Chemical basis of DNA sugar-phosphate cleavage by low-energy electrons

DNA damage by low-energy electrons (LEE) was examined using a novel system in which thin solid films of oligonucleotide tetramers (CGTA and GCAT) were irradiated with monoenergetic electrons (10 eV) under ultrahigh vacuum. The products of irradiation were examined by HPLC. These analyses permitted the quantitation of 16 nonmodified nucleobase, nucleoside, and nucleotide fragments of each tetramer resulting from the cleavage of phosphodiester and N-glycosidic bonds. The distribution of nonmodified products suggests a mechanism of damage involving initial electron attachment to nucleobase moieties, followed by electron transfer to the sugar-phosphate backbone, and subsequent dissociation of the phosphodiester bond. Moreover, virtually all the nonmodified fragments contained a terminal phosphate group at the site of cleavage. These results demonstrate that the phosphodiester bond breaks by a distinct pathway in which the negative charge localizes on the phosphodiester bond giving rise to nonmodified fragments with an intact phosphate group. Conversely, the radical must localize on the sugar moiety to give as yet unidentified modifications. In summary, the reaction of LEE with simple tetramers involved dissociative electron attachment leading to phosphodiester bond cleavage and the formation of nonmodified fragments.     

Binary relations as lattice isomorphisms

Summary In 1963, Zaretskiį established a one-to-one correspondence between the setB _X of binary relations on a set X and the set of triples of the form (W, ϕ, V) where W and V are certain lattices and ϕ: W→V is an isomorphism. We provide a multiplication for these triples making the Zaretskiį correspondence a semigroup isomorphism. In addition, we consider faithful representations ofB _X by pairs of partial transformations and also as the translational hull of its rectangular relations. Using these triples, we study idempotents, regular and completely regular elements and relationsH-equivalent to some relations with familiar properties such as reflexivity, transitivity, etc. Entrata in Redazione il 14 aprile 1998.     

Photodynamic activity of substituted zinc trisulfophthalocyanines: role of plasma membrane damage

We recently reported that variations in cellular phototoxicity among a series of alkynyl-substituted zinc trisulfophthalocyanines (ZnPcS3Cn) correlates with their hydrophobicity, with the most amphiphilic derivatives showing the highest cell uptake and phototoxicity. In this study we address the role of the plasma membrane in the photodynamic response as it relates to the overall hydrophobicity of the photosensitizer. The membrane tracker dye 1-[4(trimethylamino)phenyl]-6-phenylhexa-1,3,5-triene (TMA-DPH), which is incorporated into plasma membranes by endocytosis, was used to establish plasma membrane uptake by EMT-6 cells of the ZnPcS3C, by colocalization, and TMA-DPH membrane uptake rates after photodynamic therapy were used to quantify membrane damage. TMA-DPH colocalization patterns show plasma membrane uptake of the photosensitizers after short 1 h incubation periods. TMA-DPH plasma membrane uptake rates after illumination of the photosensitizer-treated cells show a parabolic relationship with photosensitizer hydrophobicity that correlates well with the phototoxicity of the ZnPcS3C,. After a 1 h incubation period, overall phototoxicity correlates closely with the postillumination rate of TMA-DPH incorporation into the cell membrane, suggesting a major role of plasma membrane damage in the overall PDT effect. In contrast, after a 24 h incubation, phototoxicity shows a stronger but imperfect correlation with total cellular photosensitizer uptake rather than TMA-DPH membrane uptake, suggesting a partial shift in the cellular damage responsible for photosensitization from the plasma membrane to intracellular targets. We conclude that plasma membrane localization of the amphiphilic ZnPcS3C6-C9 is a major factor in their overall photodynamic activity.     

Distributions of conduction electrons as manifested in MAS NMR of gallium nitride

A strategy is demonstrated for identifying unambiguously and characterizing quantitatively the effects of distributions of conduction electron concentrations arising from intentional or unintentional dopants in semiconductors by magic-angle spinning (MAS) NMR. The 71Ga MAS NMR spectra of a number of chemically synthesized GaN samples with no intentional doping show inhomogeneously broadened absorptions to high frequency of the main peak. These broad signals are shown, from spin-lattice relaxation time measurements as a function of shift position in a single sample, to be due to Knight shifts arising from degenerate conduction electrons. For a GaN sample with Ge as an intentional dopant at the 0.13% (wt) level, the spectrum is dramatically broadened and shifted to high frequency by up to several hundred parts per million. Analysis of the inhomogeneously broadened line shape yields a quantitative probability density function for electron carrier concentration in the bulk sample that reflects significant compositional heterogeneity due to a variety of possible sources.     

