Structural analysis of base mispairing in DNA containing oxidative guanine lesion

Classical molecular dynamics methods were used to analyze the importance of 8-oxoguanine (8-oxoG) pairing with other DNA bases in order to determine the impact of oxidative guanine lesions on DNA structure. Six lesioned molecules, each containing 8-oxoG mispaired with one of the four normal bases on the the opposite strand at the center of 40-mer DNA, and one non-damaged DNA molecule, were simulated for 2 nanoseconds of real time. The 8-oxoG lesioned bases were found to incorporate opposite all normal bases. There are observed conformational and energetical differences among these parings. 8-oxoG in anti-form creates firm hydrogen bonds with cytosine and this bonding has a strong attractive electrostatic interaction energy similar to that of a native base pair-guanine to cytosine. Meanwhile, it does not form a stable base pair with purine bases (adenine and guanine) nor with the pyrimidine base thymine. On the other hand, the 8-oxoG in syn-form was found to pair with adenine.      

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.     

The molecular orientation of DNA bases on H-passivated Si(1 1 1) surfaces investigated by means of near edge X-ray absorption fine structure spectroscopy

Layers of the DNA bases adenine, cytosine, and guanine were deposited onto hydrogen passivated Si(1 1 1) surfaces. The average tilt angles of these molecules with respect to the substrate surface were determined by the angular dependence of the Near Edge X-ray Absorption Fine Structure (NEXAFS) of the carbon K-edge. The interpretation of the NEXAFS spectra was assisted by a semi-empirical approach to the calculation of the π^∗-transition region which employs density functional theory calculations and core level photoemission data.     

Specific heat spectra for quasiperiodic ladder sequences

We performed a theoretical study of the specific heat C(T) as a function of the temperature for double-strand quasiperiodic sequences. To mimic DNA molecules, the sequences are made up from the nucleotides guanine G, adenine A, cytosine C and thymine T, arranged according to the Fibonacci and Rudin-Shapiro quasiperiodic sequences. The energy spectra are calculated using the two-dimensional Schr?dinger equation, in a tight-binding approximation, with the on-site energy exhibiting long-range disorder and non-random hopping amplitudes. We compare the specific heat features of these quasiperiodic artificial sequences to the spectra considering a segment of the first sequenced human chromosome 22 (Ch22), a real genomic DNA sequence.     

DNA damage induced by laser-hematoporphyrin derivative

Irradiation caused DNA single-strand breaks in S180 cells in the presence oflaser-hematoporphyrin derivative(HPD).The number of single strand breaks was 3.69 ×10~(10)break dolton~(-1).The analysis of base composition of DNA showed that the effect of laser-HPDirradiation on guanine was the highest,being 5-12 times as high as those of the three others(adenine,cytosine and thymine).It was different from the nature of DNA damage caused by γ-ray irradiation.     

Detection of DNA Bases Using Fe Atoms and Graphene

The adsorption of DNA bases on a magnetic probe composed of Fe atoms and graphene is studied by using firstprinciples calculations.The stability of geometry,the electronic structure and magnetic property are investigated.The results indicate that four DNA bases,i.e.,adenine,thymine,cytosine and guanine,can all be adsorbed on the probe solidly.However,the magnetic moments of the composite structure can be observed only when adenine adsorbs on the probe.In the cases of the adsorption of the other three bases,the magnetic moments of the composite structure are zero.Based on the significant change of magnetic moment of the composite structure,adenine can be distinguished conveniently from thymine,cytosine and guanine.This work may provide a new way to detect DNA bases.     

IR Vibrational spectra of H-bonded complexes of adenine, 2-aminopurine and 2-aminopurine<Superscript>+</Superscript> with cytosine and thymine: Quantum-chemical study

Using theoretical study on the B3LYP/6-311++G(d,p) level of theory, we have compared vibrational spectra of 2-aminopurine (as neutral or protonated at N1 atom species) with adenine and H-bonded complexes of 2-aminopurine (as neutral or protoned at N1 atom species) · cytosine or 2-aminopurine · thymine with adenine · cytosine and adenine · thymine base pairs. The nature of the base pairing between adenine, 2-aminopurine, 2-aminopurine⁺ and cytosine or thymine have been investigated by means of quantum-mechanical calculations. We have investigated the effect of the hydrogen bond formation on the vibrational spectra of the investigated base pairs. The main differences in the vibrational spectra as for bases so for base pairs have been observed in the high-frequency region.     

