Pyrimidine Bases In DNA Research Articles

Efficient conversion of thymine glycol into the formamide lesion in oligonucleotides

Oxidation of (5 R,6 S)-5,6-dihydro-5,6-dihydroxythymidine (thymidine glycol) with sodium periodate efficiently produced N-(2-deoxy-β- d- erythro-pentofuranosyl)formamide, a hydroxyl radical-induced decomposition product of pyrimidine bases in DNA, and this method was successfully applied to the conversion of thymine glycol in oligonucleotides into the formamide lesion.

DNA binding by Ru(II)–bis(bipyridine)–pteridinyl complexes

The interactions of five bis(bipyridyl) Ru(II) complexes of pteridinyl-phenanthroline ligands with calf thymus DNA have been studied. The pteridinyl extensions were selected to provide hydrogen-bonding patterns complementary to the purine and pyrimidine bases of DNA and RNA. The study includes three new complexes [Ru(bpy)(2)(L-pterin)](2+), [Ru(bpy)(2)(L-amino)](2+), and [Ru(bpy)(2)(L-diamino)](2+) (bpy is 2,2'-bipyridine and L-pterin, L-amino, and L-diamino are phenanthroline fused to pterin, 4-aminopteridine, and 2,4-diaminopteridine), two previously reported complexes [Ru(bpy)(2)(L-allox)](2+) and [Ru(bpy)(2)(L-Me(2)allox)](2+) (L-allox and L-Me(2)allox are phenanthroline fused to alloxazine and 1,3-dimethyalloxazine), the well-known DNA intercalator [Ru(bpy)(2)(dppz)](2+) (dppz is dipyridophenazine), and the negative control [Ru(bpy)(3)](2+). Reported are the syntheses of the three new Ru-pteridinyl complexes and the results of calf thymus DNA binding experiments as probed by absorption and fluorescence spectroscopy, viscometry, and thermal denaturation titrations. All Ru-pteridine complexes bind to DNA via an intercalative mode of comparable strength. Two of these four complexes--[Ru(bpy)(2)(L-pterin)](2+) and [Ru(bpy)(2)(L-allox)](2+)--exhibit biphasic DNA melting curves interpreted as reflecting exceptionally stable surface binding. Three new complexes--[Ru(bpy)(2)(L-diamino)](2+), [Ru(bpy)(2)(L-amino)](2) and [Ru(bpy)(2)(L-pterin)](2+)--behave as DNA molecular "light switches."

Osmium Tetroxide, 2,2′-Bipyridine: Electroactive Marker for Probing Accessibility of Tryptophan Residues in Proteins

A complex of osmium tetroxide with 2,2'-bipyridine (Os,bipy) has been applied as a chemical probe of DNA structure as well as an electroactive DNA label. The Os,bipy has been known to form covalent adducts with pyrimidine DNA bases. Besides the pyrimidines, electrochemically active covalent adducts with Os,bipy are formed also by tryptophan (W) residues in peptides and proteins. In this paper we show that Os,bipy-treated proteins possessing W residues (such as avidin, streptavidin, or lysozyme) yield at the pyrolytic graphite electrode (PGE) a specific signal (peak alphaW) the potential of which differs from the potentials of signals produced by free Os,bipy or by Os,bipy-modified DNA. No such signal is observed with proteins lacking W (such as ribonuclease A or alpha-synuclein). Subpicomole amounts of W-containing proteins modified with Os,bipy can easily be detected using adsorptive transfer stripping voltammetry with the PGE. Binding of biotin to avidin interferes with Os,bipy modification of the protein, in agreement with the location of W residues within the biotin-binding site of avidin. These Ws are accessible for modification in the absence of biotin but hidden (protected from modification) in the avidin-biotin complex. The Os,bipy-modified avidin is unable to bind biotin, and its quarternary structure is disrupted. Analogous effects were observed with another biotin-binding protein, streptavidin. Our results demonstrate that modification of proteins with Os,bipy under conditions close to physiological, followed by a simple electrochemical analysis, can be applied in the microanalysis of protein structure and interactions.

