Context-dependent mutagenesis by DNA lesions.

BACKGROUND: Detailed analyses of mutational hotspots following DNA damage provide an understanding of oncogene activation and tumor suppressor gene inactivation, and hence provide an insight into the earliest steps in the induction of cancer. A mutational hotspot might be created by preferential lesion formation, decreased lesion repair, or increased misinsertion past the lesion during DNA replication. The respective contribution of these factors might be influenced by the DNA sequence context of the hotspot. RESULTS: As a prelude to addressing the contribution of all possible nearest-neighbor contexts on the replication past O6-methylguanine (m6G) and repair of m6G in vivo, we have devised a mutation frequency (MF) detection strategy on the basis of the properties of type IIs restriction enzymes. We also report a method for constructing site-specific single-stranded viral DNA genomes that should yield identical ligation efficiencies regardless of the lesion or its surrounding sequence context. Using repair-deficient Escherichia coli, we discovered that m6G in three sequence contexts was nearly 100% mutagenic in vivo, showing that the DNA polymerase holoenzyme almost always placed a thymine base opposite m6G during replication. In partially repair-proficient cells, the Ada O6-methylguanine-DNA methyltransferase repair protein was twice as efficient on m6G when a guanine base rather than an adenine base was 5' to the lesion. CONCLUSIONS: The system allows the mutagenic potential of, theoretically, any DNA lesion that exhibits point mutations, in any varied local sequence context, to be rapidly determined. The assay demonstrates low background, high throughput, and does not require phenotypic selection, making it possible to discern the effects of sequence context on the processing of m6G.     

Molecular basis of DNA photodimerization: intrinsic production of cyclobutane cytosine dimers

Based on CASPT2 results, the present contribution establishes for the first time that cytosine photodimer formation (C< >C) is mediated along the triplet and singlet manifold by a singlet-triplet crossing, (T1/S0)X, and by a conical intersection, (S1/S0)CI, respectively. The former can be accessed in a barrierless way from a great variety of photochemical avenues and exhibits a covalent single bond between the ethene C6-C6' carbon atoms of each monomer. The efficiency of the stepwise triplet mechanism, however, would be modulated by the effectiveness of the intersystem crossing mechanism. The results provide the grounds for the understanding of the potential photogenotoxicity of endogenous and exogenous compounds via triplet-triplet sensitization, with a lower bound for cytosine oligonucleotides predicted to be 2.70 eV, and give support to the traditional view of the primary role of triplet excited states in the photochemistry of DNA, a well-known source of photoproducts in solution under triplet photosensitization conditions. The function played by singlet excimers (excited dimers) to explain both the red-shifted fluorescence and photoreaction is highlighted. A rationale on the pronounced wavelength dependence of the observed fluorescence is offered. Geometrical arrangements at the time of light irradiation close to, but energetically above, (S1/S0)CI are suggested as reactive orientations that become prone to produce C< >C directly, with no energy barrier. Because of the outstanding intrinsic ability of cytosine to form stable relaxed excimers, the system located near the bound relaxed excimer has to accumulate enough vibrational energy to surmount a small barrier of 0.2 eV to reach (S1/S0)CI, making the overall process to proceed at a slower relative rate as compared to other compounds such as thymine, which is not susceptible of forming so stable excimers.     

A triplet mechanism for the formation of thymine-thymine (6-4) dimers in UV-irradiated DNA

The reaction pathway for the photochemical formation of thymine-thymine (6-4) dimers in DNA is explored using hybrid density functional theory techniques in gas and in bulk solvent. It is concluded that the photo-induced cycloaddition displays favorable energy barriers in the triplet excited state. The stepwise cycloaddition in the triplet excited state involves the initial formation of a diradical followed by ring closure via singlet-triplet interaction. The key geometric features and electron spin densities are also discussed. The difference in barriers of H3' transfer for the lowest-lying triplet and singlet states shows that the singlet oxetane intermediate could catch the second photon to accelerate the rate of proton transfer, leading to formation of the Dewar structure. The present results provide a rationale for the formation of thymine-thymine (6-4) dimers in the triplet excited states.     

Selectivity in the photodimerization of 6-alkylcoumarins

Coumarin and 6-alkylcoumarins (alkyl = C(1) to C(16)) were photodimerized in homogeneous solvents differing in polarity and in aqueous micellar solutions. The four possible photodimers, syn head-to-head (hh), anti head-to-head, syn head-to-tail (ht), and anti head-to-tail, were identified through a combination of X-ray analysis and NMR spectroscopy. In 6-methylcoumarin the concentration-corrected dimerization (quantum) yield increases with decreasing concentration of the educt; anti-hh was formed exclusively in nonpolar solvents and upon triplet sensitization and was the main product under all conditions except for ionic micellar systems, which direct to preferred syn-hh dimerization. Long alkyl substituents, however, lead to anti-hh in polar solvents and in micelles, too. Predominating ht dimer formation was observed for nonsubstituted coumarin in polar solvents only. Thus, syn/anti and hh/ht selectivity can be steered by varying the 6-alkyl substituent. Syn-hh photodimers of 6-methylcoumarin can be photochemically split into the monomers; they partly proved thermally unstable against acids, bases, methanol, and on SiO(2) surfaces.     

