PHOTOCHEMISTRY OF 4-THIOURIDINE AND THYMINE

Abstract— When thymine is irradiated in aqueous solution with monochromatic 334-nm UV radiation in the presence of 4-thiouridine a photoproduct of thymine is formed, as shown by thin-layer chromatography and autoradiography. The quantum yield for the formation of thymine photoproduct (θ=0.017) is greater than that for cytosine photoproduct formation (θ= 0.0015). The identity of the photoproduct is not known: one possibility is the formation of an adduct between the sensitizer and the base yielding a pyrimidine-pyrimidone type of photoproduct.     

DNA BREAKAGE CAUSED BY 334-nm ULTRAVIOLET LIGHT IS ENHANCED BY NATURALLY OCCURRING NUCLEIC ACID COMPONENTS AND NUCLEOTIDE COENZYMES

Abstract— The induction of breaks in DNA in vitro caused by 334-nm UV radíation is enhanced by the following compounds (fluence enhancement factors and concentrations used in parentheses): 4-thiouridine (6.9, 1 m M ), 5-methylamino-2-thiouridine (7.5, 1 m M ), 2-thiouracil (41.0, 1 m M ), riboflavin (14.4.0.1 m M ), and the oxidized (6.8, 1 m M ) and reduced (3.4, 1 m M ) forms of nicotinamide adenine dinucleotide. Anoxia and diazobicyclo(2.2.2)octane reduce the number of DNA breaks caused by 334-nm radiation plus 4-thiouridine by 70 and 76%, respectively.     

PHOTOSENSITIZED INACTIVATION OF DNA BY MONOCHROMATIC 334-nm RADIATION IN THE PRESENCE OF 2-THIOURACIL: GENETIC ACTIVITY AND BACKBONE BREAKS

Abstract Monochromatic 334-nm radiation delivered under aerobic conditions inactivates the genetic activity (ability to transform auxotrophic recipient cells to nutritional prototrophy) of isolated transforming Bacillus subtilis DNA. The presence of superoxide dismutase (SOD), catalase, and mannitol reduces the 334-nm inactivation. The rate of inactivation of the genetic activity by 334-nm radiation is enhanced fivefold by the sensitizer 2-thiouracil (s²Ura). This enhancement is substantially reversed when the irradiations are performed in the presence of mannitol, and, to a lesser extent, SOD. Catalase slightly reduces the s²Ura enhancement of 334-nm inactivation of transforming activity. Backbone breaks induced in the same DNA by aerobic 334-nm radiation were also enhanced markedly by the presence of s²Ura; this enhancement was reversed by the presence of mannitol and, to a lesser extent, SOD during irradiation. Catalase had no effect upon s²Ura-enhanced, 334-nm-induced SSBs. Whereas DNA breakage may be responsible for a portion of the inactivation of the DNA by the photosensitized reaction between s²-Ura and 334-nm radiation, it is not the only inactivating lesion, because the yield of SSBs per lethal hit per unit length of DNA is not constant for all the irradiation conditions studied. The results support a complex role for active oxygen species in inactivation of transforming activity and DNA breakage by s²Ura-enhanced 334-nm radiation. They are also consistent with the formation of superoxide anion, hydroxyl radical, and possibly also singlet molecular oxygen, generated from ground-state molecular oxygen by reactive s²Ura in both Type I and II reactions.     

Electrochemical study of thymine dimer based on DNA charge transfer

Differential pulse voltammetry was used to study the formation and level of thymine dimer in DNA duplex modified on a gold electrode. The electrochemical signal of methylene blue coupled with ferricyanide can be obtained via DNA mediated electron transfer, which would be blocked during the formation of thymine dimer. DNA duplexes with different sequences differ in the level of thymine dimer under the same UV irradiation. Futhermore, the presence of guanine base directly preceding -TT- can effectively decrease the level of thymine dimer, possibly due to the self-repair process in which guanine participates. The proposed method can be further applied to DNA self-repair analysis.     