50 years thymine dimer

Fifty years ago thymine dimer was discovered in the Biochemical and Biophysical Laboratory of Delft Technological University, The Netherlands, by one of the authors of this review (Beukers) as the first environmentally induced DNA lesion. It is one of the photoproducts formed between adjacent pyrimidine bases in DNA by UV irradiation, currently known as cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts. Major lesions found in DNA after in vitro or in vivo UV irradiation are the cis–syn cyclobutane thymine dimer and the thymine–cytosine (6-4) photoproduct. Even after 50 years the study of photo-induced DNA lesions is still going on as is illustrated by the hundreds of papers published every year and the millions hits when browsing the internet for dimer-related information. Living organisms possess efficient and different mechanisms to repair detrimental lesions in their DNA. A unique mechanism to repair CPDs is reversion by either direct interaction with light of short wavelength or by enzymatic photoreactivation. Photophysical mechanisms that induce and reverse molecular bonds in biological macromolecules have been a main focus of research of the group in Delft in the middle of the last century. This review describes the break-through results of these studies which were the result of intense interactions between scientists in the fields of physics, organic chemistry and biochemistry. Philosophically, the “view” of the group in Delft was very appealing: since in nature photolesions are induced in DNA by the sun, how is it possible that repair of these lesions could be accomplished by the same energy source. Evolutionary, it is hardly possible to think of a more efficient repair mechanism.

Spectroscopic studies on a novel intramolecular hydrogen bond within the (6 4) photoproduct

The (6-4) photoproduct, which is one of major UV-induced lesions formed between adjacent pyrimidine bases in DNA, was characterized by using (15)N NMR, fluorescence emission, and UV/VIS absorption at various pH values. From these experiments, we identified a novel intramolecular hydrogen bond between the hydroxyl group at the C5 position of the 5' component and the N3 of the 3' pyrimidone ring within the (6-4) photoproduct.

Interactions of slow electrons with biomolecules

We report on results of computational studies of the interaction of slow electrons with the purine and pyrimidine bases of DNA, as well as with their associated nucleosides and nucleotides. The calculations focus on characterisation of the π* resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. High-level studies of the π* resonances in pyrazine, a close analogue of the pyrimidine bases, indicate that the higher-energy π* resonances in these bases may in fact contain large admixtures of core-excited character built on low-lying triplet states. Decay into such triplet states may provide a mechanism for damage to DNA.

Geometrical characterization of adenine and guanine on Cu(1 1 0) by NEXAFS, XPS, and DFT calculation

Adsorption of purine DNA bases (guanine and adenine) on Cu(1 1 0) was studied by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine-structure spectroscopy (NEXAFS), and density-functional theory (DFT) calculation. At coverages near 0.2 monolayers, Angular-resolved NEXAFS analysis revealed that adenine adsorbates lie almost flat and that guanine adsorbates are tilted up on the surface with the purine ring parallel to the atom rows of Cu(1 1 0). Referring to the previous studies on pyrimidine DNA bases [M. Furukawa, H. Fujisawa, S. Katano, H. Ogasawara, Y. Kim, T. Komeda, A. Nilsson, M. Kawai, Surf. Sci. 532–535 (2003) 261], the isomerization of DNA bases on Cu(1 1 0) was found to play an important role in the adsorption geometry. Guanine, thymine and cytosine adsorption have an amine-type nitrogen next to a carbonyl group, which is dehydrogenated into imine nitrogen on Cu(1 1 0). These bases are bonded by the inherent portion of –NH–CO– altered by conversion into enolic form and dehydrogenation. Adenine contains no CO group and is bonded to Cu(1 1 0) by participation of the inherent amine parts, resulting in nearly flatly-lying position.

Interaction of low-energy electrons with the pyrimidine bases and nucleosides of DNA

We report computed cross sections for the elastic scattering of slow electrons by the pyrimidine bases of DNA, thymine and cytosine, and by the associated nucleosides, deoxythymidine and deoxycytidine. For the isolated bases, we carried out calculations both with and without the inclusion of polarization effects. For the nucleosides, we neglect polarization effects but estimate their influence on resonance positions by comparison with the results for the corresponding bases. Where possible, we compare our results with experiment and previous calculations.

Efficiency of pyrimidine dimer formation in Escherichia coli across UV wavelengths

Inactivation of Escherichia coli as a function of ultraviolet (UV) wavelength was investigated by using the endonuclease-sensitive site (ESS) assay to quantify pyrimidine dimer formation. Ultraviolet dose-response curves were determined based on both log reduction in colony-forming units (CFU) and endonuclease-sensitive sites per kb DNA (ESS/kb) for monochromatic 254-nm low-pressure (LP) UV, polychromatic medium-pressure (MP) UV, 228 and 289-nm UV irradiation. UV irradiation from LP and MP UV sources were approx. equal in both CFU reduction and pyrimidine dimer formation at all UV doses studied; 228-nm irradiation was less effective than LP or MP, and 289-nm irradiation was the least effective in both CFU reduction and pyrimidine dimer formation. These results are in qualitative agreement with the absorption spectrum of pyrimidine bases in DNA. Results indicated an approx. linear relationship between ESS/kb and log CFU reduction. Formation of pyrimidine dimers in genomic DNA is primarily responsible for UV inactivation of E. coli. This work contributed to fundamental understanding of UV disinfection and aids in UV reactor design.