Tetraolefin stereospecific photodimerization and photopolymerization in coordination polymers

In the context of the highly desirable design and preparation of smart materials with adjustable properties based on photoreactive compounds,we report two unique photoreactive coordination polymers (CPs),{[Zn(4-Iba)₂(4-tkpvb)]·H₂O}_n(1,4-HIba=4-iodobenzoic acid,4-tkpvb=1,2,4,5-tetrakis(4-pyridylvinyl)benzene) and[Cd(1,4-bdc)(4-tkpvb)]_n(2,1,4-H₂bdc=1,4-benzenedicarboxylic acid).Depending on the metal ions and auxiliary carboxylate ligands used...     

Unsymmetrical photodimerization of a 9-aminomethylanthracene in the crystalline salt

By the salt formation with particular nonaromatic dicarboxylic acids, rapid and selective photodimerization of 9-(N,N-dimethylaminomethyl)anthracene (1) was accomplished in the solid state. For instance, the salt with trans,trans-muconic acid or acetylenedicarboxylic acid was led quantitatively to the 9,10:4',1' photodimer usy-ht-2, the first example of the unsymmetrical [4+4] photodimerization of anthracene in the solid state. The reactions were rationalized by the relevant C...C distances between the reacting carbons.     

Chemistry of 3-arylindenones: behavior in superacids and photodimerization

In superacids HSO₃F and CF₃SO₃H, it has been found that 3-arylindenones are very stable and exist as a doubly protonated species. NMR showed protonation both at the oxygen of the carbonyl group and at the C2 carbon of the indenone system. 3-Arylindenones proved however very sensitive to heat and light. Their [2+2] photodimerization under daylight has been studied.     

Exploring two-state reaction pathways in the photodimerization of cyclohexadiene.

The ground- (S0) and lowest triplet-state (T1) pathways associated with dimerization of cyclohexadiene to give [2+2] and [4+2] cycloadducts have been theoretically studied at the UBLYP and UB3LYP levels of theory with the 6-31G* basis set. The DFT energies were validated by CCSD(T) single-point energy calculations. These cycloaddition reactions follow stepwise mechanisms with formation of bis-allylic biradical (BB) intermediates. In the S0 ground state, the interaction between two cyclohexadiene molecules with formation of BB intermediate IN(S0) has a large activation enthalpy of 32.0 kcal mol(-1). On the other hand, C-C bond-formation in the lowest triplet state (T1) leading to BB intermediate IN(T1) has a low activation enthalpy of 5.0 kcal mol(-1), but the subsequent ring closure involves a very large activation enthalpy of 43.4 kcal mol(-1). Triplet-to-singlet intersystem crossing from IN(T1) to IN(S0) favors cyclization to give the corresponding [2+2] and [4+2] cycloadducts.     

Elementary steps for charge transport in DNA: thermal activation vs. tunneling

Using stacks of Watson–Crick base pairs as an important example of multichromophoric molecular assemblies, we studied charge migration in DNA with special emphasis on the mechanism of hole hopping between neighboring guanines (G) connected by the adenine–thymine (AT) bridge. The tight-binding model proposed for this elementary step shows that for short AT bridges, hole transfer between two G bases proceeds via quantum mechanical tunneling. By contrast, hopping over long bridges requires thermal activation. The condition for crossover between tunneling and thermal activation near room temperature is specified and applies to the analysis of experimental data. We show that thermal activation dominates, if the bridge between two G bases contains more than three AT pairs. Our theoretical findings predict that the replacement of AT base pairs by GC pairs increases the efficiency of hole transport only in the case of short base pair sequences. For long sequences, however, the opposite effect is expected.     

A new [2 + 2] photodimerization of 5-chloro- and 5-methyl-2-pyridone in their inclusion complexes with 1,1'-biphenyl-2,2'-dicarboxylic acid as a model for DNA damage by photodimerization of its thymine component

As a model for DNA damage by photodimerization of its thymine component, a new [2 + 2] photodimerization of 5-chloro and 5-methyl-2-pyridone to the corresponding cis-anti-dimers as their inclusion complexes with 1,1'-biphenyl-2,2'-dicarboxylic acid was found, and the mechanism of this stereoselective solid state reaction was studied by X-ray analysis.     

