Nucleo bases

H-atom abstraction has been demonstrated to be the mechanism of action of excited uranyl ions, and in this case negligible base oxidation is found. Nucleo-base (especially guanine) oxidation is the principal reaction caused by singlet oxygen and this reactive species can be generated by a number of the complexes (e.g. many Ru(II)polypyridyls and porphyrins). It is worth pointing out, however, that the yield of may be lower when the sensitiser is bound to DNA, and it is the authors view that some of the reactions claimed to proceed via 62 may be caused by direct reaction of the photo-oxidised sensitiser with the DNA. 

The hydroxyl radical can also abstract a single electron from dG to generate the base radical cation (G ). In duplex DNA, the G " " will be stabilized by its delocalization into adjacent bases. Both calculations and kinetic measurements " indicate that GG sequences have a lower oxidation potential than an isolated G. Nucleo-bases on the 3 -side of G determine the extent of G formation, and here purines are more effective than pyrimidines at lowering the oxidation potential of G, which accounts for the GG effect and that GA sites are also reactive. ... 

Hoogsteen face The Hoogsteen face refers to a part of nucleo-bases that is exposed along the major groove of DNA. The Hoogsteen face is a potential site of interaction with other molecules and especially useful for binding of a third oligonucleotide strand to form a triple helix. 

Klein, D. J., Edwards, T. E., and Ferre-D Amare, A. R. (2009). Cocrystal structure of a class I preQl riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleo-base. Nat. Struct. Mol. Biol. 16, 343—344. 

Direct UV irradiation of DNA leads to a variety of lesions at the nucleo-base. The principle products are pyrimidine cyclobutane dimers ToT, ToC, and CoC, formed in that order of preference, by [2+2] photocycloaddition of two adjacent pyrimidine nucleosides in the same oligonucleotide strand (Scheme B.21.4). With approximately 50% of the frequency of cyclobutane dimers, [2+2] dimerization involves a C=0 double bond leading to an intermediate oxetane 29, which later decomposes to the [6-4] photoproduct 30. 

Ravera M, Baracco S, Cassino C, Colangelo D, Bagni G, Sava G, Osella D (2004) Electrochemical measurements confirm the preferential bonding of the antimetastatic complex [ImH][RuCl4(DMSO)(Im)] (NAMI-A) with proteins and the weak interaction with nucleo-bases. J Inorg Biochem 98 984-990... 

Saladino R, Crestini C, Costanzo G, DiMauro E. On the prebiotic synthesis of nucleo-bases, nucleotides, oligonucleotides, pre-RNA and pre-DNA molecules. Top Curr Chem 2005 259 29-68. 

The thymidine derivatives (146) and (147) undergo cleavage of a C-C bond on irradiation. These reactions are typical Norrish Type I processes and provide a route to study C-3 -DNA radicals. Hydrogen abstraction by the radicals yields a 1 1 mixture of the threo and erythro derivatives (148). The reactions from the P-isomers (146) are generally more efficient than from the a-isomer (147). A study of the photochemical reactivity of the deoxyuridine derivative (149) has been reported. This novel compound is an electron-accepting nucleo base. It has been used as a means of cleaving DNA. The photochemical fission occurs specifically at the 5 -G of 5 GG3 sequences. 

Figure 7.1 shows D-a-ribonucleotide-adenosine-5 -triphophate. The purine nucleo-base adenine is in blue, D-ribose is in grey with two secondary, vicinal OH-groups are at the 2 and 3 -positions, and three phosphate groups are in brown linked to the primary 5 -OH of the sugar. 

The rich coordination chemistry of transition metal ions has been used not only to create metal-ligand complexes that play the role of alternative nucleo-base pairs within nucleic acid duplexes, but also to influence the secondary structure adopted by the nucleic acid, for example, hairpin, duplex, or triplex, and to create connectors for such nucleic acid structures. In this context, oligonucleotides that contain terminal ligands can lead to structures distinct from those accessible by using centrally-modified oligonucleotides, such as cyclic structures or hairpins (Fig. 3). 

MeU and 1-MeT enables formation of L containing mixed nucleo-base complexes according to... 

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