ULTRAVIOLET LIGHT IRRADIATION OF DEFINED-SEQUENCE DNA UNDER CONDITIONS OF CHEMICAL PHOTOSENSITIZATION

Abstract— The formation of cyclobutane pyrimidine dimers and UV light-induced (6-4) products was examined under conditions of triplet state photosensitization. DNA fragments of defined sequence were irradiated with 313 nm light in the presence of either acetone qr silver ion. UV irradiation in the presence of both silver ion and acetone enhanced the formation of TT cyclobutane dimers, yet no (6-4) photoproducts were formed at appreciable levels. When photoproduct formation was also measured in pyrimidine dinucleotides, only cyclobutane dimers were formed when the dinucleotides were exposed to 313 nm light in the presence of photosensitizer. The relative distribution of each type of cyclobutane dimer formed was compared for DNA fragments that were irradiated with 254, 313, or 313 nm UV light in the presence of acetone. The dimer distribution for DNA irradiated with 254 and 313 nm UV light were very similar, whereas the distribution for DNA irradiated with 313 nm light in the presence of acetone favored TT dimers. Alkaline labile lesions at guanine sites were also seen when DNA was irradiated with 313 nm light in the presence of acetone.     

Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA

Cyclobutane pyrimidine dimer (CPD) is a photoproduct formed by two stacked pyrimidine bases through a cycloaddition reaction upon irradiation. Owing to its close association with skin cancer, the mechanism of CPD formation has been studied thoroughly. Among many aspects of CPD, its formation involving 5-methylcytosine (5mC) has been of special interest because the CPD yield is known to increase with C5-methylation of cytosine. In this work, high-level quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine a previously experimentally detected pathway for CPD formation in hetero (thymine-cytosine and thymine-5mC) dipyrimidines, which is facilitated through intersystem crossing in thymine and formation of a triplet biradical intermediate. A DNA duplex model system containing a core sequence TmCG or TCG is used. The stabilization of a radical center in the biradical intermediate by the methyl group of 5mC can lead to increased CPD yield in TmCG compared with its non-methylated counterpart, TCG, thereby suggesting the existence of a new pathway of CPD formation enhanced by 5mC.     

A doorway state leads to photostability or triplet photodamage in thymine DNA

Ultraviolet irradiation of DNA produces electronic excited states that predominantly eliminate the excitation energy by returning to the ground state (photostability) or following minor pathways into mutagenic photoproducts (photodamage). The cyclobutane pyrimidine dimer (CPD) formed from photodimerization of thymines in DNA is the most common form of photodamage. The underlying molecular processes governing photostability and photodamage of thymine-constituted DNA remain unclear. Here, a combined femtosecond broadband time-resolved fluorescence and transient absorption spectroscopies were employed to study a monomer thymidine and a single-stranded thymine oligonucleotide. We show that the protecting deactivation of a thymine multimer is due to an ultrafast single-base localized stepwise mechanism where the initial excited state decays via a doorway state to the ground state or proceeds via the doorway state to a triplet state identified as a major precursor for CPD photodamage. These results provide new mechanistic characterization of and a dynamic link between the photoexcitation of DNA and DNA photostability and photodamage.     

Contribution of Cytosine‐Containing Cyclobutane Dimers to DNA Damage Produced by Photosensitized Triplet–Triplet Energy Transfer

Mutagenic cyclobutane pyrimidine dimers (CPDs) can be induced in DNA through either direct excitation or photosensitized triplet–triplet energy transfer (TTET). In the latter pathway, thymines are expected to receive the excitation energy from the photosensitizer and react with adjacent pyrimidines. By using state‐of‐the art analytical tools, we provide herein additional information on the formation of cytosine‐containing CPDs. We thus determined the yield of all possible CPDs upon TTET in a series of natural DNAs with various base compositions. We show that the distribution of CPDs cannot be explained only by excitation of individual thymines. We propose that the mechanism for TTET involves at least dinucleotides as the minimal targets. The observation of the formation of cytosine–cytosine CPDs also suggests that additional pathways are involved in this photosensitized reaction.     

