Pyrimidine dimer

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Chemical structures of thymine pyrimidine dimers Chemical structures of pyrimidine dimers.jpg
Chemical structures of thymine pyrimidine dimers

A pyrimidine dimer is a chemical species issued from a photochemical reaction involving two pyrimidine nucleobases (thymine, cytosine, or uracil) through formation of new covalent bonds. The discovery pyrimidine dimers [1] was initially prompted by the observation that ultraviolet (UV) radiation inactivates cells. [2] Over the years, experimental and theoretical studies, performed mainly on model DNA and RNA systems in solution, shed light on the primary processes underlying their formation. [3] , [4] , [5] In parallel, such dimers have been detected in living cells and skin, [6] and their impact on biological processes has been extensively characterized. [7]

Contents

Four principal classes of pyrimidine dimers have been identified: cyclobutane pyrimidine dimers (CPDs), (6–4) pyrimidone photoproducts (64PPs), their Dewar valence isomers, and the spore photoproduct (SP). Dimerization may proceed via a direct mechanism, in which UV radiation is absorbed by the nucleobases, or via an indirect photosensitized processes, requiring the action of other molecules absorbing light. [8]

The formation of a pyrimidine dimer within a DNA double helix disrupts Watson-Crick base pairing, distorts the local structure. DNA UV mutation.svg
The formation of a pyrimidine dimer within a DNA double helix disrupts Watson–Crick base pairing, distorts the local structure.

The formation of a pyrimidine dimer within a double helix disrupts Watson–Crick base pairing, distorts the local structure, [9] and compromises the accurate transmission of genetic information. If left unrepaired, such lesions can induce transcriptional and replicative errors, contributing to mutagenesis and carcinogenesis. [10] Pyrimidine dimers play a major role in the development of melanoma. [11]

Certain pyrimidine dimers can undergo photoreversal, a process that regenerates the original nucleobases. [12] [13] In living cells, repair occurs primarily through photoreactivation involving photolyase enzymes [14] , [15] or through a base excision repair mechanism. [16]

Beyond the biological significance of pyrimidine dimers as DNA lesions, reversible pyrimidine dimerization has attracted interest for applications for technological applications. [17]

Photochemistry

Among the pyrimidine dimers formed between either identical or different nucleobases, those involving two thymines have been, by far, the most extensively studied from a photochemical perspective. In addition to the dimerization of the major nucleobases, the photochemistry of the epigenetic analogs, such as 5-methylcytosine, [18] has also been investigated. While synthetic nucleic acids are more suitable for characterizing the primary processes underlying dimerization in single strands, [19] , [20] , [21] , [22] , [23] , [24] duplexes [25] and guanine quadruplexes, [26] , [27] several studies have also been conducted on purified genomic DNA. [28] , [29]

Direct mechanism

According the direct mechanism, UV photons are absorbed by the pyrimidines and the photoreaction proceeds mainly from a singlet excited state. Those states are collective, that is delocalized over both pyrimidines. [30] A minor pathway, proceeding via the thymine triplet state, formed through intersystem crossing, has also been reported for CPDs. [31] , [32]

In the case of 64PPs, the direct photochemical process leads to the formation of a reaction intermediate (oxetane), [33] which subsequently undergoes a dark reaction leading to the final dimer. The Dewar valence isomers [34] are obtained upon irradiation of 64PPs, the backbone playing an important role in the reaction. [35] Studies by time-resolved absorption spectroscopy revealed that in thymine single strands CPDs are formed within 1 picosecond, [36] while the reaction leading from the oxetane to 64PPs is completed within 4 milliseconds. [37]

Absorption spectra of DNA single (dT20, blue) and double (dA20dT20, red) strands. Absorption spectra of DNA single and double strands.jpg
Absorption spectra of DNA single (dT20, blue) and double (dA20dT20, red) strands.

The quantum yield of the dimerization reaction, Φ defined as the number of dimers formed per absorbed photon, and its dependence on the irradiation wavelength are central to these investigations. These parameters are intrinsically linked to nature of the electronic excited state populated upon photon absorption and to their relaxation. [38] , [39] In single thymine stands, ΦCPD is constant (0.05), across the main absorption band. In contrast, Φ64PP decreases continuously upon increasing wavelength. [40] No 64PPs are detected upon UVA irradiation, where DNA exhibits weak absorption, whereas CPDs are still induced albeit less efficiently (ΦCPD =7x10-4). More importantly, base pairing enhances CPD formation under UVA irradiation, the ΦCPD being higher by a factor 7, while the opposite trend is observed upon UVC irradiation. [41]

The formation of various pyrimidine dimers at 254 nm was quantified for purified genomic DNA. CPDs (total ΦCPD =10-3) are more abundant the 64PP (total Φ64PP = 3x10-4). [42] CPD formation has also reported for this natural biomolecule irradiated with UVA light. [43]

Indirect mechanism

Simplified scheme of the mechanism involved in the photosensitized formation of pyrimidine dimers. Photosenistized formation of pyrimidine dimers-2.tif
Simplified scheme of the mechanism involved in the photosensitized formation of pyrimidine dimers.