One-electron photooxidation and site-selective strand cleavage at 5-methylcytosine in DNA by sensitization with 2-methyl-1,4-naphthoquinone-tethered oligonucleotides

Photosensitized one-electron oxidation was applied to discriminate a specific base site of 5-methylcytosine (mC) generated in DNA possessing a partial sequence of naturally occurring p53 gene, using a sensitizing 2-methyl-1,4-naphthoquinone (NQ) chromophore tethered to an interior of oligodeoxynucleotide (ODN) strands. Photoirradiation and subsequent hot piperidine treatment of the duplex consisting of mC-containing DNA and NQ-tethered complementary ODN led to oxidative strand cleavage selectively at the mC site, when the NQ chromophore was arranged so as to be in close contact with the target mC. The target mC is most likely to be one-electron oxidized into the radical cation intermediate by the sensitization of NQ. The resulting mC radical cation may undergo rapid deprotonation and subsequent addition of molecular oxygen, thereby leading to its degradation followed by strand cleavage at the target mC site. In contrast to mC-containing ODN, ODN analogs with replacement of normal cytosine, thymine, adenine, or guanine at the mC site underwent less amount of such an oxidative strand cleavage at the target base site, presumably due to occurrence of charge transfer and charge recombination processes between the base radical cation and the NQ radical anion. Furthermore, well designed incorporation of the NQ chromophore into an interior of ODN could suppress a competitive strand cleavage at consecutive guanines, which occurred as a result of positive charge transfer. Thus, photosensitization by an NQ-tethered ODN led to one-electron oxidative strand cleavage exclusively at the target mC site, providing a convenient method of discriminating mC in naturally occurring DNA such as human p53 gene as a positive band on a sequencing gel.     

LETHAL ACTION OF ULTRAVIOLET AND VISIBLE (BLUE-VIOLET) RADIATIONS AT DEFINED WAVELENGTHS ON HUMAN LYMPHOBLASTOID CELLS: ACTION SPECTRA AND INTERACTION SITES

Abstract— The repair proficient human lymphoblastoid line (TK6) has been employed to construcr an action spectrum for the lethal action of ultraviolet (UV) radiation in the range254–434 nm and to examine possible interactions between longer (334, 365 and 405 nm) and shorter wavelength (254 and 313 nm) radiations. The action spectrum follows a DNA absorption spectrum fairly closely out to 360 nm. As in previously determined lethal action spectra for procaryotic and eucaryotic cell populations, there is a broad shoulder in the334–405 nm region which could reflect the existence of either (a) a non-DNA chromophore or (b) a unique photochemical reaction in the DNA over this region. Pre-treatment with radiation at 334 or 365 nm causes either a slight sensitivity to (low fluences) or protection from (higher fluences) subsequent exposure to radiation at a shorter wavelength (254 or 313 nm). Pre-irradiation at a visible wavelength (405 nm) at all fluence levels employed sensitizes the populations to treatment with 254 or 313 nm radiations. These interactions will influence the lethal outcome of cellular exposure to broad-band radiation sources.     

Reactivity of ferrocenylcarbodiimide with DNA duplex containing single-mismatched base pairs.

Ferrocenylcarbodiimide (1), which is known to react with a guanine (G) or thymine (T) base of single stranded DNA, was allowed to react with DNA duplex having a single mismatched base pair of G-T, T-T, or T-cytosine (C). Electrophoreograms of the reaction mixture showed that 1 could react with G or T base of the mismatched sites on the DNA duplex. However, 1 also reacted with the G base of the terminal site on the DNA duplex. This showed that 1 can react with an unpaired base or unstable base pair such as a terminal or mismatched base on the DNA duplex. Electrochemical mismatch detection could be achieved after hybridization of the ferrocenylated mismatched DNA duplex with a selected DNA probe-immobilized electrode. These results revealed that 1 has a potentiality of serving as a labeling reagent of mismatched bases on the DNA duplex, which is important in the search for heterozygous single nucleotide polymorphisms (SNPs).     

