Selective one-electron oxidation of duplex DNA oligomers: reaction at thymines

The one-electron oxidation of duplex DNA generates a nucleobase radical cation (electron "hole") that migrates long distances by a hopping mechanism. The radical cation reacts irreversibly with H2O or O2 to form oxidation products (damaged bases). In normal DNA (containing the four common DNA bases), reaction occurs most frequently at guanine. However, in DNA duplexes that do not contain guanine (i.e., those comprised exclusively of A/T base pairs), we discovered that reaction occurs primarily at thymine and gives products resulting from oxidation of the T-C5 methyl group and from addition to its C5-C6 double bond. This surprising result shows that it is the relative reactivity, not the stability, of a nucleobase radical cation that determines the nature of the products formed from oxidation of DNA. A mechanism for reaction is proposed whereby a thymine radical cation may either lose a proton from its methyl group or H2O/O2 may add across its double bond. In the latter case, addition may initiate a tandem reaction that converts both thymines of a TT step to oxidation products.     

Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA

Formation of the thymine dimer is one of the most important types of photochemical damage in DNA, responsible for several biological pathologies. Though specifically designed proteins (photolyases) can efficiently repair this type of damage in living cells, an autocatalytic activity of the DNA itself was recently discovered, allowing for a self-repair mechanism. In this paper, we provide the first molecular dynamics study of the splitting of thymine dimer radical anions, using a quantum mechanical/molecular mechanics (QM/MM) approach based on density functional theory (DFT) to describe the quantum region. A set of seven statistically representative molecular dynamics trajectories is analyzed. Our calculations predict an asynchronously concerted process in which C5-C5' bond breaking is barrierless while C6-C6' bond breaking is characterized by a small free energy barrier. An upper bound of 2.5 kcal/mol for this barrier is estimated. Moreover, the molecular dynamics study and the low free energy barrier involved in C6-C6' bond breaking characterize the full process as being an ultrafast reaction.     

Recognition of thymine and related nucleosides by a Zn(II)-cyclen complex bearing a ferrocenyl pendant

A cyclen derivative bearing a ferrocenyl arm (L) and a series of its ZnII complexes [ZnL(OH2)][ClO4]2 (C1), [ZnL(OH)][ClO4] (C2), and [ZnL(Cl)][ClO4].CH3CN (C3) (cyclen = 1,4,7,10-tetraazacyclododecane, L = 1-(ferrocenemethyl)-1,4,7,10-tetraazacyclododecane) have been prepared and characterized spectroscopically. An X-ray structure determination confirmed the formation of complex C1 and revealed that the coordinated water participates in hydrogen bonding with the perchlorate counter ions. The pKa value for deprotonation of the water molecule determined by potentiometric titration was found to be 7.36 +/- 0.09 at 25 degrees C and I = 0.1 (KNO3). The possibility of using complex C1 as a potential sensor for thymine derivatives in aqueous solution has been examined. Shifts in the 1H and 13C NMR resonances showed the binding occurred with thymine (T) and two thymine derivatives, thymidine (dT) and thymidine 5'-monophosphate (TMP2-). Significant shifts of the nuC=O and nuC=C vibrations of the thymine derivatives were also observed via IR spectroscopy upon complexation with the receptor. The thymine adduct, [ZnL(thymine anion)][ClO4].2H2O (C4), has been crystallized and characterized. The X-ray structure of C4 confirmed the thymine binding to the receptor, and the short Zn-N(thymine) distance of 1.975(5) A indicated clearly that the ferrocenyl arm does not affect the complexation of the DNA base. In contrast to the large spectral changes, electrochemical studies showed a small shift of the reversible potential of the redox couple Fc+/Fc (Fc = ferrocene) and subtle changes in voltammetry upon the addition of an excess of dT, TMP2-, and guanine (dG) at physiological pH, indicating the level of interaction is similar in both Fc and Fc+ forms.     