A Unique Demonstration Model of DNA

I describe a physical demonstration model of DNA for the classroom. The model comprises two types of building block that fit together through complementary shape interactions and are held in place by magnets. These building blocks, which represent the purine and pyrimidine bases of DNA, can be put together rapidly (about a minute) to produce an abstract structure that portrays several of the gross architectural features of idealized B-DNA. Thus the model is a right-handed double helix whose strands run in opposite directions and has major and minor grooves. The blocks that form the base-pair units do so specifically. These units lie perpendicular to the helical axis, there are 10 base-pair units per turn, and any sequence can be built with them. Crucially, unlike any other demonstration model currently available, the model can be replicated in situ. It is also self-supporting. The model should complement the currently available resources for teaching the structure and function of DNA.

The degenerate properties of modified purine and pyrimidine DNA bases: a density functional study

Density-functional theory was used to study the properties (binding geometries and affinities for the natural DNA bases) of various degenerate nucleobases, which bind without discrimination to the purines or pyrimidines. The data for purine mimics ( Z and K) indicates that although stronger binding strengths are calculated for pairs with cytosine compared with thymine, cytosine binds to a less stable tautomer of the nucleobase mimic. Indeed, the energy differences between the binding strengths and the tautomers effectively cancel and thereby provide a possible explanation for the observed degenerate properties of these molecules. Similar trends are found for the pyrimidine mimics ( M and P); however, the energy differences do not cancel, even upon inclusion of environmental effects.

Determination of purine and pyrimidine bases in DNA by micellar electrokinetic capillary chromatography with electrochemical detection

A method based on micellar electrokinetic capillary chromatography with electrochemical detection was developed for the determination of cytosine, 5-methylcytosine (5-MC), thymine, adenine, and guanine in the hydrolysates of DNA. The working electrode was fabricated in a novel self-positioning carbon disc electrode system that can align the capillary outlet with the working electrode without a three-dimensional micromanipulator. The five analytes could be well separated within 10 min in a 40 cm length capillary at a separation voltage of 9 kV in a 40 mmol/l borate buffer (pH 10.0) containing 100 mmol/l sodium dodecyl sulfate. Good linearity was observed between peak current and concentration of bases over three orders of magnitude with the detection limits ( S/ N=3) ranging from 1.28·10 −6 to 5.02·10 −6 mol/l. This proposed method demonstrated long-term stability and reproducibility with relative standard deviations of less than 5% for both migration time and peak current ( n=7). It has been successfully applied to determine bases including 5-MC in the hydrolysates of fish sperm DNA, calf thymus DNA, and DNA isolated from spleen cells of female mice.

Probing structure and dynamics of DNA with 2-aminopurine: effects of local environment on fluorescence.

2-Aminopurine (2AP) is an analogue of adenine that has been utilized widely as a fluorescence probe of protein-induced local conformational changes in DNA. Within a DNA strand, this fluorophore demonstrates characteristic decreases in quantum yield and emission decay lifetime that vary sensitively with base sequence, temperature, and helix conformation but that are accompanied by only small changes in emission wavelength. However, the molecular interactions that give rise to these spectroscopic changes have not been established. To develop a molecular model for interpreting the fluorescence measurements, we have investigated the effects of environmental polarity, hydrogen bonding, and the purine and pyrimidine bases of DNA on the emission energy, quantum yield, and intensity decay kinetics of 2AP in simple model systems. The effects of environmental polarity were examined in a series of solvents of varying dielectric constant, and hydrogen bonding was investigated in binary mixtures of water with 1,4-dioxane or N,N-dimethylformamide (DMF). The effects of the purine and pyrimidine bases were studied by titrating 2AP deoxyriboside (d2AP) with the nucleosides adenosine (rA), cytidine (rC), guanosine (rG), and deoxythymidine (dT), and the nucleoside triphosphates ATP and GTP in neutral aqueous solution. The nucleosides and NTPs each quench the fluorescence of d2AP by a combination of static (affecting only the quantum yield) and dynamic (affecting both the quantum yield and the lifetime, proportionately) mechanisms. The peak wavelength and shape of the emission spectrum are not altered by either of these effects. The static quenching is saturable and has half-maximal effect at approximately 20 mM nucleoside or NTP, consistent with an aromatic stacking interaction. The rate constant for dynamic quenching is near the diffusion limit for collisional interaction (k(q) approximately 2 x 10(9) M(-1) s(-1)). Neither of these effects varies significantly between the various nucleosides and NTPs studied. In contrast, hydrogen bonding with water was observed to have a negligible effect on the emission wavelength, fluorescence quantum yield, or lifetime of 2AP in either dioxane or DMF. In nonpolar solvents, the fluorescence lifetime and quantum yield decrease dramatically, accompanied by significant shifts in the emission spectrum to shorter wavelengths. However, these effects of polarity do not coincide with the observed emission wavelength-independent quenching of 2AP fluorescence in DNA. Therefore, we conclude that the fluorescence quenching of 2AP in DNA arises from base stacking and collisions with neighboring bases only but is insensitive to base-pairing or other hydrogen bonding interactions. These results implicate both structural and dynamic properties of DNA in quenching of 2AP and constitute a simple model within which the fluorescence changes induced by protein-DNA binding or other perturbations may be interpreted.