A quantum chemical study of reactions of DNA bases with sulphur mustard: a chemical warfare agent

Reactions of the sulphonium ion of sulphur mustard (SM⁺¹) at the N7, N3 and O6 sites of guanine, N7, N3 and N1 sites of adenine, O2 and N3 sites of cytosine and O2 and O4 sites of thymine were studied theoretically in gas phase and aqueous media employing density functional theory (DFT) and second order Møller–Plesset perturbation (MP2) theory. The B3LYP, B3PW91 and B1B95 functionals of DFT and the 6-31+G* and AUG-cc-pVDZ basis sets were used in the calculations. Basis set superposition error was treated using the counterpoise method by single point energy calculations at the B3LYP/6-31+G* level in gas phase. The present study explains the mechanism of alkylation of the DNA bases and shows that SM⁺¹ would form stable adducts at the endocyclic nitrogen sites of the DNA bases, and at the O6 site of guanine and the O2 site of cytosine. Formation of adducts at the N7 site of guanine and N3 site of adenine are found to be most favored and next most favored respectively, which agrees with experimental observations.     

Affinity labeling of a single guanine bulge

We have developed a conceptually new method for the selective labeling of duplex DNA containing a guanine bulge with a masked form of fluorescent 2-amino-1,8-naphthyridine. A naphthyridine derivative 2 tethering DNA-alkylating epoxide was synthesized from (S)-epichlorohydrin and naphthyridine derivative 1, which selectively binds to the guanine bulge duplex. HPLC analysis of the labeling reaction of bulge duplex d(GTT GTGTTG GA)/d(CAA CA A ACC T) (TGT/A_A) with 2 showed a formation of 2-TGT adduct for the guanine bulge. The reaction proceeded for the guanine bulge and a reduced efficiency for the cytosine bulge, but not at all for adenine and thymine bulges. The site of covalent bond formation in 2-TGT was unambiguously identified at the guanine two bases away from the bulge by the use of MALDI-TOF MS analysis of the oligomer fragments produced by strand scission. The labeling reaction was also observed for the guanine bulge flanking two G-C base pairs (CGC/G_G), producing a 2:1 adduct (2.2-CGC). Upon hydrolysis of 2-TGT and 2.2-CGC with concentrated hydrogen chloride, a release of fluorescent 2-aminonaphthyridine from the adduct was clearly detected, verifying a concept of an affinity labeling of the guanine bulge with a masked fluorescent chromophore. The affinity labeling targeting of the guanine bulge is a conceptually novel method for the postsynthetic labeling of DNA. Hybridization, to the target sequence, of a probe DNA possessing one extra guanine especially between two cytosines provides a unique site for the labeling by masked fluorophore 2. The technique may have broad application in genetic typing without using a conventional synthesis of fluorescent-labeled DNA oligomers.     

Inhibition of sulfur incorporation to transfer RNA by ultraviolet-A radiation in Escherichia coli

tRNA sulfurtransferase activity was assayed in Escherichia coli cell extracts obtained from bacterial suspensions exposed to a sub-lethal dose of ultraviolet-A radiation (fluence 148 kJ m(-2)) imparted at a low fluence rate (41 W m(-2)). We found that the irradiation reduced the enzymatic activity to one fourth of the control value, indicating that ultraviolet-A exposure inhibits the synthesis of 4-thiouridine, the most abundant thionucleoside in E. coli tRNA. Changes in the tRNA content of 4-thiouridine and its derived photoproduct 5-(4'-pyrimidin 2'-one) cytosine were studied in bacteria growing under ultraviolet-A irradiation. In these conditions the accumulation of photoproduct was limited, and the kinetics of this process was non-coincident with disappearance of 4-thiouridine. The results, which are compatible with the fact that ultraviolet-A induces an inhibition of the 4-thiouridine synthesis, suggest that the effect of radiation on tRNA modification is relevant to tRNA photo-inactivation in growing bacteria.     