DFT study on the nucleophilic addition reaction of water and ammonia to the thymine radical cation

The nucleophilic addition reactions of water and ammonia molecules toward the C5-C6 double bond of thymine radical cations were investigated using density functional theory. We predicted that the nucleophilic addition favored the C5-site of thymine radical cations, in contrast to the previous experimental observations in bulk solution where the addition product to the C6-site was dominant. Considering the molecular orbital factors, we estimated the relative reactivity of the C5- and C6-sites of thymine radical cations for the nucleophilic addition of ammonia. We found that the C5 was more reactive than the C6 for the small-size clusters of Thy1(NH3)n+, n = 0-2, in the gas phase and even in aqueous solution, though the difference in the reactivity between the two sites became smaller as the number of ammonia molecules increased. This variation of the reactivity was attributed to the electron density redistribution within the thymine radical cations induced by the ammonia molecules as a nucleophile. We suggest that the dominance of the C6-addition product in bulk solution is mainly due to the higher stability of the C6-addition product by solvation, rather than to the higher reactivity of the C6-site for the nucleophilic addition.     

An ab initio MO study on the thymine dimer and its radical cation

Ab initio SCF calculations with the 6-31G basis set for the thymine dimer (cys-syn form) and the thymine dimer radical cation are reported. The fusion of the thymine bases at the C5 and C6 positions involves the formation of a cyclobutane ring with puckering. The puckering causes a notable difference in the electronic structures of the two bases of the thymine dimer. The density of the HOMO orbital of the thymine dimer is localized on the O2, N1, and C6 atoms of both thymine rings, with the higher density on one of the rings. The HOMO orbital has a bonding character on the C6(SINGLEBOND)C6 bond. In the thymine dimer radical cation, the unpaired electron is localized mainly on the lengthened C6(SINGLEBOND)C6 bond with the higher density on one of the C6 atoms and to a lesser extent on the N1 atoms of both rings. © 1996 John Wiley & Sons, Inc.     

Theoretical study of the effect of radiation on thymine

The possible effects of radiation exposure to DNA are studied by investigations for the thymine residue. Detailed analysis of the various addition and other products is undertaken theoretically, using the semiempirical AM1 procedure. The results agree with the experimental finding that the loss of hydrogen on radiation exposure occurs from the C₅-methyl group and hydroxyl radical addition occurs at C₆, yielding the ‘5-yl’ radical. This radical is nonplanar, the axial conformer being slightly preferred over the equatorial one. In contrast, the other possible radical, the ‘6-yl’ radical, is almost planar. These results are important in understanding the conformational changes in DNA as a consequence of radiation exposure.     

A stereocontrolled access to ring-fused piperidines through a formal [2+2+2] process

[reaction: see text] A formal [2+2+2] process has been devised that allows the stereocontrolled formation of ring-fused piperidines from allylsilanes possessing an oxime moiety. The cascade involves an intermolecular radical addition of an alpha-iodoacetate onto an allylsilane double bond, which is followed by a 5-exo-trig cyclization onto an oxime and is completed by the formation of the amide bond by nucleophilic attack of the amine onto the ester function.     

Diphosphanylketenimines: new reagents for the synthesis of unique phosphorus heterocycles

Two consecutive [3+2] cycloaddition reactions of the diphosphanylketenimine (PPh(2))(2)C[double bond]C[double bond]NPh (3), involving the phosphanyl groups, with two equivalents of the electron-poor alkynes dimethyl acetylenedicarboxylate or methyl acetylenecarboxylate give rise to the formation of the bicyclic 1 lambda(5),3 lambda(5)-diphospholes 5 a,b, which contain a phosphorane unit with five carbon substituents attached to the phosphorus center. Compound 3 undergoes cyclodimerization by crystallization, affording the unsymmetrical dimer 6, which is converted back to 3 by heating in toluene. Compound 6 can be oxidized stepwise on the three trivalent phosphorus atoms by treatment with H(2)O(2) affording 7, 9, and the transient species 10, which are transformed into their corresponding ketenimine monomers either spontaneously (10) or by heating in toluene (7, 9). In this way, the compound (O[double bond]PPh(2))(PPh(2))C[double bond]C[double bond]NPh (8) is quantitatively obtained. Compound 8 readily reacts with the alkynes MeO(2)CC[triple bond]CCO(2)Me and MeO(2)CC[triple bond]CH, and with phenyl isocyanate and ethyl isothiocyanate through regiospecific [3+2] cycloaddition processes furnishing several lambda(5)-phosphole and lambda(5)-azaphosphole derivatives. Finally, the reaction of 8 with N-methylpropargylamine yields the new 2,3-dihydro-1,4-lambda(5)-azaphosphinine 15 through a cycloaddition process involving two functional groups from each molecule.     

