Uracil in RNA

A. Biotin Incorporate in base thymine in DNA probe sequence or uracil in RNA probe sequence... 

As with proteins, the nucleic acid polymers can denature, and they have secondary structure. In DNA, two nucleic acid polymer chains are twisted together with their bases facing inward to form a double helix. In doing so, the bases shield their hydrophobic components from the solvent, and they form hydrogen bonds in one of only two specific patterns, called base pairs. Adenine hydrogen bonds only with thymine (or uracil in RNA), and guanine pairs only with cytosine. Essentially every base is part of a base pair in DNA, but only some of the bases in RNA are paired. The double-helix structure... 

The major bases found in nucleic acids are adenine and guanine (purines) and uracil, cytosine, and thymine (pyrimidines). Thymine is found primarily in DNA, uracil in RNA, and the others in both DNA and RNA. Their structures, along with their chemical parent compounds, purine and pyrimidine, are shown in Figure 10.1, which also indicates other biologically important purines that are not components of nucleic acids. Hypoxanthine, orotic acid, and xanthine are biosynthetic and/or degradation intermediates of purine and pyrimidine bases, whereas xanthine derivatives—caffeine, theophylline, and theobromine—are alkaloids from plant sources. Caffeine is a component of coffee beans and tea, and its effects on metabolism are mentioned in Chapter 16. Theophylline is found in tea and is used therapeutically in asthma, because it is a smooth muscle relaxant. Theobromine is found in chocolate. It is a diuretic, heart stimulant, and vasodilator. 

The 5-chloro, 5-bromo and 5-iodo derivatives of uracil are base analogues of thymine and, in cellular systems, can replace the latter in DNA u >. Furthermore, 5-iodo-2 -deoxyuridine is an antiherpes agent currently used for treatment of ocular herpes keratitis. By contrast, 5-fluorouracil can replace uracil in RNA, and, together with 5-fluoro-2 -deoxyuridine, is employed in tumour chemotherapy. All the foregoing are also known mutagens, and 5-bromouracil and its deoxyriboside are widely employed in studies on mutagenesis U9). 

Another key difference between RNA and DNA is the presence of thymine in DNA instead of the uracil in RNA. Thymine is simply uracil with an additional methyl group. The four common bases of DNA are cytosine, thymine, adenine, and guanine. 

The three pyrimidine bases are the simpler and they are uracil (U), thymine (T), and cytosine (C). Cytosine is found in DNA and RNA, uracil in RNA only, and thymine in DNA only. 

These purines and pyrimidines join to the sugar-phosphate backbones of nucleic acids through repeating /3-linked AT-glycosidic bonds involving the N9 position of purines and the N1 position of pyrimidines. There are two classes of nucleic acids ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). DNA and RNA differ in one of their nitrogenous base components (uracil in RNA, thymine in DNA) and in their sugar (ribose) moiety, as indicated in Fig. V-2. 

A heterocyclic base, guanine, adenine, cytosine, uracil (in RNA), or thymine (in DNA). The sugar is substituted at Cl by the base, which is attached by a / glycosyl Cl -N link. 

Base pairing The hydrogen bonds formed between complementary bases that are part of the polynucleotide chains of nucleic acids. The base pairing is specific in that adenine will base pair with thymine (uracil in RNA) and guanine will pair with cytosine. 

The five-carbon sugar in RNA is ribose, and the sugar in DNA is 2 -deox)Tribose. The only difference between these two sugars is the absence of an hydroxyl group on the 2 carbon of 2 -deoxyribose. The purines in both DNA and RNA are adenine and guanine. Both DNA and RNA contain the pyrimidine cytosine however, the fourth base is thymine in DNA and uracil in RNA. The chemical compositions of DNA and RNA are summarized in Table 24.1. 

Purines are bases found in the nucleosides and nucleotides that make up nucleic acids. In nucleic acids, the purines match up with specific pyrimidine bases. The matching between purines and pyrimidines forms "base-pairs" in which adenine pairs with thymine (in DNA) or uracil (in RNA). Guanine pairs with the base cytosine in either nucleic acid. 

Rates with Other Nucleic Acid Derivatives. The -OH reaction rates with uridine, UMP, and adenine are compared in Table VI with those for uracil obtained using the same CNS" competition method. Uridine and 2, 3 -UMP (mixed) at neutral pH show lower corrected OH reaction rates of 2.9 X 109M"1 sec. 1 and 3.5 X 109M 1 sec."1 respectively, indicating that the ribose sugar and phosphate groups are not highly reactive sites for -OH attack. Adenine, the complementary purine base to uracil in RNA has a much lower -OH reactivity than uracil of 1.9 X... 

It is impossible for DNA to act as a direct template in the ordering of amino acids in protein synthesis, because almost all DNA is located in the nucleus and protein synthesis occurs in the cytoplasm. The genetic information in DNA is transcribed to the intermediate RNA molecule that moves to the cytoplasm, where it directs the synthesis of the gene product on the ribosomes. The RNA differs chemically from the DNA in that the sugar molecule is ribose and thymine in DNA is replaced by uracil in RNA. Structurally, RNA is predominantly a single-stranded molecule with short, double helical regions providing some three-dimensional structure. 

RNA is similar to DNA, although RNA nucleotides contain ribose rather than the deoxyribose found in DNA. Three bases found in DNA nucleotides are also found in RNA adenine (A), guanine (G), and cytosine (C). Thymine in DNA is replaced by uracil in RNA ... 

Pu = purine base cytosine and thymidine for DNA (uracil in RNA) Fragments from 5 end labeled a-d Fragments from 3 end labeled w-z... 

Complementary structures two structures which define one another, e.g. the 2 polynucleotide chains in the DNA duplex. The base pairs adenine/thymine (or adenine/uracil in RNA) and guanine/cytosine are complementary, so that by base pairing the nucleotide sequence of one polynucleotide chain defines a unique sequence in the complementary strand. 

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