A5–4 PYRIMIDINE-PYRIMIDONE PHOTOPRODUCT PRODUCED FROM MIXTURES OF THYMINE AND 4-THIOURIDINE IRRADIATED WITH 334 nm LIGHT

The nucleoside 4-thiouridine, present in some bacterial tRNA species, is known to be a chromophore and a target for near-UV light-induced growth delay and also mediates both photoprotection and near-UV cell killing in various bacterial strains. To investigate the photoreaction of 4-thiouridine with DNA or its precursors, we irradiated aqueous mixtures of thymine and 4-thiouridine with 334 nm light and then separated photoproducts using two or more stages of reversed-phase high performance liquid chromatography. The two equally abundant major photoproducts were analyzed by UV absorbance spectrophotometry, fast-atom bombardment and electron-impact mass spectrometry, and ¹H- and ¹³C-NMR spectroscopy, and have been identified as two diastereomers of 6-hydroxy-5-[1-(β-D-erythro-pentofuranosyl)-4′-pyrimidin-2′-one]dihydrothymine (o⁶hThy[5-4]Pdo), of molecular weight = 370.32. These two diastereomers, although stable at room temperature or below, are interconvertible by heating (90d?C for 5 min) in aqueous solution. The possible biological significance of this photoproduct is discussed, and an application as a crosslinker for oligonucleotides to selectively block replication is suggested.     

Solution structure of a DNA duplex containing a guanine-difluorotoluene pair: a wobble pair without hydrogen bonding?

The incorporation of synthetic nucleoside analogues into DNA duplexes provides a unique opportunity to probe both structure and function of nucleic acids. We used 1H and 19F NMR and molecular dynamics calculations to determine the solution structures of two similar DNA decamer duplexes, one containing a central G-T mismatched or "wobble" base pair, and one in which the thymine in this base pair is replaced by difluorotoluene (a thymine isostere) creating a G-F pair. Here, we show that the non-hydrogen-bonding G-F pair stacks relatively well into the helix and that the distortions caused by each non-Watson-Crick G-T or G-F base pair are quite localized to a three base pair site around the mismatch. A detailed structural analysis reveals that the absence of hydrogen bonding introduces more dynamic motion into the G-F pair relative to G-T and permits the G-F pair to exhibit stacking and conformational features characteristic of both a Watson-Crick base pair (on the guanine containing strand) and a wobble base pair (on the strand containing the difluorotoluene). We used these results to posit a rationale for recognition and repair of mismatch sites in DNA.     

AN EPR STUDY OF π-CATION RADICALS IN DINUCLEOSIDE PHOSPHATES AND DNA PRODUCED BY PHOTOIONIZATION

In this work we have produced the π-cation radicals of a number of nucleotides, dinucleoside phosphates, and DNA in aqueous glasses (8M NaCIO₄) by photoionization and investigated these species by EPR spectroscopy. Results found for nucleotides and dinucleoside phosphates containing one type of DNA base, e.g. TpT, GpG, or dApdA, were used in the analysis of spectra found for mixed dinucleoside phosphates, e.g. TpdG. For TpdG and TpdA in neutral glasses photoionization takes place from the purine base and no transfer of charge to the pyrimidine base is found. In basic conditions both the adenine and thymine π-cations are observed in TpdA. In both neutral and basic conditions the results found for mixed dinucleoside phosphates containing guanine show that the guanine cation is formed preferentially by photolysis. This result was found to extend to DNA. Photolysis of DNA in 8M NaC1O₄ produced principally the guanine cation. Computer simulations using parameters determined by other workers from a study of γ-irradiated oriented DNA closely match the spectrum found in this work attributed to the guanine cation in dinucleoside phosphates and DNA. This work thus confirms the presence of the guanine cation in γ-irradiated DNA.     

8-Oxoguanine enhances bending of DNA that favors binding to glycosylases

Molecular dynamics (MD) simulations were carried out on the DNA oligonucleotide GGGAACAACTAG:CTAGTTGTTCCC in its native form and with guanine in the central G(19):C(6) base pair replaced by 8-oxoguanine (8oxoG). A box of explicit water molecules was used for solvation, and Na(+) counterions were added to neutralize the system. The direction and magnitude of global bending were assessed by a technique used previously to analyze simulations of DNA containing a thymine dimer. The presence of 8oxoG did not greatly affect the magnitude of DNA bending; however, bending into the major groove was significantly more probable when 8oxoG replaced G(19). Crystal structures of glycosylases bound to damaged-DNA substrates consistently show a sharp bend into the major groove at the damage site. We conclude that changes in bending dynamics that assist the formation of this kink are a part of the mechanism by which glycosylases of the base excision repair pathway recognize the presence of 8oxoG in DNA.     