Ultraviolet Irradiation Produces Novel Endonuclease Ill-Sensitive Cytosine Photoproducts at Dipyrimidine Sites

Ultraviolet light irradiation of DNA in vitro and in vivo induces cyclobutane dimers, (6–4) pyrimidine-pyrimi-done photoproducts and a variety of minor products. Using a denned DNA fragment, we have identified two classes of sites that can be cleaved by Escherichia coli endonuclease III: single cytokines whose heat lability corresponds to that of cytosine hydrates and more heat-stable dipyrimidines containing cytosine. The dipyrimidine products are induced at sites suggestive of (6–4) photoproducts but are not recognized as (6–4) photoproducts by radioimmunoassay. Use of oligonucleotides containing a single cyclobutane thymine dimer, a (6–4) photoproduct or the Dewar photoisomer of the (6–4) photoproduct also indicated that these products are not substrates for endonuclease III. We have therefore identified a minor UV photoproduct that has the same sequence specificity as the two major dipyrimidine photoproducts; it may be a minor isomer, a unique derivative or an oxidative lesion confined to dipyrimidine sites. Its biological significance is not yet known but may be masked by the preponderance of major products at the same sites. Its occurrence at the particular site in dipyrimidine sequences involved in the mutagenic action of UV photoproducts suggests that it may play a role in generating C to T transitions that are common UV-induced mutations.     

PHOTOSENSITIZED INACTTVATION OF INFECTIOUS DNA BY UROCANIC ACID, INDOLEACRYLIC ACID AND RHODIUM COMPLEXES

Naked, infectious single-stranded (ss) and double-stranded (ds) DNA from phages SI3 and G4 were irradiated with 308 nm UV radiation in the absence and presence of several photobiologically active compounds: E - and Z -urocanic acid ( E - and Z -UA), their methyl esters ( E - and Z -MU), E - and Z-indoleacrylic acid ( E - and Z -IA), cis -dichlorobis(1,10-phenanthroline)rhodium(III) chloride (cDCBPR) and tris(1,10-phenanthroline)rhodium (III) perchlorate (TPR). E -urocanic acid protects against cyclobutane pyrimidine dimer formation in ssDNA but concomitantly photosensitizes the formation of other lesions that inactivate ssDNA. Z -urocanic acid also protects ssDNA against such dimerization but without the associated sensitized damage. The methyl ester isomers behave similarly. There is no such differential activity observed for the IA isomers, both of which sensitize the inactivation of ssDNA. Photostationary state mixtures of both UA and IA efficiently sensitize the inactivation of dsDNA, and cDCBPR strongly protects ssDNA from UV damage, while TPR is a significant sensitizer. Both of these metal complexes sensitize the inactivation of dsDNA slightly. For all compounds, cyclobutane pyrimidine dimers were the predominant lethal lesions produced by sensitization of the dsDNA, but they were not the major lethal lesions created by sensitization of the ssDNA. In the case of dsDNA, both UA and IA created pyrimidine dimers with a high degree of potential for mutagenesis, as determined by an assay that monitors the frequency of mutations following the spontaneous deamination of cytosine in photodimers.     

In Vivo Spectrum of UVC‐induced Mutation in Mouse Skin Epidermis May Reflect the Cytosine Deamination Propensity of Cyclobutane Pyrimidine Dimers

Although ultraviolet radiation (UVR) has a genotoxicity for inducing skin cancers, the skin may tolerate UVC component because the epidermal layer prevents this short wavelength range from passing through. Here, UVC genotoxicity for mouse skin was evaluated in terms of DNA damage formation and mutagenicity. UVC induced UVR photolesions and mutations remarkably in the epidermis but poorly in the dermis, confirming the barrier ability of the epidermis against shorter UVR wavelengths. Moreover, the epidermis itself responded to UVC mutagenicity with mutation induction suppression, which suppressed the mutant frequencies to a remarkably low, constant level regardless of UVC dose. The mutation spectrum observed in UVC‐exposed epidermis showed a predominance of UV‐signature mutation, which occurred frequently in 5′‐TCG‐3′, 5′‐TCA‐3′ and 5′‐CCA‐3′ contexts. Especially, for the former two contexts, the mutations recurred at several sites with more remarkable recurrences at the 5′‐TCG‐3′ sites. Comparison of the UVC mutation spectrum with those observed in longer UVR wavelength ranges led us to a mechanism that explains why the sequence context preference of UV‐signature mutation changes according to the wavelength, which is based on the difference in the mCpG preference of cyclobutane pyrimidine dimer (CPD) formation among UVR ranges and the sequence context‐dependent cytosine deamination propensity of CPD.     

