Nucleobase dimers

Table 1.2 Nucleobase dimer binding energies [kcal/mol], binding energy statistics, and a summary of geometricai errors.

In addition, we provided a brief comparison between nucleobase dimer and trimer binding energies and geometries as computed with mDC, other semiempirical models, a molecular mechanical force field, and several ab initio methods. mDC was shown to reproduce the high-level ab initio and experimental results with the greatest accuracy. 

Nir E, Kleinermanns IHK, de Vries MS (2003) The nucleobase cytosine and the cytosine dimer investigated by double resonance laser spectroscopy and ab initio calculations. Phys Chem Chem... 

Although the reduction potentials of DNA bases and UV induced DNA lesions inside a DNA double strand or inside the active site of a DNA photolyase, together with the reduction potential of the photoexcited FADH- in the photolyases, are not known, currently available redox potentials indicate that the single electron reduction of a nucleobase or a UV induced dimer lesion by a reduced and deprotonated flavin coenzyme is a weakly exothermic process. The reduced and deprotonated FADH- in its photoexcited state is... 

Incorporation of an artificial flavin nucleobase and of a cyclobutane pyrimidine dimer building block into DNA DNA double strands, DNArPNA hybrid duplexes, and DNA-hairpins, provided compelling evidence that an excess electron can hop through DNA to initiate dimer repair even at a remote site. The maximum excess electron transfer distance realised so far in these defined Donor-DNA-Acceptor systems is 24 A. New experiments are now in progress to clarify whether even larger transfer distances can be achieved. 

Figure 24 Interactions between the nucleobases involve dimers of stacked AT pairs that are slipped so as to...

LCA toward amino acids and nucleic bases has also been measured. Wesdemiotis and Cerda measured the alkali metal ion affinities of nucleobases in the gas phase from the dissociation of metal ion-bound heterodimers [nucleobase + B]M+, in which B represents a reference base of known affinity and M is an alkali metal. By assessing the dimer decomposition for two different internal energies, entropy is deconvoluted from enthalpy and LCA values are obtained. For guanine, cytosine, adenine, thymine and uracil, the corresponding Li+-nucleobase bond energies are as follows 57.2, 55.5, 54.1,... 

Each WCP dimer model consists of two purine bases (G and A) and two pyrimidine bases (C and T). According to the calculations, the two highest-lying orbitals HOMO and HOMO-1 of each duplex are mainly locahzed on the purine nucleobases, whereas the two occupied MOs following at lower energies, HOMO-2 and HOMO-3, are locahzed on pyrimidine nucleobases. Therefore, the purine-purine electronic coupling provides the dominant contribution to the hole transfer matrix elements, irrespective whether the bases belong to the same or to opposite strands. 

Comparing matrix elements of simple models of two purine nucleobases with those calculated for WCP dimers (Table 3), one wonders about the effect of pyrimidine nucleobases on the electronic coupling matrix elements of hole transfer in DNA [14, 73]. 

A number of studies are concerned with the free-radical reactions of typical nucleobase lesions. For example, the cyclobutane-type Thy dimer can be split by one-electron reduction [Heelis et al. 1992 reactions (307) and (308)], a process that is relevant to the repair of this typical UV-damage by the photoreactivating enzyme (photolyase, for a review see Carrell et al. 2001, for the energetics of the complex reaction sequence, see Popovic et al. 2002). At 77 K, the dimer radical anion is sufficiently long-lived to be detectable by EPR (Pezeshk et al. 1996). 

Thymidine cyclobutane dimers are important photoproducts formed by short-wave UV irradiation (2 = 290-320 nm) of DNA, by [2 + 2] cycloaddition between two adjacent thymine nucleobases in the same oligonucleotide strand (Scheme 4.5.1) [1]. They lead to profound biological effects in vivo, including mutation, cancer, and cell death [2] (Box 21). In a wide range of organisms the repair of these lesions in DNA is accomplished by enzymes (the photolyases), which regenerate undamaged thymidines by means of a photoinduced electron-transfer process [3]. 

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