Single,double, and multiple double strand breaks induced in DNA by 3-100 eV electrons

Nonthermal secondary electrons with initial kinetic energies below 100 eV are an abundant transient species created in irradiated cells and thermalize within picoseconds through successive multiple energy loss events. Here we show that below 15 eV such low-energy electrons induce single (SSB) and double (DSB) strand breaks in plasmid DNA exclusively via formation and decay of molecular resonances involving DNA components (base, sugar, hydration water, etc.). Furthermore, the strand break quantum yields (per incident electron) due to resonances occur with intensities similar to those that appear between 25 and 100 eV electron energy, where nonresonant mechanisms related to excitation/ionizations/dissociations are shown to dominate the yields, although with some contribution from multiple scattering electron energy loss events. We also present the first measurements of the electron energy dependence of multiple double strand breaks (MDSB) induced in DNA by electrons with energies below 100 eV. Unlike the SSB and DSB yields, which remain relatively constant above 25 eV, the MDSB yields show a strong monotonic increase above 30 eV, however with intensities at least 1 order of magnitude smaller than the combined SSB and DSB yields. The observation of MDSB above 30 eV is attributed to strand break clusters (nano-tracks) involving multiple successive interactions of one single electron at sites that are distant in primary sequence along the DNA double strand, but are in close contact; such regions exist in supercoiled DNA (as well as cellular DNA) where the double helix crosses itself or is in close proximity to another part of the same DNA molecule.     

Part-whole number knowledge in preschool children

Ability to reflect on a number as an object of thought, and to isolate its constituent parts, is basic to a deep knowledge of arithmetic, as well as much practical and applied mathematical problem solving. Part-whole reasoning and counting are closely related in children’s numerical development. The mathematical behavior of young children in part-whole problem settings was examined by using a dynamic problem situation, in which a small set of items was partitioned such that one of the subsets remained perceptually inaccessible. Issues addressed include the problem solving strategies successful children used, adaptations children make in response to successive administrations of the task over time, and characterizations of children’s mathematical thinking based on their responses to the task.     

Comparison between X-ray photon and secondary electron damage to DNA in vacuum

Both monolayer and thick (20 microm) films of dry pGEM-3Zf(-) plasmid DNA deposited on tantalum foil were exposed to Al Kalpha X-rays (1.5 keV) for various times in an ultrahigh vacuum chamber. For monolayer DNA, the damage was induced mainly by low energy secondary electrons (SEs) emitted from the tantalum. For the thick films, DNA damage was induced chiefly by X-ray photons. Different forms of plasmid DNA were separated and quantified by agarose gel electrophoresis. The exposure curves for the formation of nicked circular (single strand break, SSB), linear (double strand break, DSB), and interduplex cross-link forms 1 and 2 were obtained for both monolayer and thick films of DNA, respectively. The lower limits of G values for SSB and DSB induced by SEs were derived to be 86 +/- 2 and 8 +/- 2 nmol J(-1), respectively. These values are 1.5 and 1.6 times larger than those obtained with 1.5 keV photons. The projected X-ray energy dependence of the low energy electron (LEE) enhancement factor for the SSB and DSB in monolayer DNA is also discussed. This new method of investigation of the SE-induced damage to large biomolecules allows direct comparison of the yield of products induced by high energy photons and LEEs under identical experimental conditions.     

DNA strand breaks induced by 0-4 eV electrons: the role of shape resonances

Collisions of 0-4 eV electrons with thin DNA films are shown to produce single strand breaks. The yield is sharply structured as a function of electron energy and indicates the involvement of pi* shape resonances in the bond breaking process. The cross sections are comparable in magnitude to those observed in other compounds in the gas phase in which pi* electrons are transferred through the molecule to break a remote bond. The results therefore support aspects of a theoretical study by Barrios et al. [J. Phys. B 106, 7991 (2002)]] indicating that such a mechanism could produce strand breaks in DNA.     

The synthesis and structural characterization of the new ternary nitrides: Ca4TiN4 and Ca5NbN5

The ternary nitrides, Ca₄TiN₄ and Ca₅NbN₅, were synthesized in sealed niobium tubes using lithium nitride as a flux at 900 and 1050 °C, respectively. The structures of both compounds were solved from single-crystal X-ray diffraction data. Ca₄TiN₄ is the first example of a calcium group IV nitride; it crystallizes in the triclinic space group (No. 2) with cell parameters a=5.9757(5) Å, b=6.0129(5) Å, c=6.0116(12) Å, α=71.565(4)°, β=79.471(4)°, γ=68.258(4)° and Z=2. Ca₄TiN₄ is isostructural with Na₄TiO₄ and contains tetrahedral TiN₄ units connected through edges and corners to CaN₄ tetrahedra and CaN₅ square pyramids. Ca₅NbN₅ crystallizes in the monoclinic space group C2/m (No. 12) with cell parameters a=11.922(7) Å, b=6.878(5) Å, c=8.936(7) Å, β=101.22(3)° and Z=4. Ca₅NbN₅ is isostructural with Ba₅NbN₅; the structure contains NbN₄ tetrahedra that share vertices with CaN₅ trigonal bipyramids.