG8, the radical cation must traverse five A/T base pairs. Electrochemical measurements in solution have shown that the purine bases (A and G) have considerably lower Eox than the pyrimidines (C and T), with the Eox of G estimated to be about 0.25 V below that of A [20]. It is not very likely that the Eox of bases in DNA will be the same as they are in solution, but it is generally assumed that the order of Eox will remain the same. Consequently, the radical cation at Gi of AQ-DNA(l) must traverse a bridge of five A bases to reach GG8. The process whereby the radical cation crosses such bridges has been a major point of debate in consideration of long distance radical cation migration mechanisms in DNA this issue will be discussed fully below. 

Scheme 1 UV-light induced formation of the two major photo lesions in DNA. T=T cyclobutane pyrimidine dimer. (6-4)-photo product (6-4)-lesion, formed after ring opening of an oxetane intermediate, which is the product of a Paterno-Buchi reaction...

Nucleotide A subunit of DNA or RNA consisting of a purine (adenine and guanine) or a pyrimidine base [thymine (DNA only), uracil (RNA only) and cytosine], a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA). 

Thymine (T) A nitrogenous pyrimidine base found in DNA but not in RNA it bonds with adenine (A) to form the A-T base pair. 

Nucleic acids can contain of any one of three kinds of pyrimidine ring systems (uracil, cytosine, or thymine) or two types of purine derivatives (adenine or guanine). Adenine, guanine, thymine, and cytosine are the four main base constituents found in DNA. In RNA molecules, three of these four bases are present, but with thymine replaced by uracil to make up the fourth. Some additional minor derivatives are found in messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA), particularly the N4,N4-dimethyladenine and N7-methylguanine varieties. 

Figure 1.42 The three pyrimidine bases common to nucleic acid construction. Cytosine and thymine are found in DNA, while in RNA, uracil residues replace thymine. The associated sugar groups are bound in N-glycosidic linkages to the N-l nitrogen.

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