Ring opening of the cyclobutane in a thymine dimer radical anion

The reactions of hydrated electrons (e(aq) (-)) with thymine dimer 2 and thymidine have been investigated by radiolytic methods coupled with product studies, and addressed computationally by means of BB1K-HMDFT calculations. Pulse radiolysis revealed that one-electron reduction of the thymine dimer 2 affords the radical anion of thymidine (5) with t(1/2)<35 ns. Indeed, the theoretical study suggests that radical anion 3, in which the spin density and charge distribution are located in both thymine rings, undergoes a fast partially ionic splitting of the cyclobutane with a half-life of a few ps. This model fits with the in vivo observation of thymine dimer repair in DNA by photolyase. gamma-Radiolysis of thymine dimer 2 demonstrates that the one-electron reduction and the subsequent cleavage of the cyclobutane ring does not proceed by means of a radical chain mechanism, that is, in this model reaction the T(-)* is unable to transfer an electron to the thymine dimer 2.     

Nickel-catalyzed

Oxabenzonorbornadienes 1 and 2 and azabenzonorbornadiene 3 undergo [2+2] cycloaddition with alkynes (PhC triple bond Ph, PhC triple bond CMe, PhC triple bond CCO2Et, PhC triple bond CCH(OEt)2, and HC triple bond C(CH2)4Me) in the presence of [Ni(PPh3)2Cl2], PPh3, and Zn powder in toluene to afford the corresponding exo-cyclobutene derivatives 4a-e, 5a-e, and 6 in fair to excellent yields. Under similar conditions. EtCO2C triple bond CCO2Et does not react with 1 in toluene to give the [2+2] cycloaddition product, but in acetonitrile, the catalytic [2+2] cycloaddition proceeds and cycloadduct 4 f is isolated in 83% yield. At high temperature, these cyclobutene derivatives readily undergo ring expansion to yield the corresponding 8-membered carbocyclic dienes. Thus, flash vacuum pyrolysis of 4a, 4d, 4f, 6, and 14 at 500 degrees C affords dienes 13a-d and 15 in 70-96% yields. This interesting ring expansion may be viewed as the insertion of an alkyne moiety into the carbon-carbon double bond of a cyclic olefin resulting in the enlargement of the ring by two carbons. Compound 13a is readily deoxygenated by TiCl4 and Zn in THF to give a cyclooctatetraene derivative 16 in 89% yield.     

Photoinduced reductive repair of thymine glycol: implications for excess electron transfer through DNA containing modified bases

Photoinduced reduction of thymine glycol in oligodeoxynucleotides was investigated using either a reduced form of flavin adenine dinucleotide (FADH(-)) as an intermolecular electron donor or covalently linked phenothiazine (PTZ) as an intramolecular electron donor. Intermolecular electron donation from photoexcited flavin (FADH(-)) to free thymidine glycol generated thymidine in high yield, along with a small amount of 6-hydroxy-5,6-dihydrothymidine. In the case of photoreduction of 4-mer long single-stranded oligodeoxynucleotides containing thymine glycol by *FADH(-), the restoration yield of thymine was varied depending on the sequence of oligodeoxynucleotides. Time-resolved spectroscopic study on the photoreduction by laser-excited N,N-dimethylaniline (DMA) suggested elimination of a hydroxyl ion from the radical anion of thymidine glycol with a rate constant of approximately 10(4) s(-1) generates 6-hydroxy-5,6-dihydrothymidine (6-HOT(*)) as a key intermediate, followed by further reduction of 6-HOT(*) to thymidine or 6-hydroxy-5,6-dihydrothymdine (6-HOT). On the other hand, an excess electron injected into double-stranded DNA containing thymine glycol was not trapped at the lesion but was further transported along the duplex. Considering redox properties of the nucleobases and PTZ, competitive excess electron trapping at pyrimidine bases (thymine, T and cytosine, C) which leads to protonation of the radical anion (T(-)(*), C(-)(*)) or rapid back electron transfer to the radical cation of PTZ (PTZ(+)(*)), is presumably faster than elimination of the hydroxyl ion from the radical anion of thymine glycol in DNA.     

