Cyclobutane pyrimidine dimers

Zhang RB, Eriksson LA (2006) A triplet mechanism for the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA. J Phys Chem B 110 7556-7562... 

Scheme 1 UV-light induced formation of the two major photo lesions in DNA. T=T cyclobutane pyrimidine dimer. (6-4)-photo product (6-4)-lesion, formed after ring opening of an oxetane intermediate, which is the product of a Paterno-Buchi reaction...

Scheme 2 Mechanism of repair of cyclobutane pyrimidine dimers (CPD) by a CPD photolyase. 8-HDF 8-hydroxy-5-deazaflavin, ET electron transfer. FADH reduced and de-protonated flavin-coenzyme...

These experiments proved that a light-excited, reduced flavin is indeed able to photoreduce cyclobutane pyrimidine dimers and that these dimers undergo a spontaneous cycloreversion. The quantum yield of about 0=5% clarified that the overall dimer splitting process is highly efficient, even in these simple model systems ((]) photolyase 70%). 

Whatever the reason may be behind the strict necessity to deprotonate the flavin donor, the reduced and deprotonated flavin was established in these model studies to be an efficient electron donor, able to reduce nucle-obases and oxetanes. In the model compounds 1 and 2 the pyrimidine dimer translates the electron transfer step into a rapidly detectable chemical cycloreversion reaction [47, 48], Incorporation of a flavin and of a cyclobutane pyrimidine dimer into DNA double strands was consequently performed in order to analyse the reductive electron transfer properties of DNA. 

Incorporation of a flavin electron donor and a thymine dimer acceptor into DNA double strands was achieved as depicted in Scheme 5 using a complex phosphoramidite/H-phosphonate/phosphoramidite DNA synthesis protocol. For the preparation of a flavin-base, which fits well into a DNA double strand structure, riboflavin was reacted with benzaldehyde-dimethylacetale to rigidify the ribityl-chain as a part of a 1,3-dioxane substructure [49]. The benzacetal-protected flavin was finally converted into the 5 -dimethoxytri-tyl-protected-3 -H-phosphonate ready for the incorporation into DNA using machine assisted DNA synthesis (Scheme 5a). For the cyclobutane pyrimidine dimer acceptor, a formacetal-linked thymine dimer phosphoramidite was prepared, which was found to be accessible in large quantities [50]. Both the flavin base and the formacetal-linked thymidine dimer, were finally incorporated into DNA strands like 7-12 (Scheme 5c). As depicted in... 

Scheme 5 a Flavin-H-phosphonate and formacetal-linked thymine dimer phospho-ramidite used for the synthesis of the flavin and dimer containing DNA-strands 7-12. b Representation of a reduced flavin- and formacetal-linked cyclobutane pyrimidine dimer containing DNA strand, which upon irradiation (hv) and electron transfer (ET) performs a cycloreversion (CR) of the dimer unit, c Depiction of the investigated oligonucleotides... 

Flavin-cyclobutane pyrimidine dimer and flavin-oxetane model compounds like 1-3 showed for the first time that a reduced and deprotonated flavin is a strong photo-reductant even outside a protein environment, able to transfer an extra electron to cyclobutane pyrimidine dimers and oxetanes. There then spontaneously perform either a [2n+2n cycloreversion or a retro-Paternd-Buchi reaction. In this sense, the model compounds mimic the electron transfer driven DNA repair process of CPD- and (6-4)-photolyases. 

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. 

Vink, A. A. et al., The inhibition of antigen-presenting activity of dendritic cells resulting from UV irradiation of murine skin is restored by in vitro photorepair of cyclobutane pyrimidine dimers, Proc. Natl. Acad, Sci. USA 94, 5255-5260, 1997. 

Most microorganisms have redundant pathways for the repair of cyclobutane pyrimidine dimers— making use of DNA photolyase and sometimes base-excision repair as alternatives to nucleotide-excision repair—but humans and other placental mammals do not. This lack of a back-up to nucleotide-excision repair for the removal of pyrimidine dimers has led to speculation that early mammalian evolution involved small, furry, nocturnal animals with little need to repair UV damage. However, mammals do have a path-... 

Direct Repair Several types of damage are repaired without removing a base or nucleotide. The best-characterized example is direct photoreactivation of cyclobutane pyrimidine dimers, a reaction promoted by DNA photolyases. Pyrimidine dimers result from an ultraviolet light-induced reaction, and photolyases use energy derived from absorbed light to reverse the dam-... 

Figure 12.1 Structures of (a) cyclobutane pyrimidine dimer (ToT), (b) pyrimidine (6-4) pyrimidone photoproduct ((6-4)pp). (c) The scheme of the catalytic cycle for the repairing of ToT dimers by DNA photolyase 114]...

There are two major types of DNA damage following UV radiation cyclobutane pyrimidine dimers (CPD) and pyrimidine-pyrimidone (6-4) photoproducts that are often simply called (6-4) photoproducts. Formation of these UV lesions may be influenced by the DNA sequence. Nevertheless, in general, CPDs are more abundant than (6-4) photoproducts in UV irradiated DNA. For example, in UVC-irradiated DNA, the overall ratio of CPDs to (6-4) photoproducts is about 3 1. 

Spore Photoproduct Lyase. The DNA in spores is in A-form because of dehydration. As a consequence, when spores are exposed to UV, the stereochemistry of the bases is not conducive to the formation of cyclobutane pyrimidine dimers or (6-4) photoproducts. Instead, UV induces the formation of 5-thyminyl-5,6-dihydrothymine or spore photoproduct (SP). This lesion is repaired by a 40-kDa enzyme called SP lyase. The enzyme is an iron-sulfur [4Fe-4S] protein that employs S-adenosyl-methionine (AdoMet) as a catalytic cofactor and carries out repair by a radical mechanism (6) (Fig. 2). In this mechanism, the reduced [Fe-S] center cleaves AdoMet to generate a 5 -deoxyadenosyl radical intermediate and methionine. The radical then abstracts an H-atom from C-6 of the SP. The resulting substrate radical undergoes bond cleavage to generate a product radical. The latter abstracts an H-atom from the 5 deoxyadenosine to form canonical thymines and a 5 deoxyadenosyl radical. Finally, the catalytic cycle is closed by electron transfer back to the [Fe-S] cluster concomitant with the formation of AdoMet (6). 

Nucleotide excision repair is the primary repair system for the removal of DNA damage caused by chemicals that produce bulky adducts or by the UV component of sunlight, which produces cyclobutane pyrimidine dimers (Pyr< >Pyr) and (6-4) photoproducts in DNA (1). These lesions, as well as other bulky lesions induced by chemical carcinogens, are removed by... 

The literature documents various situations in which C deamination is enhanced. These situations include the presence of C in cyclobutane pyrimidine dimers (a form of DNA damage caused by exposure to UV radiation see later discussion) or in mis-pairings with other bases or with alkylated bases (1). Cytosine deamination is also promoted in the presence of nitrons acid, a reaction that although not considered in this review, has lent much to our understanding of possible chemical mechanisms of spontaneous deamination (1). 

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