DNA and RNA Nucleosides

Cohen B, Crespo-Hemandez CE, Kohler B (2004) Strickler-berg analysis of excited singlet state dynamis in DNA and RNA nucleosides. Faraday Discuss 127 137... 

Transient absorption experiments have shown that all of the major DNA and RNA nucleosides have fluorescence lifetimes of less than one picosecond [2—4], and that covalently modified bases [5], and even individual tautomers [6], differ dramatically in their excited-state dynamics. Femtosecond fluorescence up-conversion studies have also shown that the lowest singlet excited states of monomeric bases, nucleosides, and nucleotides decay by ultrafast internal conversion [7-9]. As discussed elsewhere [2], solvent effects on the fluorescence lifetimes are quite modest, and no evidence has been found to date to support excited-state proton transfer as a decay mechanism. These observations have focused attention on the possibility of internal conversion via one or more conical intersections. Recently, computational studies have succeeded in locating conical intersections on the excited state potential energy surfaces of several isolated nucleobases [10-12]. 

Badouard, C., Masuda, M., Nishino, H., Cadet,)., Favier, A., and Ravanat, ).-L (2005) Detection of chlorinated DNA and RNA nucleosides by HPLC coupled to mass spectrometry as potential biomarkers of inflammation. J. Chromatogr. B, 827, 26-31. 

As described above, Zn -cyclen complex 8 is a highly selective host in aqueous solution at physiological pH for dT and U among the DNA and RNA nucleosides. In the resulting... 

DNA and RNA are formed of nucleotides. Each nucleotide or nucleoside is composed of a purine or pyrimidine base linked to the 1-position of a ribose sugar in the case of RNA and a 2 -deoxyribose sugar in the case of DNA.155 The 5 position is phosphorylated in the case of a nucleotide, while the nucleoside is not phosphorylated therefore, nucleotides are nucleoside phosphates. Phosphorylation can include one, two, or three phosphate groups. The most familiar example of a phosphorylated nucleotide is phosphorylated adenosine, which occurs as the mono-, di-, and triphosphate (AMP, ADP, and ATP, respectively) and is a principal means of energy storage in biological systems. 

Table 2.2 Nitrogenous Bases, Nucleosides, Nucleotides, and Sugars Found in DNA and RNA...

Those nucleosides found in the nucleic acids DNA and RNA involve the joining of ribose of deoxyribose to a purine or a pyrimidine base. One such nucleoside is adenosine, in which a nitrogen of adenine is linked to carbon 1 of the pentose, ribose. In this form it is a component of RNA but as a phosphory-lated derivative of adenosine (e.g. ATP), which is a high energy compound, it fulfils an important role in metabolism. The dinucleotides NAD and NADP are two cofactors necessary for many enzymic transformations and these also contain /V-glycosides of ribose phosphate. Other important nucleosides are found... 

Adenosine A nucleoside that is composed of adenine and d-ribose. Adenosine or adenosine derivatives play many important biological roles in addition to being components of DNA and RNA. Adenosine itself is a neurotransmitter. [NIH]... 

Nucleotides are needed for DNA and RNA synthesis (DNA replication and transcription) and for energy transfer. Nucleoside triphosphates (ATP and GTP) provide energy for reactions that would otherwise be extremely unfevorable in the cell. 

Excess purine nucleotides or those released from DNA and RNA by nucleases are catabolized first to nucleosides (loss of P.) and then to free purine bases (release of ribose or deoxyribose). Excess nucleoside monophosphates may accumulate when ... 

Figure 4.15 k summary of the fate of nucleosides that are produced from RNA digestion in the lumen of the intestine. The nucleosides produced from RNA in the lumen are absorbed by the enterocytes and then transported from the intestine into the blood from where they are taken up by cells (especially proliferating cells, e.g. in the bone marrow) to form nucleotides for DNA and RNA synthesis. (See Chapter 10) NTP is nucleoside triphosphate. 

DNA and RNA synthesis De novo formation of purine and pyrimidine nucleotide Nucleoside diphosphate reductase Thymidylate synthase Polymerase reactions Chapter 20... 

The bases are either monocyclic pyrimidines or bicyclic purines (see Section 14.1). Three pyrimidine bases are encountered in DNA and RNA, cytosine (C), thymine (T) and uracil (U). Cytosine is common to both DNA and RNA, but uracil is found only in RNA and thymine is found only in DNA. In the nucleic acid, the bases are linked through an A-glycoside bond to a sugar, either ribose or deoxyribose the combination base plus sugar is termed a nucleoside. The nitrogen bonded to the sugar is that shown. 

C-Glycosides are typified by barbaloin, a component of the natural purgative drag cascara, but, as a group, the M-glycosides are perhaps the most important to biochemistry. Al-Glycosidic linkages are found in the nucleosides, components of DNA and RNA (see Section 14.1). In addition, nucleosides are essential parts of the structures of crucial biochemicals such as ATP, coenzyme A, NAD+, etc. The amine in these types of compound is part of a purine or pyrimidine base (see Section 14.1). 

Ribavirin is a synthetic analog of nucleosides. It is effective against many DNA and RNA viruses, such as viral influenza and herpes. The mechanism of its action is not completely known. However, it is highly likely that it is not the same for all viruses. It has been tried on a number of AIDS patients with various results. A synonym of this drag is virazoll. 

Fluorinated analogues of nucleosides are drugs that interact with enzymes involved in the synthesis of DNA and RNA (cf. Chapter 7). They are developed for treatment of cancer and viral infections. Fluorine atoms can be present either on the base moiety or on the sugar one. 

Several other major classes of enzymes, among them the nucleic acid polymerases, activate ATP (and other NTPs) in a completely different manner. Similar to transphos-phoiylation enzymes, they utilize two metal ions for catalysis. However, steric interactions are purposely employed in order to reverse the preferred binding situation. A MaMp y motif is generated which weakens the P —O—P,5 linkage This allows a nucleoside monophosphate group to be transferred (under liberation of PPi), a process which is essential in the biosynthesis of DNA and RNA sequences. 

Compounds based on the purine structure are classified as purines. Adenine is one of the two purines found in DNA and RNA. The other is guanine. Adenine and guanine are called bases in reference to DNA and RNA. A nucleic acid base attached to ribose forms a ribonucleoside. Adenine combined with ribose produces the nucleoside adenosine. When an oxygen atom is removed from the second carbon of ribose, the sugar unit formed is... 

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