NONRECIPROCAL SYNERGISTIC LETHAL INTERACTION BETWEEN 365-nm and 405-nm RADIATION IN WILD TYPE and uvrA STRAINS OF ESCHERICHIA COLI*

Abstract— Lethality by 405-nm radiation in three repair-proficient and two uvrA strains of Escherichia coli that belong to two isogenic series was greatly enhanced by prior exposures to 365-nm radiation at fluences greater than 1 times 10₆Jm_-2. Fluences at 365 nm that yielded a surviving fraction of 0.10 (>1 times 10₆ Jm_-2) in the 5 strains tested resulted in the following 405-nm fluence enhancement factors (FEF, ratio of the 405-nm F₃₇ in the absence of a prior 365-nm irradiation to that in the presence): strain K.12 AB1157 (wild type), 8.7; strain B/r (wild type), 52; strain WP2 (wild type), 25; strain WP2s (uvrA), 13; strain K.12 AB1886 (uvrA), 15. The maximal 405-nm FEF value obtained after a prior 365-nm irradiation at greater fluences was 83 in the wild-type strain B/r. Enhancement of anoxic 405-nm radiation after a prior aerobic 365-nm exposure was not detectable, suggesting that prior aerobic irradiation at 365-nm increased the effects of damage produced at 405 nm by means of an oxygen-dependent process. Single-strand breaks (or alkali-labile bonds) were produced by 405-nm radiation at 3.0 times 10_-5 breaks per 2.5 times 10₉ daltons per Jm_-2 in the polA strain P3478; pyrimidine dimers were not detected by biological assay (photoreactivation) at 405 nm. Although the introduction of different DNA lesions produced by 365- and 405-nm radiations cannot be ruled out, we propose that the strong synergistic effect of 365-nm irradiation on 405-nm lethality is the consequence of pronounced inhibition by 365-nm radiation of components of the DNA-repair systems that can mend or bypass damage produced by 405-nm radiation.     

Oligonucleotide cross-linking with copper ions. Spectral and quantum chemical study

Copper(II) complexes with synthetic oligonucleotides consisting of repeating adenine–thymine and guanine–cytosine complementary base pairs have been studied by UV spectroscopy and simulated by DFT quantum chemical calculations at the B3LYP/6-311G++(d,p) level of theory with inclusion of solvation (hydration) effects. The obtained data suggest selective interaction of copper(II) ions with guanine–cytosine complementary pairs, followed by DNA cross-linking at those sites.     

2-Aminopurine flipped into the active site of the adenine-specific DNA methyltransferase M.TaqI: crystal structures and time-resolved fluorescence

We report the crystal structure of the DNA adenine-N6 methyltransferase, M.TaqI, complexed with DNA, showing the fluorescent adenine analog, 2-aminopurine, flipped out of the DNA helix and occupying virtually the same position in the active site as the natural target adenine. Time-resolved fluorescence spectroscopy of the crystalline complex faithfully reports this state: base flipping is accompanied by the loss of the very short ( approximately 50 ps) lifetime component associated with fully base-stacked 2-aminopurine in DNA, and 2-aminopurine is subject to considerable quenching by pi-stacking interactions with Tyr108 in the catalytic motif IV (NPPY). This proves 2-aminopurine to be an excellent probe for studying base flipping by M.TaqI and suggests similar quenching in the active sites of DNA and RNA adenine-N6 as well as DNA cytosine-N4 methyltransferases sharing the conserved motif IV. In solution, the same distinctive fluorescence response confirms complete destacking from DNA and is also observed when the proposed key residue for base flipping by M.TaqI, the target base partner thymine, is substituted by an abasic site analog. The corresponding cocrystal structure shows 2-aminopurine in the active site of M.TaqI, demonstrating that the partner thymine is not essential for base flipping. However, in this structure, a shift of the 3' neighbor of the target base into the vacancy left after base flipping is observed, apparently replicating a stabilizing role of the missing partner thymine. Time-resolved fluorescence and acrylamide quenching measurements of M.TaqI complexes in solution provide evidence for an alternative binding site for the extra-helical target base within M.TaqI and suggest that the partner thymine assists in delivering the target base into the active site.     