Metabolism of [2-14C]thymine and [2-14C]thymidine in germinating black gram (Phaseolus mungo) seeds

The metabolism of [2-14C]thymine and [2-14C]thymidine in the cotyledons and embryonic axes of black gram (Phaseolus mungo) seedlings was investigated. Both [2-14C]thymine and [2-14C]thymidine degraded extensively into [14C]CO2. The rate of release of [14C]CO2 from [2-14C]thymine was much greater than that from [2-14C]thymidine. Radioactivity from both precursors was also observed beta-ureidoisobutyric acid. This indicated that thymine was degraded by the reductive pathway of pyrimidine degradation. Small amounts of [2-14C]thymine and [2-14C]thymidine were salvaged for deoxyribonucleotide and DNA synthesis. The highest incorporation of [2-14C]thymine and [2-14C]thymidine into the DNA fraction was observed in 24 hour-old cotyledons where net DNA synthesis was not observed. These precursors seem to be utilised for DNA synthesis of organelles of the cotyledonary cells, probably mitochondria. In embronic axes, [2-14C]thymine is more effectively salvaged for DNA synthesis than [2-14C]thymine. The incorporation rate increased during the early phase of germination and attained its maximum at 48 h after which it decreased. No thymidine kinase activity was detected in either cotyledons or in the embryonic axes. Thymidine salvage seems to be catalysed by nucleoside phosphotransferase which is present both in the cotyledons and in the embryonic axes. This suggests that, in contrast to other pyrimidine and purine bases and nucleosides, no specific salvage system for thymine and thymidine is present in black gram seedlings.     

Synthesis and characterization of a [3-15N]-labeled cis-syn thymine dimer-containing DNA duplex

Cis-syn thymine dimers are the major photoproducts of DNA and are the principal cause of mutations induced by sunlight. To better understand the nature of base pairing with cis-syn thymine dimers, we have synthesized a decamer oligodeoxynucleotide (ODN) containing a cis-syn thymine dimer labeled at the N3 of both T's with 15N by two efficient routes from [3-15N]-thymidine phosphoramidite. In the postsynthetic irradiation route, an ODN containing an adjacent pair of [3-15N]-labeled T's was irradiated and the cis-syn dimer-containing ODN isolated by HPLC. In the mixed building block route, a mixture of cis-syn and trans-syn dimer-containing ODNs was synthesized from a mixture of [3-15N]-labeled thymine dimer phosphoramidites after which the cis-syn dimer-containing ODN was isolated by HPLC. The N3-nitrogen and imino proton signals of an (15)N-labeled thymine dimer-containing decamer duplex were assigned by 2D 1H-15N heterocorrelated HSQC NMR spectroscopy, and the 15N-1H coupling constant was found to be 1.8 Hz greater for the 5'-T than for the 3'-T. The larger coupling constant is indicative of weaker H-bonding that is consistent with the more distorted nature of the 5'-base pair found in solution state NMR and crystallographic structures.     

Quinone sensitized electron transfer photooxidation of nucleic acids: chemistry of thymine and thymidine radical cations in aqueous solution

The 2-methyl-1,4-naphthoquinone (MQ) sensitized photooxidation of nucleic acid derivatives has been studied by laser flash photolysis and steady state methods. Thymine and thymidine, as well as other DNA model compounds, quench triplet MQ by electron transfer to give MQ radical anions and pyrimidine or purine radical cations. Although the pyrimidine radical cations cannot be directly observed by flash photolysis, the addition of N,N,N',N'-tetramethyl-1,4-phenylenediamine (TMPD) results in the formation of the TMPD radical cation via scavenging of the pyrimidine radical cation. The photooxidation products for thymine and thymidine are shown to result from subsequent chemical reactions of the radical cations in oxygenated aqueous solution. The quantum yield for substrate loss at limiting substrate concentrations is 0.38 for thymine and 0.66 for thymidine. The chemistry of the radical cations involves hydration by water leading to C(6)-OH adduct radicals of the pyrimidine and deprotonation from the N(1) position in thymine and the C(5) methyl group for thymidine. Superoxide ions produced via quenching of the quinone radical anion with oxygen appear to be involved in the formation of thymine and thymidine hydroperoxides and in the reaction with N(1)-thyminyl radicals to regenerate thymine. The effects of pH were examined in the range pH 5-8 in both the presence and absence of superoxide dismutase. Initial C(6)-OH thymine adducts are suggested to dehydrate to give N(1)-thyminyl radicals.     