Spin-resolved transport properties of DNA base multi-functional electronic devices

By using density functional theory in combination with non-equilibrium Green's function method, we have investigated the spin-polarized electronic transport properties of four DNA base devices, namely, adenine (A), cytosine (C), guanine (G) and thymine (T). The results show the spin-polarized transport properties can be effectively regulated by adopting different bases, and thymine based device can exhibit high-efficiency spin-filtering, negative differential resistance, spin rectifying behaviors and switching effect by tuning the external magnetic field. We find that the variation in the degree of localization of the frontier molecular orbitals at different biases is responsible for these interesting phenomena. These effects can be explained by the spin-resolved transmission spectrum and the spatial distribution of molecular orbitals around the Fermi level. Our results suggest that thymine base holds great potential application in designing multi-functional spin molecular device.     

Two-dimensional self-assembly of DNA base molecules on Cu(111) surfaces

We present scanning tunneling microscope images of the self-assembled nucleic-acid base molecules on the surfaces of Cu(111). The images reveal that the chemical inertness of the Cu(111) substrate allows the molecules to diffuse over the surface to self-assemble themselves spontaneously into their own unique structure: adenine into one-dimensional (1D) molecular chains, thymine into 2D islands, guanine into 2D square lattices, and cytosine into 1D zig-zag molecule-cluster networks. We find that molecular orbital calculations reproduce some of the observed self-assembly, and suggest that base-base interaction induced by hydrogen bonding is essential to this phenomenon.     

乙酸对DNA空间结构微观损伤的Raman光谱特征

利用Raman光谱技术从分子水平研究了乙酸对鲱鱼精DNA空间结构微观损伤的特征。实验结果表明,鲱鱼精DNA被乙酸浸润处理后,Raman特征频率与强度均发生了不同程度的变化。证明了乙酸对DNA的损伤是整个分子,包括骨架磷酸基团、脱氧核糖及碱基。不仅是DNA的构象,而且其构型也发生了变化：氢键断裂,B型构象被修改,DNA单、双链断裂,碱基也受到了严重损伤。其碱基损伤严重程度依次为胞嘧啶、胸腺嘧啶、鸟嘌呤和腺膘呤。     

Electronic density of states in sequence dependent DNA molecules

We report in this work a numerical study of the electronic density of states (DOS) in π-stacked arrays of DNA single-strand segments made up from the nucleotides guanine G, adenine A, cytosine C and thymine T, forming a Rudin-Shapiro (RS) as well as a Fibonacci (FB) polyGC quasiperiodic sequences. Both structures are constructed starting from a G nucleotide as seed and following their respective inflation rules. Our theoretical method uses Dyson’s equation together with a transfer-matrix treatment, within an electronic tight-binding Hamiltonian model, suitable to describe the DNA segments modelled by the quasiperiodic chains. We compared the DOS spectra found for the quasiperiodic structure to those using a sequence of natural DNA, as part of the human chromosome Ch22, with a remarkable concordance, as far as the RS structure is concerned. The electronic spectrum shows several peaks, corresponding to localized states, as well as a striking self-similar aspect.     

Surface‐enhanced Raman scattering‐based approach for DNA detection at low concentrations via polyvinyl alcohol‐protected silver grasslike patterns

A simple method is demonstrated to detect DNA at low concentrations on the basis of surface‐enhanced Raman scattering (SERS) via polyvinyl alcohol‐protected silver grasslike patterns (PVA‐Ag GPs) grown on the surface of the common Al substrate. By the SERS measurements of sodium citrate and thymine, the PVA‐Ag GPs are shown to be an excellent SERS substrate with good activity, stability and reproducibility. With the use of the tested molecule of thymine, the enhancement factor of the PVA‐Ag GPs is up to ~1.4 × 10⁸. The PVA‐Ag GPs are also shown to be an excellent SERS substrate with good biocompatibility for DNA detection, and the detection limit is down to ~10⁻⁵ mg/g. Meanwhile, the assignations of the Raman bands and the adsorption behaviors of the DNA molecules are also analyzed. In this work, the geometry optimization and the wavenumber analysis of adenine–Ag and guanine–Ag complexes for the ground states are performed using density functional theory, B3LYP functional and the LanL2DZ basis set. The transition energies and the oscillator strengths of adenine–Ag and guanine–Ag for the lowest six singlet excited states were calculated by using the time‐dependent density functional theory method with the same functional and basis set. The results show that the charge transfer in the adenine–Ag and guanine–Ag complexes should be the chemical factor for the SERS of the DNA molecules. Lastly, this method may be employed in large‐scale preparation of substrates that have been widely applied in the Raman analysis of DNA because the fabrication process is simple and inexpensive. Copyright © 2011 John Wiley & Sons, Ltd.     