Histone H1- and other protein- and amino acid-hydroperoxides can give rise to free radicals which oxidize DNA

Exposure of amino acids, peptides and proteins to radicals, in the presence of oxygen, gives high yields of hydroperoxides. These materials are readily decomposed by transition metal ions to give further radicals. We hypothesized that hydroperoxide formation on nuclear proteins, and subsequent decomposition of these hydroperoxides to radicals, might result in oxidative damage to associated DNA. We demonstrate here that exposure of histone H1 and model compounds to gamma-radiation in the presence of oxygen gives hydroperoxides in a dose-dependent manner. These hydroperoxides decompose to oxygen- and carbon-centred radicals (detected by electron paramagnetic resonance spectroscopy) on exposure to Cu(+) and other transition metal ions. These hydroperoxide-derived radicals react readily with pyrimidine DNA bases and nucleosides to give adduct species (i.e. protein-DNA base cross-links). Product analysis has demonstrated that radicals from histone H1-hydroperoxides, and other protein and amino acid hydroperoxides, can also oxidize both free 2'-deoxyguanosine and intact calf thymus DNA to give the mutagenic oxidized base 7, 8-dihydro-8-oxo-2'-deoxyguanosine (8-hydroxy-2'-deoxyguanosine, 8-oxodG). The yield of 7,8-dihydro-8-oxo-2'-deoxyguanosine is proportional to the initial protein-hydroperoxide concentration, and corresponds (for histone H1-hydroperoxide, 280 microM) to approx. 1. 4% conversion for free 2'-deoxyguanosine (200 microM), and 0.14% for 2'-deoxyguanosine in DNA (70 microgram/ml). Evidence has also been obtained with DNA for reaction at cytosine and thymine, but not adenine; the lack of damage to the latter may result from damage transfer to 2'-deoxyguanosine residues. These studies demonstrate that initial radical-induced damage to nuclear proteins can give rise to subsequent DNA damage; the latter includes both DNA-protein cross-links and formation of oxidized DNA bases.

Assay for reactive oxygen species-induced DNA damage: measurement of the formamido and thymine glycol lesions

A 32P-postlabeling assay has been developed for the simultaneous detection of the thymine glycol lesion and the formamido remnant of pyrimidine bases in DNA exposed to reactive oxygen species (ROS). The formamido lesion is a principal lesion produced in X-irradiated DNA oligomers when oxygen is available to mediate the damage process. Production of the well-known thymine glycol lesion is less dependent on the concentration of oxygen. These two lesions have the common property that they make the phosphoester bond 3′ to the modified nucleoside resistant to hydrolysis by nuclease P1. Our assay uses 32P-postlabeling to measure these lesions in the form of modified dimers obtained from DNA by nuclease P1 digestion. Appropriate carriers and internal standards have been chemically synthesized to improve the reliability and accuracy of the assay. The measurements were accomplished on 1-μg samples of DNA.

DNA–psoralens molecular recognition using molecular dynamics

Furocoumarins are an important class of compounds for photochemotherapy used in the treatment of numerous diseases characterised by hyperproliferative conditions. Their photosensitising activity has been related to the ability to form covalent linkage with the pyrimidine bases of DNA upon UV-A irradiation. Using the published experimental data of the 3D-structure of the furan-side monoadduct between the 4′-(hydroxymethyl)-4,5′,8-trimethylpsoralen and the DNA oligonucleotide d(GCGTACGC) 2 as starting point, a computational procedure to study the dark intercalation complexes by molecular dynamics was built and then preliminary validated on another psoralen. This docking procedure provides a tool to better understand the mechanism of the DNA-intercalation of these linear furocoumarins and it can be useful in the design of new photochemotherapeutic agents with an improved therapeutic profile.