Interaction between thymine dimer and flavin-adenine dinucleotide: a DFT and direct ab initio molecular dynamics study

The interaction between the fully reduced flavin-adenine dinucleotide (FADH (-)) and thymine dimer (T) 2 has been investigated by means of density functional theory (DFT) calculations. The charges of FADH (-) and (T) 2 were calculated to be -0.9 and -0.1, respectively, at the ground state. By photoirradiation, an electron transfer occurred from FADH (-) to (T) 2 at the first excited state. Next, the reaction dynamics of electron capture of (T) 2 have been investigated by means of the direct ab initio molecular dynamics (MD) method (HF/3-21G(d) and B3LYP/6-31G(d) levels) in order to elucidate the mechanism of the repair process of thymine dimer caused by the photoenzyme. The thymine dimer has two C-C single bonds between thymine rings (C 5-C 5' and C 6-C 6' bonds) at the neutral state, which is expressed by (T) 2. After the electron capture of (T) 2, the C 5-C 5' bond was gradually elongated and then it was preferentially broken. The time scale of the C-C bond breaking and formation of the intermediate with a single bond (T) 2 (-) was estimated to be 100-150 fs. The present calculations confirmed that the repair reaction of thymine dimer takes place efficiently via an electron-transfer process from the FADH (-) enzyme.     

Trapping reactions of an intermediate containing a tungsten-phosphorus triple bond with alkynes

The thermolysis of the phosphinidene complex [Cp*P[W(CO)5]2] (1) in toluene in the presence of tBuC(triple bond)CMe leads to the four-membered ring complexes [[[eta2-C(Me)C(tBu)]Cp*(CO)W(mu3-P)[W(CO)3]][eta4:eta1:eta1-P[W(CO)5]WCp*(CO)C(Me)C(tBu)]] (4) as the major product and [[W[Cp*(CO)2]W(CO)2WCp*(CO)[eta1:eta1-C(Me)C(tBu)]](mu,eta3:eta2:eta1-P2[W(CO)5]] (5). The reaction of 1 with PhC(triple bond)CPh leads to [[W(Co)2[eta2-C(Ph)C(Ph)]][(eta4:eta1-P(W(CO)5]W[Cp*(CO)2)C(Ph)C(Ph)]] (6). The products 4 and 6 can be regarded as the formal cycloaddition products of the phosphido complex intermediate [Cp*(CO)2W(triple bond)P --> W(CO)5] (B), formed by Cp* migration within the phosphinidene complex 1. Furthermore, the reaction of 1 with PhC(triple bond)CPh gives the minor product [[[eta2:eta1-C(Ph)C(Ph)]2[W(CO)4]2][mu,eta1:eta1-P[C(Me)[C(Me)]3C(Me)][C(Ph)](C(Ph)]] (7) as a result of a 1,3-dipolaric cycloaddition of the alkyne into a phosphaallylic subunit of the Cp*P moiety of 1. Compounds 4-7 have been characterized by means of their spectroscopic data as well as by single-crystal X-ray structure analysis.     

