Electronic excited States of polynucleotides: a study by electroabsorption spectroscopy.

Electroabsorption spectra were obtained for single-stranded polynucleotides poly(U), poly(C), poly(A), and poly(G) in glycerol/water glass at low temperature, and the differences in permanent dipole moment (Deltamu) and polarizability (Deltaalpha) were estimated for several spectral ranges covering the lowest energy absorption band around 260 nm. In each spectral range, the electrooptical parameters associated with apparent features in the absorption spectrum exhibit distinct values representing either a dominant single transition or the resultant value for a group of a relatively narrow cluster of overlapping transitions. The estimated spacing in energy between electronic origins of these transitions is larger than the electronic coupling within the Coulombic interaction model which is usually adopted in computational studies. The electroabsorption data allow us to distinguish a weak electronic transition associated with a wing in polynucleotide absorption spectra, at an energy below the electronic origin in absorption spectra of monomeric nucleobases. In poly(C) and poly(G), these low-energy transitions are related to increased values of Deltamu and Deltaalpha, possibly indicating a weak involvement of charge resonance in the respective excited states. A model capable of explaining the origin of low-energy excited states, based on the interaction of pipi* and npi* transitions in neighboring bases, is introduced and briefly discussed on the grounds of point dipole interaction.

Driven translocation of a polynucleotide chain through a nanopore: a continuous time Monte Carlo study.

Using the continuous time Monte Carlo method, we simulated the translocation of a polynucleotide chain driven through a nanopore by an electric field. We have used two models of driven diffusion due to the electric field. The chain may have strong interaction with the pore, and depends on which end of the chain first enters the pore. Depending on this interaction, in both cases, the distribution of times for the chain to pass through the pore in our model is found to have three peaks, as observed in the experiment of Kasianowicz Brandin, Branton, and Deamer [Proc. Natl. Acad. Sci. USA 93, 13770 (1996)].

The reaction of triplet 2-methyl-1,4-naphthoquinone (menadione) with DNA and polynucleotides.

The photoreaction of 2-methyl-1,4-naphthoquinone (MQ, menadione) with DNA and polynucleotides in argon-saturated aqueous solution (pH 7) was studied. Results from laser flash photolysis experiments indicate that triplet quinone reacts with DNA and polyA but not detectably with polyU by one-electron oxidation of the bases of the nucleic acid with formation of the radical anion of the quinone. Irradiation of argon-saturated solutions containing MQ and DNA or polynucleotides (polyU, polyA, polyG or polyC) with 334 nm light leads to an increase in molecular weight for single-stranded DNA, polyA and to a much less extent for polyU. This finding indicates crosslink formation with quantum yields in the range of 10(-5)-10(-3).

[DNA apurinization and apyrimidinization of gamma-irradiated silkworm embryos at different developmental stages]. / Issledovanie apurinizatsii i apirimidinizatsii DNK gamma-obluchennykh émbrionov tutovogo shelkopriada na raznykh stadiiakh razvitiia.

A study was made of the formation and repair of apurine-apyrimidine (AP) sites in DNA of gamma-irradiated 3- and 7-day embryos of Bombyx mori differing drastically in radiosensitivity. The number of AP-sites in DNA immediately after irradiation was much larger in DNA of 3-day embryos than in DNA of 7-day embryos. The kinetics of the postirradiation recovery of AP sites in DNA of 3- and 7-day Bombyx mori embryos was heterogeneous and varied significantly.

[A comparative study of the DNA structural damages and synthesis in embryos of the silkworm Bombyx mori irradiated with gamma rays at different developmental stages]. / Sravnitel'noe issledovanie strukturnykh povrezhdenii i sinteza DNK v émbrionakh tutovogo shelkopriada Bombyx mori, obluchennykh gamma-luchami na raznykh stadiiakh razvitiia.

Studies have been made on formation and reparation of apurine-apyrimidine (AP) regions, monothread DNA ruptures, as well as on inhibition and recovery of DNA synthesis in gamma-irradiated 3- and 7-day embryos of the silkworm which sharply differ in their radiosensitivity. It was shown that in 3-day embryos, the number of AP regions and DNA ruptures immediately after irradiation is significantly higher than in 7-day embryos. DNA synthesis is more radiosensitive in 3-day embryos as compared to that in 7-day ones. Kinetics of postradiation recovery of regions and DNA ruptures in 3- and 7-day embryos is heterogeneous and significantly different. However, radiation inhibition and postradiation recovery of DNA synthesis in irradiated 3- and 7-day embryos are associated mainly with postradiation survival of these embryos.

Laser (two-quantum) photolysis of polynucleotides and nucleoproteins: quantitative processing of results.

The paper offers and substantiates a technique for quantitative processing of the photochemical reactions in polynucleotides, nucleoproteins and their components caused by the action of powerful ultraviolet laser pulse radiation.

The kinetics of radiation-induced strand breakage in polynucleotides in the presence of oxygen: a time-resolved light-scattering study.