Photoactivated 8-methoxypsoralen treatment causes a peptide-dependent increase in antigen display by transformed lymphocytes

Ex vivo exposure of malignant human T cells to photoactivated 8-methoxypsoralen (8-MOPa), followed by their i.v. return, appears to vaccinate patients against tumor-associated antigens of cutaneous T cell lymphoma in a procedure termed photopheresis. The molecular basis of this Food and Drug Administration-approved therapy, administered in 100 centers worldwide, is unclear. Most of the attention to the mechanism of action of the drug has focused on its capacity to form covalent cross-links with pyrimidine bases of DNA, thereby inhibiting cellular proliferation. Because immunologic factors appear to be important in the clinical response and could potentially serve as a model for immunotherapy of other malignancies, we explored the possibility that 8-MOP-treated cells display increased quantities of antigenic peptides at their cell surface. In this work, human B-lymphoblastoid tissue culture lines were exposed to 8-MOPa and expression of cell surface class I major histocompatibility complex proteins assessed, since CD8 T cells recognize antigenic moieties in the context of class I molecules. A peak 200-300% increase in MHC class I expression in 8-MOPa-treated cells occurred at 20 hr. 8-MOPa was far more effective in inducing this increase in class I MHC than other modalities, including mitomycin C, gamma-irradiation, ultraviolet B or heat or cold shock. This increase in surface class I MHC molecules appears to be driven by the degradation of cytoplasmic proteins into small peptides, followed by the transport of these peptides to MHC class I molecules in the endoplasmic reticulum. The data suggest that 8-MOPa treatment may augment the immunogenicity of tumor and/or antigen-presenting cells by enhancing processing and transport of class I MHC antigenic peptides.

Chemical display of thymine residues flipped out by DNA methyltransferases.

The DNA cytosine-C5 methyltransferase M. Hha I flips its target base out of the DNA helix during interaction with the substrate sequence GCGC. Binary and ternary complexes between M. Hha I and hemimethylated DNA duplexes were used to examine the suitability of four chemical methods to detect flipped-out bases in protein-DNA complexes. These methods probe the structural peculiarities of pyrimidine bases in DNA. We find that in cases when the target cytosine is replaced with thymine (GTGC), KMnO4proved an efficient probe for positive display of flipped-out thymines. The generality of this procedure was further verified by examining a DNA adenine-N6 methyltransferase, M. Taq I, in which case an enhanced reactivity of thymine replacing the target adenine (TCGT) in the recognition sequence TCGA was also observed. Our results support the proposed base-flipping mechanism for adenine methyltransferases, and offer a convenient laboratory tool for detection of flipped-out thymines in protein-DNA complexes.

DNA breaks and oxidized DNA pyrimidine bases in cells of rectal mucosa from patients with alcohol abuse

DNA breaks and oxidized DNA pyrimidine bases in cells of rectal mucosa from patients with alcohol abuse

Oxidative DNA base damage in renal, hepatic, and pulmonary chromatin of rats after intraperitoneal injection of cobalt(II) acetate.

DNA base damage was studied in renal, hepatic, and pulmonary chromatin of male and female F344/NCr rats that had been given either 50 or 100 mumol of Co(II) acetate/kg body wt in a single ip dose and killed 2 or 10 days later. Control rats received 200 mumol of sodium acetate/kg body wt. Chromatin was isolated from organs and analyzed by gas chromatography/mass spectrometry with selected ion monitoring. The following 11 products derived from purine and pyrimidine bases in DNA were quantified: 5-hydroxy-5-methylhydantoin, 5-hydroxyhydantoin,5-(hydroxymethyl)uracil(5-OHMe-Ura),5- hyd roxycytosine(5-OH- Cyt),thymine glycol, 5,6-dihydroxycytosine,4,6-diamino-5-formamido-pyrimidine (FapyAde),2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua),7,8-dihydro-8-oxoadenine,2-oxoadenine, and 7,8-dihydro-8-oxoguanine. The response was organ-specific. Eight of the DNA base products in renal chromatin of Co(II)-treated rats (mostly 5-OH-Cyt and other pyrimidine products), five in hepatic chromatin (mostly FapyGua and other purine products), and two in pulmonary chromatin (5-OHMe-Ura > FapyAde) were increased by 30% to more than 200% over control levels with increasing Co(II) dose. The renal and hepatic, but not pulmonary, DNA base damage tended to increase with time. No significant differences in response were found between male and female rats. The bases determined were typical products of hydroxyl radical attack on DNA, suggesting a role for this radical in the mechanism(s) of DNA damage caused by Co(II) in vivo. Some of these bases have been shown previously to be promutagenic. The present results imply involvement of oxidative DNA base damage in Co(II)-induced genotoxic and carcinogenic effects.