FORMATION OF CYCLOBUTANE THYMINE DIMERS PHOTOSENSITIZED BY PYRIDOPSORALENS: A TRIPLET-TRIPLET ENERGY TRANSFER MECHANISM

The 365 nm irradiation of thymine thin films in the presence of pyridopsoralens is shown to induce the formation of cyclobutane thymine dimers, in contrast to other compounds such as 8- and 5-methoxypsoralen. In order to elucidate the mechanism of such a photosensitized reaction, we have determined the energy of the lowest triplet state (T1) of these compounds, using phosphorescence spectroscopy and CNDO/S quantum chemistry calculations. The T1 energy values were found to be significantly higher for pyridopsoralens--up to 0.3 eV--than for 8- and 5-methoxypsoralen (approximately 2.8 eV), which are not able to photoinduce cyclobutane thymine dimers. The determination of the relative efficiency of cyclobutane thymine dimer formation was performed using chromatographic analysis. A good correlation was found between the energy of the T1 state of the psoralen derivatives and the related cyclobutane thymine dimer formation. Moreover, the photosensitized cyclobutane thymine dimer formation appeared to be temperature-dependent. Our results are consistent with a mechanism involving a triplet energy transfer from the pyridopsoralen to thymine.     

UVB-induced Cyclobutane Pyrimidine Dimer Frequency Correlates with Skin Cancer Mutational Hotspots in p53

Abstract— Ultraviolet light has been identified as the major carcinogen in skin cancer and the p53 tumor suppressor gene is a major target for UV-induced mutations. The mutations are probably caused by unrepaired UV-induced cyclobutane pyrimidine dimers (CPD) and possibly by the less frequent pyrimidine (6-4) pyrimidone photoproducts. While hot spots for p53 mutations in human nonmela-noma skin tumors correspond quite well to slow spots for CPD repair in cultured cells irradiated with the model mutagen 254 nm UVC (which is not present in terrestrial sunlight), they do not all coincide with sequences that are initially frequently damaged by 254 nm UVC. Using LMPCR (ligation-mediated polymerase chain reaction), we show that environmentally relevant UVB light induces CPD at CC and PyrmC positions much more frequently than does UVC light, and that all eight skin cancer hot spots in p53 are also hot spots for UVB-induced CPD. Our results show that methylation of dipyrimidine sites (PyrmCpG) is associated with an increase rate of CPD formation upon UVB irradiation. Consequently, DNA methylation may increase the mutagenic potential of UVB and explains that several p53 mutation hot spots are found at PyrmCpG. The distribution patterns of CPD formation and the photofootprint patterns found along exons 5 and 6 of p53 gene are suggestive of DNA folding into nucleosomes.     

Biological consequences of cyclobutane pyrimidine dimers.

In the skin many molecules may absorb ultraviolet (UV) radiation upon exposure. In particular, cellular DNA strongly absorbs shorter wavelength solar UV radiation, resulting in various types of DNA damage. Among the DNA photoproducts produced the cyclobutane pyrimidine dimers (CPDs) are predominant. Although these lesions are efficiently repaired in the skin, this CPD formation results in various acute effects (erythema, inflammatory responses), transient effects (suppression of immune function), and chronic effects (mutation induction and skin cancer). The relationships between the presence of CPD in skin cells and the subsequent biological consequences are the subject of the present review.     

Binding of distamycin A to UV-damaged DNA

We have found that distamycin A can bind to DNA duplexes containing the (6-4) photoproduct, one of the major UV lesions in DNA, despite the changes, caused by photoproduct formation, in both the chemical structure of the base moiety and the local tertiary structure of the helix. A 20-mer duplex containing the target site, AATT.AATT, was designed, and then one of the TT sequences was changed to the (6-4) photoproduct. Distamycin binding to the photoproduct-containing duplex was detected by CD spectroscopy, whereas specific binding did not occur when the TT site was changed to a cyclobutane pyrimidine dimer, another type of UV lesion. Distamycin binding was analyzed in detail using 14-mer duplexes. Curve fitting of the CD titration data and induced CD difference spectra revealed that the binding stoichiometry changed from 1:1 to 2:1 with photoproduct formation. Melting curves of the drug-DNA complexes also supported this stoichiometry.     

Base flipping of the thymine dimer in duplex DNA

Exposure of two adjacent thymines in DNA to UV light of 260-320 nm can result in the formation of the cis,syn-cyclobutane pyrimidine dimer (CPD). The structure of DNA containing an intrahelical CPD lesion has been previously studied experimentally and computationally. However, the structure of the extrahelical, flipped-out, CPD lesion, which has been shown to be the structure that binds to the CPD repair enzyme, DNA photolyase, has yet to be reported. In this work the structure of both the flipped-in and the flipped-out CPD lesions in duplex DNA is reported. These structures were calculated using 8 ns molecular dynamics (MD) simulations. These structures are then used to define the starting and ending points for the base-flipping process for the CPD lesion. Using a complex, two-dimensional pseudodihedral coordinate, the potential of mean force (PMF) for the base-flipping process was calculcated using novel methodology. The free energy of the flipped-out CPD is roughly 6.5 kcal/mol higher than that of the flipped-in state, indicating that the barrier to flipping out is much lower for CPD than for undamaged DNA. This may indicate that the flipped-out CPD lesion may be recognized by its repair enzyme, DNA photolyase, whereas previous studies of other damaged, as well as nondamaged, bases indicate that they are recognized by enzymes in the intrahelical, flipped-in state.     