Vacuum ultraviolet ellipsometry investigation of ultrathin organic films and their heterostructures

Thin layers and multilayer structures of the DNA bases guanine and cytosine on ZnO substrates were prepared by organic molecular beam deposition under ultra-high vacuum conditions and measured in situ by means of vacuum ultraviolet spectroscopic ellipsometry at the synchrotron source BESSY. Using the dielectric function of the individual layers the optical response of the G/C and C/G heterostructures was modeled. Deviations between simulated and experimental data were mainly attributed to the ordering of cytosine over guanine in the G/C and C/G structures and to the influence of the substrate.     

Newton-Leibniz integration for ket-bra operators in quantum mechanics (IV)—Integrations within Weyl ordered product of operators and their applications

We show that the technique of integration within normal ordering of operators [Hong-yi Fan, Hai-liang Lu, Yue Fan, Ann. Phys. 321 (2006) 480-494] applied to tackling Newton-Leibniz integration over ket-bra projection operators, can be generalized to the technique of integration within Weyl ordered product (IWWOP) of operators. The Weyl ordering symbol is introduced to find the Wigner operator’s Weyl ordering form Δ(p,q) =  δ(p − P)δ(q − Q) , and to find operators’ Weyl ordered expansion formula. A remarkable property is that Weyl ordering of operators is covariant under similarity transformation, so it has many applications in quantum statistics and signal analysis. Thus the invention of the IWWOP technique promotes the progress of Dirac’s symbolic method.     

核酸碱基和核苷的高效液相色谱——表面增强拉曼光谱在线联机分析研究

本文将反相高效液相色谱(RP——HPLC)与表面增强拉曼光谱(SERS)联机,对三个核嘧啶、四个核嘌呤和两个核嘧啶及其核苷混合物进行在线联机分析研究。在流动条件下,对影响 SERS 测定的因素,如激光照射、温度、pH 值、流速、记忆效应,以及联机系统的接口装置等进行了讨论。文中给出了联机测得的三维和二维 SERS 色谱图。     

Entanglement in One-Dimensional Anderson Model with Long-Range Correlated Disorder

By using the measure of concurrence, the entanglement of the ground state in the one-dimensional Anderson model is studied with consideration of the long-range correlations. Three kinds of correlations are discussed. We compare the effects of the long-rang Gaussian and power-law correlations between the site energies on the concurrence, and demonstrate the existence of the band structure of the concurrence in the power-law case. The emergence of the sharp kink on the concurrence curve shown in the intraband or in the interband indicates the position at which the localization extent of the state may have the severe variation. We use the Rudin-Shapiro model to describe the site energy distribution of the nucleotides of the DNA chain： guanine （G）, adenine （A）, cytosine（C）, thymine （T）. This model is a tetradic quasiperiodic sequence and is shown to be long-range correlated. Our results show that correlations between the site energies increase the concurrences.     

ARPES and STS investigation of noble metal Shockley states: Confinement in vicinal Au(1 1 1) surfaces and self-organized nanostructures

Spectroscopic effects associated with the superperiodic surface structure have been observed in Au(1 1 1) vicinal surfaces and nanostructured systems. In the vicinal Au(23 23 21) surface, high resolution angle resolved photoemission spectroscopy shows the opening of several gaps in the surface band structure, whereas scanning tunneling spectroscopy reveals the energy dependence of the electronic density. These combined spectroscopic data allow to determine the reconstruction potential by deducing their first Fourier components. We also demonstrate that due to the peculiar growth on this Au vicinal surface, we can obtain a self-assembled superlattice of triangular Ag islands. The high ordering of the nanostructures leads to homogenous electronic properties.     

A first-principles study on DNA sequencing using graphene quantum dot

In this paper, we propose a new device based on graphene quantum dot (GQD) to interrogate nucleotide in a DNA molecule. We have conducted non-equilibrium Green’s function together with the density functional theory simulations to show zero transmission curves for a system which includes nucleobases. The simulation results indicates several characteristic peaks in the electron transmission curve for any single base on the quantum dot which can be utilized to distinguish between bases. Number and positions of the peaks, as well as their amplitude, depend on the type of the bases and their relative position to the dot. Thus, this structure shows remarkable distinction characteristic in zero bias transmission curve and can yield minimal ambiguity in the adenine, cytosine, guanine and thymine nucleotide detection. Due to stacking of nucleobases on the graphene and consequent attenuation in directional fluctuations, stable measurement is also expected.     

Sonoelectrochemical determination of nucleosides and nucleotides

We summarize our recent work on sonovoltammetric studies of adenine, guanine, thymine, cytosine and their corresponding nucleosides and nucleotides. Ultrasound is found to be an excellent tool to enhance the reliability of determinations of purine and pyrimidine derivatives and can lead to improved analytical performance characteristics and lower detection limits.