DNA nucleobases

As for nucleic acid applications, the syntheses and fluorescent properties of the DNA nucleobase replacements like the l,2,3-triazolo[4,5-rf]pyrimidine 2-deoxyribofuranosides 87... 

Structural and biological impact of radical addition reactions with DNA nucleobases... 

Bamatraf MMM, O Neill P, Rao BSM (1998) Redox dependence of the rate of interaction of hydroxyl radical adducts of DNA nucleobases with oxidants consequences for DNA strand breakage. J Am Chem Soc 120 11852-11857... 

To evaluate the participation of hydrogen bonding in DNA replication selectivity mechanisms Kool described a seminal functional strategy based on chemically modified DNA polymerase substrates [3a,d,g], He developed nucleotide analogs in which the polar natural DNA nucleobases are replaced by non-polar aromatic molecules, which closely mimic the shape and size of the natural nucleobases but have at least significantly diminished ability to form stable hydrogen bonds (Figure 4.1.4). 

In the present chapter we will describe some examples in which barrierless minimum energy reaction paths along the potential hypersurfaces of several systems will be shown to connect initially excited singlet states with the triplet manifold. Those examples include the isoalloxazine molecule and different DNA nucleobases. 

In this chapter we have reviewed computations that help to explain the photostability and lifetimes of the DNA nucleobases, using cytosine and the cytosine-guanine Watson-Crick base-pair as examples. 

A more suitable model, mimicking the DNA environment to a better extent, is the 9-methyladenine-l-methylthymine (MAMT) base pair, since in DNA nucleobases are bonded to deoxyribose (through the C-N bond) via these methylated positions. 

The ability to calculate redox potentials has powerfid implications. For example, elecfrocatalytic reactions of metal complexes, such as Ru(bpy)3 +, with DNA nucleobases, such as guanine, provide a sensitive method for detection of nucleic acids on surfaces in electrochemical DNA chips (see Nucleic Acid-Metal Ion Interactions) In these reactions, voltammetric oxidation of Ru(bpy)3 + to Ru(bpy)3 + in the presence of guanine produces an enhancement in the oxidative current due to the reaction of Ru(III) with guanine (Figure 2). On surfaces, the extent of elecfrocatalytic enhancement is indicative of the quantity of bound nucleic acid levels of DNA as low as 40 attomoles have been detected using related methods. ... 

Beside Hg, other late transition metal ions (e.g., Ag and Au ) can coordinate to DNA nucleobases to form interstrand cross-links. Several DNA coordination modes have been suggested for Ag ions, including coordination to the purine N1 and the pyrimidine N3 (86). At Ag /base pair ratios <0.5, the metal ion coordinates to the N7 position of purines, in particular to guanine, while at a Ag /bp ratio of 0.5, Ag forms cross-links between the two strands of the duplex by binding to two nucleobases (89). The Au " " ion was also shown to coordinate to solvent-exposed GC base pairs in RNA duplexes to form a G-Au-C bridge that resembles T-Hg-T (88). 

The existence was also observed of a characteristic affinity of reported to the phosphodiesteric centers and the intrastrand DNA nucleobases. The binding tendency at the intra-strand nucleobases increases in the order ... 

Molecules containing sulfur or nitrogen donor atoms can serve as ligands to form stable complexes with the relatively kinetically inert Pt(II) center (for a review see Ref. 60). It is likely that cisplatin binds to many cellular components, the result of which is general toxicity, but coordination to the heterocyclic nitrogen atoms of DNA nucleobases is most likely responsible for its antitumor activity. 

The ability to calculate redox potentials has powerful implications. For example, electrocatalytic reactions of metal complexes, such as Ru(bpy)3 +, with DNA nucleobases, such as guanine, provide a sensitive method for detection of nucleic acids on surfaces in electrochemical DNA chips see Nucleic Acid-Metal Ion Interaction In these reactions. 

Some of these activated species like HO Cu -hydroperoxo, or Cu -hydroxo have been also proposed in the case of the oxidations of the DNA nucleobases (55). Various mechanisms like HO addition on a double-bound, hydrogen abstraction on the methyl groups or electron transfer induce nucleobases oxidations and copper complexes are oxidant enough to perform them, but, in the presence of excess of reductants, such as in the conditions often used during DNA oxidation by copper complexes, oxidized nucleobases (base radicals and radical cations) may be reduced back to undamaged species. Thus the ability of copper complexes to oxidize nucleobases could be underestimated. 

There is a revival in the study of nucleic acid bases and mixtures thereof at the hquid-solid interface. Besenbacher et al. investigated in detail the self-assembly of pure and mixed assemblies of adenine and thymine [44]. The unique aspect of the current approach is the intimate relation between experiment and molecular modehng reveahng unprecedented insight in the self-assembly properties of nucleic acids. The motivation behind the detailed study of these multicomponent systems is the potential of DNA nucleobases to complex proteins and other biological systems. 

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