Structure and dynamics of poly(T) single-strand DNA: implications toward CPD formation

The formation of cyclobutane pyrimidine dimers between adjacent thymines by UV radiation is thought to be the first event in a cascade leading to skin cancer. Recent studies showed that thymine dimers are fully formed within 1 ps of UV irradiation, suggesting that the conformation at the moment of excitation is the determining factor in whether a given base pair dimerizes. MD simulations on the 50 ns time scale are used to study the populations of reactive conformers that exist at any given time in T18 single-strand DNA. Trajectory analysis shows that only a small percentage of the conformations fulfill distance and dihedral requirements for thymine dimerization, in line with the experimentally observed quantum yield of 3%. Plots of the pairwise interactions in the structures predict hot spots of DNA damage where dimerization in the ssT18 is predicted to be most favored. The importance of hairpin formation by intra-strand base pairing for distinguishing reactive and unreactive base pairs is discussed in detail. The data presented thus explain the structural origin of the results from the ultrafast studies of thymine dimer formation.     

Crystal Structure of the T(6‐4)C Lesion in Complex with a (6‐4) DNA Photolyase and Repair of UV‐Induced (6‐4) and Dewar Photolesions

UV‐light irradiation induces the formation of highly mutagenic lesions in DNA, such as cis‐syn cyclobutane pyrimidine dimers (CPD photoproducts), pyrimidine(6‐4)pyrimidone photoproducts ((6‐4) photoproducts) and their Dewar valence isomers ((Dew) photoproducts). Here we describe the synthesis of defined DNA strands containing these lesions by direct irradiation. We show that all lesions are efficiently repaired except for the T(Dew)T lesion, which cannot be cleaved by the repair enzyme under our conditions. A crystal structure of a T(6‐4)C lesion containing DNA duplex in complex with the (6‐4) photolyase from Drosophila melanogaster provides insight into the molecular recognition event of a cytosine derived photolesion for the first time. In light of the previously postulated repair mechanism, which involves rearrangement of the (6‐4) lesions into strained four‐membered ring repair intermediates, it is surprising that the not rearranged T(6‐4)C lesion is observed in the active site. The structure, therefore, provides additional support for the newly postulated repair mechanism that avoids this rearrangement step and argues for a direct electron injection into the lesion as the first step of the repair reaction performed by (6‐4) DNA photolyases.     

Effects of cytosine methylation on pyrimidine dimer formation in DNA

The relative induction of cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4)pyrimidone photoproducts ([6-4]PD) was quantified in the duplex homopolymers polydeoxyadenosine:polydeoxythymidine, polydeoxyguanosine:polydeoxycytidine and polydeoxyguanosine:polydeoxy-5-methylcytidine irradiated with UVC or UVB radiation. Cytosine methylation significantly increased the yield of cytosine (6-4)PD after irradiation with UVC light and of cytosine CPD and (6-4)PD after irradiation with UVB light. The data suggest that CPD and (6-4)PD are preferentially induced at 5-methylcytosine bases in DNA of cells exposed to sunlight and comprise a major component of the mutation spectrum leading to the initiation of sunlight-induced skin cancer.     

Intermolecular Interactions in Photodamaged DNA from Density Functional Theory Symmetry‐Adapted Perturbation Theory

The intermolecular interactions of the photodamaged cyclobutane pyrimidine dimer (CPD) lesion with adjacent nucleobases in the native intrahelical DNA double strand are investigated at the level of density functional theory symmetry‐adapted perturbation theory (DFT‐SAPT) and compared to the original (or repaired) case with pyrimidines (TpT) instead of CPD. The CPD aggregation is on average destabilized by about 6 kcal mol^?1 relative to that involving TpT. The effect of destabilization is asymmetric, that is, it involves a single H‐bonding (Watson–Crick (WC) type) base‐pair interaction.     

