Dinucleotide structures

Fig. 1 Dinucleotide structures (as found in respective dino-cleotides). (A) morpholino analog (B) normal DNA or RNA (C) phosphorothioate analog of DNA (D) peptide nucleic acid.

The isolation, mass and NMR characterization of the lesions was performed with the dinucleotide model compound d(GpT) since the chromatographic separation of the products of guanine oxidation was followed easily by UV-VIS spectrophotometry (thymine base was not modified by the oxidation) and the very polar oxidized guanine residues could be retained on the reverse phase HPLC column by the dinucleotide structure of the substrate. The oxidation of the guanine moiety of a dinucleoside monophosphate under appropriate conditions afforded the imidazolone (Iz) and the dehydro-guanidinohydantoin derivative 35 in amounts compatible with NMR analysis (261). However, 35 is not stable and was first stabilized in two ways for the... 

Nicotinic acid- DPN has been termed desamido DPN. We have preferred to use the term nicotinic acid-" DPN which indicates that nicotinic acid has been substituted for nicotinamide in the dinucleotide structure, since there are many analogs of DPN which have been prepared now in which... 

Packer M J, M P Dauncey and C A Hunter 2000. Sequence-dependent DNA Structure Dinucleotide Conformational Maps. Journal of Molecular Biology 295 71-83. 

FIGURE 15 5 Structure of NAD the oxidized form of the coenzyme nicotinamide adenine dinucleotide The functional part of the coen zyme is framed in red... 

Oxidation of P-nicotinamide adenine dinucleotide (NADH) to NAD+ has attracted much interest from the viewpoint of its role in biosensors reactions. It has been reported that several quinone derivatives and polymerized redox dyes, such as phenoxazine and phenothiazine derivatives, possess catalytic activities for the oxidation of NADH and have been used for dehydrogenase biosensors development [1, 2]. Flavins (contain in chemical structure isoalloxazine ring) are the prosthetic groups responsible for NAD+/NADH conversion in the active sites of some dehydrogenase enzymes. Upon the electropolymerization of flavin derivatives, the effective catalysts of NAD+/NADH regeneration, which mimic the NADH-dehydrogenase activity, would be synthesized [3]. 

Several classes of vitamins are related to, or are precursors of, coenzymes that contain adenine nucleotides as part of their structure. These coenzymes include the flavin dinucleotides, the pyridine dinucleotides, and coenzyme A. The adenine nucleotide portion of these coenzymes does not participate actively in the reactions of these coenzymes rather, it enables the proper enzymes to recognize the coenzyme. Specifically, the adenine nucleotide greatly increases both the affinity and the speeifieity of the coenzyme for its site on the enzyme, owing to its numerous sites for hydrogen bonding, and also the hydrophobic and ionic bonding possibilities it brings to the coenzyme structure. 

Riboflavin, or vitamin B2, is a constituent and precursor of both riboflavin 5 -phosphate, also known as flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD). The name riboflavin is a synthesis of the names for the molecule s component parts, ribitol and flavin. The structures of riboflavin. 

This thiol-disulfide interconversion is a key part of numerous biological processes. WeTJ see in Chapter 26, for instance, that disulfide formation is involved in defining the structure and three-dimensional conformations of proteins, where disulfide "bridges" often form cross-links between q steine amino acid units in the protein chains. Disulfide formation is also involved in the process by which cells protect themselves from oxidative degradation. A cellular component called glutathione removes potentially harmful oxidants and is itself oxidized to glutathione disulfide in the process. Reduction back to the thiol requires the coenzyme flavin adenine dinucleotide (reduced), abbreviated FADH2. 

Newman, Melvin S., 93 Newman projection, 93 molecular model of, 93 Nicotinamide adenine dinucleotide, biological oxidations with, 625-626 reactions of, 725 structure of, 725, 1044 Nicotinamide adenine dinucleotide (reduced), biological reductions with, 610-611... 

Flavin adenine dinucleotide (FAD) Scheme 10.15 Chemical structures of FMN and FAD. 

Niacin. Figure 2 Structure of the coenzymes NAD+ (nicotinamide-adenine dinucleotid) and NADP+ (nicotinamide-adenine dinucleotid phosphate). 

Vitamin B2. Figure 2 Structure of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). 

The molyhdopterin cofactor, as found in different enzymes, may be present either as the nucleoside monophosphate or in the dinucleotide form. In some cases the molybdenum atom binds one single cofactor molecule, while in others, two pterin cofactors coordinate the metal. Molyhdopterin cytosine dinucleotide (MCD) is found in AORs from sulfate reducers, and molyhdopterin adenine dinucleotide and molyb-dopterin hypoxanthine dinucleotide were reported for other enzymes (205). The first structural evidence for binding of the dithiolene group of the pterin tricyclic system to molybdenum was shown for the AOR from Pyrococcus furiosus and D. gigas (199). In the latter, one molyb-dopterin cytosine dinucleotide (MCD) is used for molybdenum ligation. Two molecules of MGD are present in the formate dehydrogenase and nitrate reductase. 

The aldehyde oxidoreductase from Desulfovibrio gigas shows 52% sequence identity with xanthine oxidase (199, 212) and is, so far, the single representative of the xanthine oxidase family. The 3D structure of MOP was analyzed at 1.8 A resolution in several states oxidized, reduced, desulfo and sulfo forms, and alcohol-bound (200), which has allowed more precise definition of the metal coordination site and contributed to the understanding of its role in catalysis. The overall structure, composed of a single polypeptide of 907 amino acid residues, is organized into four domains two N-terminus smaller domains, which bind the two types of [2Fe-2S] centers and two much larger domains, which harbor the molybdopterin cofactor, deeply buried in the molecule (Fig. 10). The pterin cofactor is present as a cytosine dinucleotide (MCD) and is 15 A away from the molecular surface,... 

FIGURE 10.1 The structural formula of riboflavin and partial structures of riboflavin compounds. The latter show only those portions of the molecule that differ from riboflavin. 1 — Riboflavin (RF), 2 — flavin mononucleotide or 5 -riboflavin monophosphate (FMN or 5 -FMN), 3 — flavin adenine dinucleotide (FAD). 

Zinc-containing alcohol dehydrogenases take up two electrons and a proton from alcohols in the form of a hydride. The hydride acceptor is usually NAD(P) (the oxidized form of nicotinamide adenine dinucleotide (NADH) or its phosphorylated derivative, NADPH). Several liver alcohol dehydrogenases have been structurally characterized, and Pig. 17.8 shows the environment around the catalytic Zn center and the bound NADH cofactor. 

Figure 14-3. Transesterification reaction of the dinucleotide model where the nucleophile-containing ribose sugar is modelled by a tetrahydrofurane structure, whereas the cleaving sugar is further simplified and modelled as a simple primary alcohol (ethanol)...

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