Coerced photodimerization reaction in the solid state through amine salt formation

Photodimerization of fumaric or several γ-form trans-cinnamic acids proceeded successfully in the solid state through amine salt formation with ammonia or some aromatic heterocyclic amines (especially, imidazole). It appears that this success is due to a small size or a planar structure of the amine. A layered or a channel-type clathrate crystal structure was revealed, respectively.     

Regioselective photodimerization of cinnamic acids in water: Templation with cucurbiturils

Cinnamic acids upon irradiation in solution undergo geometric isomerization while dimerizing to different dimers in the crystalline state. Controlling the nature of the dimer formed upon irradiation remains a challenging task. We have aligned a variety of cinnamic acid molecules in a head-head fashion employing cucurbit[8]uril, a weakly water soluble host as a template. The water solubility of cucurbit[8]uril is enhanced by inclusion of water soluble cinnamic acids and positions the olefins in an arrangement that favors the formation of syn head-head cyclobutanes in near quantitative yields. This methodology works in both solid state as well as in aqueous solution. Irradiation of cinnamic acid complexes with gamma-cyclodextrin has been carried out as a comparison. We find that while cucurbit[8]uril functions well both in solid state and aqueous solution, cyclodextrin works best as solid complexes only. Consistent with the postulated requirement of large cavities for templating olefins to dimerization, irradiation of complexes of cinnamic acid with cucurbit[7]uril resulted in only the corresponding cis isomers.     

The role of orientational defects in the photodimerization of 1,5-dichloroanthracene

The photodimerization of 1,5-dichloroanthracene is discussed with particular reference to the mechanism by which the ratio of head-to-head and head-to-tail dimer differs between reaction in the solid and in solution. It is shown that in certain crystallographic space groups linear and planar imperfections will not, of themselves, produce regions of packing suitable for the formation of the “non-topochemical” dimer. A novel type of point defect which may account for the solid state reactivity is described and the extra lattice energy that is associated with this defect calculated.     

Site-selective DNA alkylation of GG steps by naphthaldiimide derivatives possessing enantiomeric epoxide

We have synthesized an enantiomeric pair of novel DNA alkylating agents consisting of a naphthaldiimide intercalator and a chiral epoxy side chain. These naphthaldiimide derivatives have high DNA binding affinity and selectively alkylate 5'G of the GG steps for (S)-epoxide and 3'G for (R)-epoxide.     

A study in Crystal engineering: Solid-state photodimerization of chloro- and methyl-coumarins

Use of chloro and methyl substitution in crystal engineering and their interchangeability in terms of mode of packing have been examined in a series of substituted coumarins. Photoreactivity in the solid state lists been correlated with the crystallograhic structures of these coumarins. The packing of chloro-substituted aromatic compounds has been investigated by analysing the arrangement of 132 compounds. Results substantiate the use of the chloro group as a steering agent and show that the chloro and methyl groups are not always interchangeable.     

A theoretical study of the reaction pathway in the photodimerization of anthracene

The approximation proposed by Salem to calculate the interaction energy between conjugated systems has been used to obtain different potential surfaces for anthracene photodimerization in order to establish the reaction pathway.     

Reversible photodimerization of coumarin derivatives dispersed in poly(vinyl acetate)

Four photoreactive coumarin derivatives were successfully synthesized from 7-hydroxy-coumarin and 7-hydroxy-4-methylcoumarin, i.e., 7-propionyloxy-4-methylcoumarin (M₁), 7-palmitoyloxy-4-methylcoumarin (M₂), 7-propionyloxycoumarin (M₃), and 7-palmitoy-loxycoumarin (M₄). Reversible photodimerization (350 or 300 nm) and photocleavage (254 nm) of these coumarin derivatives dispersed in poly(vinyl acetate) (PVAc) were investigated by tracing their UV absorbance variations at 310 nm. The M₂ and M₄ with long palmitoyl chain show much better photoreaction reversibility than M₁ and M₃ with short propionyl chain. Moreover, photodimerization rate (under 350 nm) of M₂ is greater than 200 times of that of M₁. This has been explained by the formation of suitable conformation for revers-ible photodimerization due to the hydrophobic interactions. Photodimerization of M₂ is ca. 3 times quicker than that of M₄, indicating 4-methyl substitution enhances pho-todimerization. The influence of photodimerization wavelength (350 and 300 nm) and photosensitizer (benzophenone) have also been investigated in detail. © 1995 John Wiley & Sons. Inc.     

Enantioselective [2 + 2] photodimerization reactions of coumarins in solution

[reaction: see text] The [2 + 2]photodimerization reactions of coumarin to an optically active anti-head-to-head dimer in the presence of an optically active host compound in cyclohexane solution proceeded with high enantioselectivity.