ULTRAVIOLET ACTION SPECTRA FOR PHOTOBIOLOGICAL EFFECTS IN CULTURED HUMAN LENS EPITHELIAL CELLS

Abstract— The action spectrum for cell killing by UV radiation in human lens epithelial (HLE) cells is not known. Here we report the action spectrum in the 297–365 nm region in cultured HLE cells with an extended lifespan (HLE B-3 cells) and define their usefulness as a model system for photobiological studies. Cells were irradiated with monochromatic radiation at 297, 302, 313, 325, 334 and 365 nm. Cell survival was determined using a clonogenic assay. Analysis of survival curves showed that radiation at 297 nm was six times more effective in cell killing than 302 nm radiation; 297 nm radiation was more than 260, 590, 1400 and 3000 times as effective in cell killing as 313, 325, 334 and 365 nm radiation, respectively. The action spectrum was similar in shape to that for other human epithelial cell lines and rabbit lens epithelial cells. The effect of UV radiation on crystallin synthesis was also determined at different wavelengths. To determine whether exposure to UV radiation affects the synthesis of β-crystallin, cells were exposed to sublethal fluences of UV radiation at 302 and 313 nm, labeled with [³⁵S]methionine and the newly synthesized βY-crystallin was analyzed by immunoprecipitation and western blotting using an antibody to β-crystallin. The results show a decrease in crystallin synthesis in HLE cells irradiated at 302 and 313 nm at fluences causing low cytotoxicity. The effect of radiation on membrane perturbation was determined by measuring enhancement of synthesis of prostaglandin E₂ (PGE₂). Synthesis of PGE₂ occurs at all UV wavelengths tested in the 297–365 nm region. The slope of the PGE₂ response curves was higher than that of cell killing curves in cultured HLE cells. These data show that cultured HLE cells with extended lifespan are a suitable system for investigating photobiological responses of cells to UV radiation.     

Bulged Guanine is Uniquely Sensitive to Damage Caused by Visible‐Light Irradiation of Ethidium Bound to DNA: A Possible Role in Mutagenesis

The interaction of ethidium bromide (=3,8‐diamino‐5‐ethyl‐6‐phenylphenanthridinium bromide; EB) with a series of duplex DNA oligomers having single‐base bulges and single‐base mis‐pairs was investigated (Fig. 1). Physical and spectroscopic analysis reveals no definitive evidence for selective binding of EB at the bulge or mis‐pair. However, irradiation of the bound EB with VIS light leads to lesions in the DNA selectively in the sequence having a bulged guanine. This reaction is attributed to the formation of an exciplex between the lowest excited singlet state of the EB and the bulged guanine. The exciplex is trapped by H₂O, which initiates a sequence of reactions that lead to piperidine‐requiring strand cleavage at this site. Significantly, the damaged bulged guanine is not recognized by E. coli formamidopyrimidine glycosylase (Fpg), which is part of a base‐excision repair system for oxidative damage to DNA. Thus, DNA containing a bulged guanine and having a bound intercalator may be irreparably damaged by exposure to VIS light, even though normal duplex DNA is relatively inert under these conditions.     

Oxidation of DNA Bases Influenced by the Presence of Other Bases

Electrochemical detection of DNA is a highly important topic. Here we show that the electrochemical responses of one DNA base (guanine, adenine, cytosine or thymine), in terms of oxidation potential, current intensity, peak width and resolution can be highly influenced by the presence of other DNA bases at electrochemically reduced graphene oxide (ER‐GO) as well as standard glassy carbon electrode. We have observed that the effects were more significant for adenine base on ER‐GO and cytosine base on glassy carbon (GC) electrode. Differences in responses were generally low in a mixture of four different DNA bases but interestingly, deviations become significantly larger when only one or two other bases were present. Our findings are of paramount importance for future developments in DNA detection and analysis since individual DNA bases are not present in isolation in nature or in typical biosensing systems.