Valence anion of thymine in the DNA pi-stack

Most of theoretical data on the stability of radical anions supported by nucleic acid bases have been obtained for anions of isolated nucleobases, their nucleosides, or nucleotides. This approach ignores the hallmark forces of DNA, namely, hydrogen bonding and pi-stacking interactions. Since these interactions might be crucial for the electron affinities of nucleobases bound in DNA, we report for the first time on the stability of the thymine valence anion in trimers of complementary bases possessing the regular B-DNA geometry but differing in base sequence. In order to estimate the energetics of electron attachment to a trimer, we developed a thermodynamic cycle employing all possible two-body interaction energies in the neutral and anionic duplex as well as the adiabatic electron affinity of isolated thymine. All calculations were carried out at the MP2 level of theory with the aug-cc-pVDZ basis set. The two-body interaction energies were corrected for the basis set superposition error, and in benchmark systems, they were extrapolated to the basis set limit and supplemented with correction for higher order correlation terms calculated at the CCSD(T) level. We have demonstrated that the sequence of nucleic bases has a profound effect on the stability of the thymine valence anion: the anionic 5'-CTC-3' (6.0 kcal/mol) sequence is the most stable configuration, and the 5'-GTG-3' (-8.0 kcal/mol) trimer anion is the most unstable species. On the basis of obtained results, one can propose DNA sequences that are different in their vulnerability to damage by low energy electron.     

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.     

Molecular dynamics simulation of thymine glycol-lesioned DNA reveals specific hydration at the lesion

One nanosecond molecular dynamics (MD) simulation of a thymine glycol (TG)-lesioned part of human lymphoblast AG9387 was performed to determine structural changes in DNA molecule caused by the presence of a lesion. These changes can be significant for proper recognition of lesions by a repair enzyme. Thymine glycol is the DNA oxidative lesion formed by addition of OH radicals to C5 and C6 atoms of the thymine base. This lesion is known as causing Cockayne Syndrome-inherited genetic disorder. Distribution of water molecules in a hydration shell around the DNA molecule was analyzed for its contribution to the recognition of the TG lesion by the repair enzyme. The results of MD simulation show there is a specific DNA structural configuration formed at the lesion. After 500 ps the DNA is bent in a kink at the TG site. This change dislocates the glycosyl bond at C5' to a position closer to the DNA surface, and thus its atoms are more exposed to the surrounding water shell. The increased number of water molecules that are close to the TG site indicates that the glycosyl bond may be easily contacted by the repair enzyme. In addition, the higher number of water molecules at the TG site substantiates the importance of water-mediated hydrogen bonds created between the repair enzyme and the DNA upon formation of the complex. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1723-1731, 2001     

Chemical reduction of 2,4,6-tricyano-1,3,5-triazine and 1,3,5-tricyanobenzene. Formation of novel 4,4',6,6'-Tetracyano-2,2'-bitriazine and its radical anion

Chemical reduction of 2,4,6-tricyano-1,3,5-triazine, TCT, results in the formation of an unstable radical anion that undergoes immediate dimerization at a ring carbon to form [C(12)N(12)](2-), [TCT](2)(2-), characterized by a long 1.570 (4) A central C[bond]C. [TCT](2)(2-) can decompose into the radical anion of 4,4',6,6'-tetracyano-2,2'-bitriazine, [TCBT]*-, the one-electron reduced form of planar (D(2h)) TCBT, which is also structurally characterized as the [TMPD][TCBT] charge-transfer complex (TMPD = N,N,N',N'-tetramethyl-p-phenylenediamine) with a 1.492 (2) A central sp(2)[bond]sp(2) C[bond]C. Although crystals could not be obtained for the radical anion [TCBT]*-, the electrochemistry (E degrees = +0.03 V), EPR (g = 2.003, (2)A((14)N) = 3.347 G, and (4)A((14)N) = 0.765 G and a line width of 0.24 G), and theoretical calculations support the formation of [TCBT]*-. In addition, thermolysis of [TCT](2)(2-) yields [TCBT]*-. Chemical reduction of 2,4,6-tricyanobenzene, TCB, forms an unstable radical anion that immediately undergoes dimerization at a ring carbon to form [C(12)H(6)N(6)](2-), [TCB](2)(2-), which has a long 1.560 (5) A central C[bond]C. Reaction of TCT with tetrathiafulvalene (TTF) forms structurally characterized [TTF][TCT], and in the presence of water, TCT hydrolyzes to 2,4-dicyano-6-hydroxy-s-triazine, DCTOH. In contrast, the reaction of TCT with TMPD forms [TMPD][TCT], which in the presence of water forms structurally characterized [HTMPD](+)[DCTO](-).