On the photoproduction of DNA/RNA cyclobutane pyrimidine dimers

The UV photoreactivity of different pyrimidine DNA/RNA nucleobases along the singlet manifold leading to the formation of cyclobutane pyrimidine dimers has been studied by using the CASPT2 level of theory. The initially irradiated singlet state promotes the formation of excimers between pairs of properly oriented nucleobases through the overlap between the ?? structures of two stacked nucleobases. The system evolves then to the formation of cyclobutane pyrimidine dimers via a shearing-type conical intersection activating a [2?+?2] photocycloaddition mechanism. The relative location of stable excimer conformations or alternative decay channels with respect to the reactive degeneracy region explains the differences in the photoproduction efficiency observed in the experiments for different nucleobases sequences. A comparative analysis of the main structural parameters and energetic profiles in the singlet manifold is carried out for thymine, uracil, cytosine, and 5-methylcytosine homodimers. Thymine and uracil dimers display the most favorable paths, in contrast to cytosine. Methylation of the nucleobases seems to increase the probability for dimerization.     

N4‐Methylation of Cytosine Drastically Favors the Formation of (6‐4) Photoproducts in a TCG Context

Methylation of cytosine is a common biological process both in prokaryotic and eukaryotic cells. In addition to 5‐methylcytosine (5mC), some bacterial species contain in their genome N⁴‐methylcytosine (N4mC). Methylation at C5 has been shown to enhance the formation of pyrimidine dimeric photoproducts but nothing is known of the effect of N4 methylation on UV‐induced DNA damage. In the present work, we compared the yield and the nature of bipyrimidine photoproducts induced in a series of trinucleotides exhibiting a TXG sequence where X is either T, C, 5mC or N4mC. HPLC associated to tandem mass spectrometry was used to quantify cyclobutane pyrimidine dimers (CPD), (6‐4) photoproducts (64PP) and their Dewar valence isomer. Methylation at position N4 was found to drastically increase the reactivity of C upon exposure to both UVC and UVB and to favor the formation of 64PP. In contrast methylation at C5 increased the yield of CPD at the expense of 64PP. In addition, enhancement of photoreactivity by C5 methylation was much higher in the UVB than in the UVC range. These results show the drastic effect of the methylation site on the photochemistry of cytosine.     

CONTRASTING STRUCTURAL IMPACTS INDUCED BY cis-syn CYCLOBUTANE DIMER AND (6–4) ADDUCT IN DNA DUPLEX DECAMERS: IMPLICATION IN MUTAGENESIS AND REPAIR ACTIVITY

Abstract—
The relative biological importance of cis-syn cyclobutane dimer and pyrimidine(6–4)pyr-imidone photoadduct ([6–4] photoadduct) appears to be dependent on the biological species, dipyrimidine sites and the local conformational variation induced at the damaged sites. The single-stranded deoxyn-ucleotide 10-mers containing the site-specific (6–4) adduct or cis-syn cyclobutane dimer of thymidylyl (3'-5')-thymidine were generated by direct photolysis of d(CGCATTACGC) with UVC (220–260 nm) irradiation or UVB (260–320 nm) photosensitization. Three-dimensional structures of the duplex cis-syn and (6–4) decamers of d(CGCATTACGC)d(GCGTAATGCG) were determined by NMR spectroscopy and the relaxation matrix refinement method. The NMR data and structural calculations establish that Watson-Crick base pairing is still intact at the cis-syn dimer site while the hydrogen bonding is absent at the 3'-side of the (6–4) lesion where the T → C transition mutation is predominantly targeted. Overall conformation of the duplex cis-syn decamer was B-DNA and produced a 9° bending in the DNA helix, but a distinctive base orientation of the (6–4) lesion provided a structural basis leading to 44° helical bending. The observed local structure and conformational rigidity at the (6–4) adduct of the thymidylyl(3'-5')-thymidine (T-T [6–4]) lesion site suggest the potential absence of hydrogen bonding at the 3' sides of the (6–4) lesion with a substituted nucleotide during replication under SOS conditions. Contrasting structural distortions induced by the T-T (6–4) adduct with respect to the T-T cis-syn cyclobutane pyrimidine photodimer may explain the large differences in mutation spectrum and repair activities between them.     

UV INDUCED (6-4) PHOTOPRODUCTS ARE DISTRIBUTED DIFFERENTLY THAN CYCLOBUTANE DIMERS IN NUCLEOSOMES

We have compared the distributions of two stable UV photoproducts in nucleosome core DNA at the single-nucleotide level using a T4 polymerase-exonuclease mapping procedure. The distribution of pyrimidine-pyrimidone (6-4) dimers was uncovered by reversing the major UV photo-product, cis-syn cyclobutane pyrimidine dimer, with E. coli DNA photolyase and photoreactivating light. Whereas the distribution of total UV photoproducts in nucleosome core DNA forms a striking 10.3 base periodic pattern, the distribution of (6-4) dimers is much more random throughout the nucleosome core domain. Therefore, histone-DNA interactions in nucleosomes strongly modulate formation of the major class of UV-induced photoproducts, while having either a constant effect or no effect on (6-4) dimer formation.