Synthesis and detection of dna damage

The biological effects of DNA alkyl adducts are difficult to evaluate at the cellular level due to their instability. Synthesis of oligonucleotides that contain a single N7-alkylguanine has become a vital tool to achieve the above goal. However, the instability of N7-alkyguanines is not compatible with the phosphoramidite chemistry used by solid-phase oligonucleotide synthesis either. Development of chemically stable analogues of unstable DNA lesions enables accurate study of polymerase bypass. The design and successful synthesis of N7-hydroxyethyl-9-deaza-2′-deoxyguanosine and N7-oxoethyl-9-deaza-2′-deoxyguanosine as the stable analogues of N7-hydroxyethyl- 2\u27-deoxyguanosine and N7-oxoethyl-2′-deoxyguanosine, respectively, are reported. The synthesis of these two nucleosides whose N7 side chains are protected by TBS for the convenience of conversion to phosphoramidites are also developed. The C-glycosidic bonds of these compounds are demonstrated to be stable under strong acidic and basic conditions. These analogues will become versatile tools to study the replication and repair of DNA alkylation damages. DNA oxidation product 8-oxoGua has been suggested as a biomarker for early cancer diagnosis. An artificial receptor for the free base of 8-oxoGua on a triplex DNA backbone was previously developed. However, accurate detection of 8-oxoGua in urine samples was affected by the presence of a large excess of guanine. Herein, a unique strategy to convert such a receptor to a colorimetric biosensor by conjugating DNA strands to gold nanoparticles (GNP) is developed. Binding of 8-oxoGua to the receptor caused the conjugation of GNP, resulting in diagnostic red-to-purple color changes. The presence of multiple binding cavities enhances the binding-induced stabilization effect and widened the temperature window used for detection. By simply incubating our sensor with a sample, 8-oxoGua can be detected at submicromolar concentrations with a UV-vis spectrometer or even by naked eye. The detection limit in a urine matrix is determined as 126 nM and the response range covers a major portion of the biologically relevant concentration range

Dynamical topology and statistical properties of spatiotemporal chaos

For spatiotemporal chaos described by partial differential equations, there are generally locations where the dynamical variable achieves its local extremum or where the time partial derivative of the variable vanishes instantaneously. To a large extent, the location and movement of these topologically special points determine the qualitative structure of the disordered states. We analyze numerically statistical properties of the topologically special points in one-dimensional spatiotemporal chaos. The probability distribution functions for the number of point, the lifespan, and the distance covered during their lifetime are obtained from numerical simulations. Mathematically, we establish a probabilistic model to describe the dynamics of these topologically special points. In despite of the different definitions in different spatiotemporal chaos, the dynamics of these special points can be described in a uniform approach.Comment: 6 pages, 5 figure

Electronic structures and magnetic orders of Fe-vacancies ordered ternary iron selenides TlFe1.5_{1.5}Se2_2 and AFe1.5_{1.5}Se2_2 (A=K, Rb, or Cs)

By the first-principles electronic structure calculations, we find that the ground state of the Fe-vacancies ordered TlFe$_{1.5}$Se$_2$ is a quasi-two-dimensional collinear antiferromagnetic semiconductor with an energy gap of 94 meV, in agreement with experimental measurements. This antiferromagnetic order is driven by the Se-bridged antiferromagnetic superexchange interactions between Fe moments. Similarly, we find that crystals AFe$_{1.5}$Se$_2$ (A=K, Rb, or Cs) are also antiferromagnetic semiconductors but with a zero-gap semiconducting state or semimetallic state nearly degenerated with the ground states. Thus rich physical properties and phase diagrams are expected.Comment: Add results about AFe$_{1.5}$Se$_2$ (A=K, Rb, or Cs);4 pages and 7 figure

Electron-phonon coupling and superconductivity in LiB1+x_{1+x}C1−x_{1-x}

By means of the first-principles density-functional theory calculation and Wannier interpolation, electron-phonon coupling and superconductivity are systematically explored for boron-doped LiBC (i.e. LiB$_{1+x}$C$_{1-x}$), with $x$ between 0.1 and 0.9. Hole doping introduced by boron atoms is treated through virtual-crystal approximation. For the investigated doping concentrations, our calculations show the optimal doping concentration corresponds to 0.8. By solving the anisotropic Eliashberg equations, we find that LiB$_{1.8}$C$_{0.2}$ is a two-gap superconductor, whose superconducting transition temperature, T$_c$, may exceed the experimentally observed value of MgB$_2$. Similar to MgB$_2$, the two-dimensional bond-stretching $E_{2g}$ phonon modes along $\Gamma$-$A$ line have the largest contribution to electron-phonon coupling. More importantly, we find that the first two acoustic phonon modes $B_1$ and $A_1$ around the midpoint of $K$-$\Gamma$ line play a vital role for the rise of T$_c$ in LiB$_{1.8}$C$_{0.2}$. The origin of strong couplings in $B_1$ and $A_1$ modes can be attributed to enhanced electron-phonon coupling matrix elements and softened phonons. It is revealed that all these phonon modes couple strongly with $\sigma$-bonding electronic states.Comment: 7 pages, 10 figures, accepted for publication in EP