In the indirect mechanism triplet states play a key role. Photons, typically in the UVA range, are absorbed by a photosensitizer whose triplet state is populated via intersystem crossing. Subsequently, the electric excitation energy is transferred to a pyrimidine triplet state which then triggers dimerization. Both CPDs and the SP are formed via this pathway. In contrast, there is no evidence that photosensitization leads to 64PPs or their Dewar valence isomers. [44]

A large variety of photosensitizes, such as benzophenones, phthalimides or fluoroquinolones, have been tested in order to study the requirements for photosensitization. In practice, their triplet energy must be higher than those of the pyrimidine triplet states and their quantum yield for intersystem crossing must be sufficiently high. In addition to external agents, 64PPs already present in DNA, have the ability to photosensitize CPD formation via the triplet state of pyrimidone. [45] Sensitization may be preceded by triplet energy migration within the double helix; migration distances up to 105 Å have been reported. [46]

Biological effects

Mutagenesis

Mutagenesis, the process of mutation formation, is significantly influenced by translesion polymerases which often introduce mutations at sites of pyrimidine dimers. [47] This occurs in prokaryotes through the SOS response to mutagenesis and in eukaryotes through other methods. As thymine–thymine CPDs are the most common lesions induced by UV, translesion polymerases show a tendency to incorporate adenines opposite these dimers, resulting in accurate replication. Cytosines that are part of CPDs, however, are susceptible to deamination, leading to cytosine to thymine transitions and contributing to the mutation process. [48]

DNA repair

Melanoma, a type of skin cancer Melanoma.jpg
Melanoma, a type of skin cancer

Pyrimidine dimers introduce local conformational changes in the DNA structure, which allows recognition of the lesion by repair enzymes. [49] In most organisms (excluding placental mammals such as humans) they can be repaired by photoreactivation. [50] Photoreactivation is a repair process in which photolyase enzymes reverse CPDs using photochemical reactions. In addition, some photolyases can also repair 6-4 photoproducts of UV induced DNA damage. Photolyase enzymes utilize flavin adenine dinucleotide (FAD) as a cofactor in the repair process. [51]

The UV dose that reduces a population of wild-type yeast cells to 37% (assuming a Poisson distribution of hits) is the same as the UV dose that causes an average of one lethal hit to each of the cells of the population. [52] The number of pyrimidine dimers induced per haploid genome at this dose was measured as 27,000. [52] A mutant yeast strain defective in the three known pyrimidine dimer repair pathways was also tested for UV sensitivity. In this case, only one to two unrepaired pyrimidine dimers per haploid genome are lethal to the cell. [52] These findings thus indicate that the repair of thymine dimers in wild-type yeast is highly efficient.[ citation needed ]

Nucleotide excision repair (NER), sometimes termed "dark reactivation", is a more general mechanism for repair of lesions and is the most common form of DNA repair for pyrimidine dimers in humans. This process works by using cellular machinery to locate the dimerized nucleotides and excise the lesion. Once the CPD is removed, there is a gap in the DNA strand that must be filled. DNA machinery uses the undamaged complementary DNA strand as a template to synthesize the matching nucleotides and consequently fill in the gap on the damaged strand. [53]

Xeroderma pigmentosum (XP) is a rare genetic disease in humans that is caused by UV damage to genes that code for NER proteins, resulting in the inability for the cell to combat pyrimidine dimers that form. Individuals with XP are also at a much higher risk of cancer, with a >5,000-fold increased risk of developing skin cancers compared to the general population. [54] Some common features and symptoms of XP include skin discoloration and the formation of multiple tumors proceeding UV exposure. [55]

A few organisms have other ways to perform repairs:

Another type of repair mechanism that is conserved in humans and other non-mammals is translesion synthesis. Typically, the lesion associated with the pyrimidine dimer blocks cellular machinery from synthesizing past the damaged site. However, in translesion synthesis, translesion polymerases can replicate past the CPD, allowing both replication and transcription machinery to continue past the lesion. One specific translesion DNA polymerase, DNA polymerase η, is deficient in individuals with Xeroderma pigmentosum. [57]

Technological applications

Beyond their role as DNA photolesions, pyrimidine dimers have been investigated as functional photochemical motifs in engineered materials. In such systems, controlled dimer formation and cleavage are used to modulate material properties with spatial resolution.

In the late 20th century, thymine moieties incorporated into polymer films were shown to undergo reversible photodimerization upon UV irradiation. [58] , [59] These studies established pyrimidine photodimerization as a crosslinking mechanism in photoresponsive polymers and photorecording materials.

Subsequent work demonstrated pyrimidine dimer formation in solid films deposited on quartz substrates via photosensitized indirect mechanisms. [60] Site-specific thymine dimerization has also been applied in DNA nanotechnology. For instance, the formation of cyclobutane pyrimidine dimers between predefined thymidine sites in DNA nanostructures increases structural rigidity and stability, facilitating handling and transfer in aqueous environments. [61] Other researchers used the process to created photoswitchable amphiphilic systems. [62]

In the 2020s, reversible thymine photodimerization in grafted copolymers was employed in the development of self-healing coatings, including materials intended for photovoltaic applications. [63] The efficiency of light-induced healing in rigid membranes and coatings was further enhanced through the incorporation of photosensitizers that promote dimer formation and photoreversion. [64]

See also

References

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