The time-resolved light-scattering changes of aqueous, aerated solutions of poly-C, poly-U and poly-A at pH 7.8, following pulse irradiation, have been studied as indices of strand break formation. With doses of 4-24 Gy/pulse a number of kinetically distinct components have been detected. For the poly-pyrimidines an immediate and fast reduction (tau 1/2 less than or equal to 50 microseconds) in light-scattering intensity (LSI), accounting for approximately 20% of the total LSI change, is followed by a much slower loss (k1 approximately 1.6 s-1) which constitutes their major LSI change. For poly-A a similar fast component is observed, present to an extent equivalent to the one noted with poly-C; it constitutes, however, over 50% of the purine polynucleotide's total response, with the remainder of the change being a slower loss (tau 1/2 approximately 0.09 s). Optical pulse radiolysis studies of poly-C and poly-U, in support of the LSI investigations, show that transient absorbances in a region assigned to base peroxyl radicals decay in a complex fashion, with some at a rate equivalent to that for the slow (major) component of LSI loss. These observations support a proposal that the rate-limiting step of major strand breakage for these polynucleotides, in the presence of oxygen, is a base peroxyl radical-mediated abstraction of a H-atom from an adjacent sugar moiety (Bothe et al. 1986), with the resulting sugar peroxyl radicals then leading to strand break formation at a rate equivalent to that for loss of the initial, fast LSI components. These latter processes are attributed to strand breaks arising from the direct interaction of .OH with the polynucleotide sugar phosphate backbone.

Base sequence specificity of a monoclonal antibody binding to (6-4)photoproducts.

The DNA base sequence specificity of the 64M-1 monoclonal antibody, which recognizes ultraviolet (UV)-induced (6-4)photoproducts, was characterized. The 64M-1 antibody strongly bound to UV-poly(dU) as well as to UV-poly(dT), and weakly to UV-poly(dC), UV-poly(me5dC) and UV-poly(rU). A competitive inhibition assay using UV-oligo(dT)8, UV-oligo(dTdC)4, UV-oligo(dC)8, UV-PvuI linker (GCGATCGC) and UV-PvuII linker (GCAGCTGC) indicated that the main (6-4)photoproducts detected by the 64M-1 antibody in UV-irradiated DNA are TT(6-4)photoproducts and TC(6-4)photoproducts. Comparison between dTpdT(6-4)photoproduct and dTpdC(6-4)photoproduct showed that the affinity of the 64M-1 antibody for dTpdT(6-4)photoproduct was about 5 times higher than that for dTpdC(6-4)photoproduct. The antibody also binds to isolated TT(6-4)photoproducts.

Extent of formation of a dimeric adenine photoproduct in polynucleotides and DNA.

Quantum yields are reported for the formation of a dimeric adenine photoproduct, A = A, in adenine homopolymers and DNA irradiated at 254 nm. The A = A content of irradiated samples was assayed by using reversed-phase HPLC to isolate the 4,6-diamino-5-guanidinopyrimidine (DGPY) which is produced from A = A on acid hydrolysis. Acid hydrolysates derived from DNA radiolabelled with [14C] 2'-deoxyadenosine were spiked with unlabelled DGPY before fractionation on HPLC and the recovered material was further purified by chromatography on Sephadex G-10 followed by co-crystallization with DGPY sulphate. Although A = A is formed with a relatively high quantum yield of 1.6 X 10(-3) mol einstein-1 in single-stranded poly(dA) the photoaddition reaction is strongly quenched in base-paired poly(dA).poly(dT) and undetectable in poly(rA).poly(dT). Respective quantum yields of 6 X 10(-5) and 9 X 10(-6) were estimated for the formation of A = A in single- and double-stranded E. coli DNA implying that the photoproduct has very limited biological significance. From studies with d(ApG), d(GpA), ApG, GpA, d(A)20 and d(A4G)4 it is concluded that adjacent guanine and adenine bases do not form a photoadduct analogous to A = A and also that guanine residues have no local or long-range quenching effect on photodimerization within A-A doublets.

DNA strand scission and apurinic sites induced by photoactivated aflatoxins.

Covalent binding of photoactivated aflatoxins to DNA in vitro under close-to-physiological conditions resulted in the formation of apurinic sites and in strand scission. Linearized pBR322 DNA was randomly fragmented, and supercoiled DNA was relaxed during the binding reaction. A primary amine facilitated fragmentation and relaxation. Quantitative measurements of relaxation revealed that the probability of a binding event to be converted into a DNA chain break was approximately 3-5% in the absence of a primary amine. The presence of the latter increased the probability approximately 2- to 3-fold. The results are compatible with the model that photoactivated aflatoxins bind to guanines on DNA; some of these guanine adducts are released, creating apurinic sites. The latter are converted into DNa chain breaks at physiological pH and temperature. Thus, apurinic sites and DNA chain breaks must be considered as quantitatively important (genotoxic) DNA damage induced by aflatoxins.

Interaction of phospholipid liposomes with a DNA model compound in irradiated systems.

Phospholipid liposomes of different unsaturated fatty acid compositions were irradiated either in the presence of a double-stranded polynucleotide, or alone and then mixed with the polynucleotide. Changes in the structure of the polynucleotide were estimated by measuring its ability to form a fluorescent intercalation complex with ethidium bromide. The results imply that radiation-induced peroxidation of the polyunsaturated fatty acids of the phospholipid followed by transfer of damage to the polynucleotide was a very minor process in these systems. The results are discussed in terms of .OH radical attack on the phospholipids at the polar head group or at saturated positions of the fatty acid chains near the water lipid interface. The intermediates produced by this process may then damage the polynucleotide.