In vitro synthesis of uniform poly(dG)–poly(dC) by Klenow exo(−) fragment of polymerase I

In this paper, we describe a production procedure of the one-to-one double helical complex of poly(dG)–poly(dC), characterized by a well-defined length (up to 10 kb) and narrow size distribution of molecules. Direct evidence of strands slippage during poly(dG)–poly(dC) synthesis by Klenow exo(−) fragment of polymerase I is obtained by fluorescence resonance energy transfer (FRET). We show that the polymer extension results in an increase in the separation distance between fluorescent dyes attached to 5′ ends of the strands in time and, as a result, losing communication between the dyes via FRET. Analysis of the products of the early steps of the synthesis by high-performance liquid chromatography and mass spectroscopy suggest that only one nucleotide is added to each of the strand composing poly(dG)–poly(dC) in the elementary step of the polymer extension. We show that proper pairing of a base at the 3′ end of the primer strand with a base in sequence of the template strand is required for initiation of the synthesis. If the 3′ end nucleotide in either poly(dG) or poly(dC) strand is substituted for A, the polymer does not grow. Introduction of the T-nucleotide into the complementary strand to permit pairing with A-nucleotide results in the restoration of the synthesis. The data reported here correspond with a slippage model of replication, which includes the formation of loops on the 3′ ends of both strands composing poly(dG)–poly(dC) and their migration over long-molecular distances (μm) to 5′ ends of the strands

Local vibrations in real crystals with combined defects

The conditions of formation and the main characteristics of local vibrations due to the presence of light impurities Al, Mg, and Mn in the bulk and on the close-packed [111] surface of the fcc crystal lattice of silver are investigated. The influence of surface roughness is analyzed. Analytical approximations are obtained which describe the frequency and intensity of the local vibrations at the impurity atom and its nearest neighborhood to high accuracy. The proposed analytical approximations provide a practical way of determining the parameters of the defect structure and the interatomic interactions from the experimentally determined characteristics of the local vibrations

Long-lived fluorescence of homopolymeric guanine–cytosine DNA duplexes

International audienceThe fluorescence spectrum of the homopolymeric double helix poly(dG)·poly(dC) is dominated by emission decaying on the nanosecond time-scale, as previously reported for the alternating homologue poly(dGdC)·poly(dGdC). Thus, energy trapping over long periods of time is a common feature of GC duplexes which contrast with AT duplexes. The impact of such behaviour on DNA photodamage needs to be evaluated

Optical Properties of Guanine Nanowires: Experimental and Theoretical Study

International audienceLong nanowires formed by ca. 800 guanine tetrads (G4-wires) are studied in phosphate buffer containing sodium cations. Their room temperature optical properties are compared to those of the monomeric chromophore 2-deoxyguanine monophosphate (dGMP). When going from dGMP to G4-wires, both the absorption and the fluorescence spectra change. Moreover, the fluorescence quantum yield increases by a factor of 7.3 whereas the average fluorescence lifetime increases by more than 2 orders of magnitude, indicating emission associated with weakly allowed transitions. The behavior of G4-wires is interpreted in the light of a theoretical study performed in the frame of the exciton theory combining data from molecular dynamics and quantum chemistry. These calculations, carried out for a quadruplex composed of three tetrads, reveal the existence of various exciton states having different energies and oscillator strengths. The degree of delocalization of the quadruplex Franck−Condon excited states is larger than those found for longer duplexes following the same methodology. The slower excited-state relaxation in G4-wires compared to dGMP is explained by emission from exciton states, possibly limited on individual tetrads, whose coherence is reserved by the reduced mobility of guanines due to multiple Hoogsteen hydrogen bonds

Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin–biotin recognition

We describe a method for the preparation of novel long (hundreds of nanometers), uniform, inter-molecular G4-DNA molecules composed of four parallel G-strands. The only long continuous G4-DNA reported so far are intra-molecular structures made of a single G-strand. To enable a tetra-molecular assembly of the G-strands we developed a novel approach based on avidin–biotin biological recognition. The steps of the G4-DNA production include: (i) Enzymatic synthesis of long poly(dG)-poly(dC) molecules with biotinylated poly(dG)-strand; (ii) Formation of a complex between avidin-tetramer and four biotinylated poly(dG)-poly(dC) molecules; (iii) Separation of the poly(dC) strands from the poly(dG)-strands, which are connected to the avidin; (iv) Assembly of the four G-strands attached to the avidin into tetra-molecular G4-DNA. The average contour length of the formed structures, as measured by AFM, is equal to that of the initial poly(dG)-poly(dC) molecules, suggesting a tetra-molecular mechanism of the G-strands assembly. The height of tetra-molecular G4-nanostructures is larger than that of mono-molecular G4-DNA molecules having similar contour length. The CD spectra of the tetra- and mono-molecular G4-DNA are markedly different, suggesting different structural organization of these two types of molecules. The tetra-molecular G4-DNA nanostructures showed clear electrical polarizability. This suggests that they may be useful for molecular electronics

Loffe-Regel' crossover and boson peaks in disordered solid solutions and similar anomalies in heterogeneous crystalline structures

Low-frequency features of the phonon spectra of disordered solid solutions and heterogeneous crystalline structures are analyzed at the microscopic level. It is shown that boson-peak type excitations can arise in disordered solid solutions whose sites have only translational degrees of freedom. Thus it is established that such excitations appear mainly because of the additional positional dispersion of sound waves which is due to the disordering. The influence of boson-peak excitations on the low-temperature specific heat is investigated. It is found that in a number of cases the specific heat is more sensitive to excitations of this kind than the low-frequency density of states is. It is shown that anomalies similar to Ioffe-Regel' crossover and boson peaks can also arise in disordered heterogeneous crystalline structures with a complicated lattice

Delocalizing effect of the Hubbard repulsion for electrons on a two-dimensional disordered lattice

We study numerically the ground-state properties of the repulsive Hubbard model for spin-1/2 electrons on two-dimensional lattices with disordered on-site energies. The projector quantum Monte Carlo method is used to obtain very accurate values of the ground-state charge density distributions with $N_p$ and $N_p+1$ particles. The difference in these charge densities allows us to study the localization properties of an added particle. The results obtained at quarter-filling on finite clusters show that the Hubbard repulsion has a strong delocalizing effect on the electrons in disordered 2D lattices. However, numerical restrictions do not allow us to reach a definite conclusion about the existence of a metal-insulator transition in the thermodynamic limit in two-dimensions.Comment: revtex, 7 pages, 7 figure

Effect of particle size on the flocculation behaviour of ultra-fine clays in salt solutions

The Athabasca oil sands deposit in Alberta contains ~5 \u3a7 10\u2079 m\ub3 of bitumen accessible by surface mining. During bitumen separation from the mined ore, ultra-fine (<300 nm) aluminosilicate clays only a few layers thick (U/F) are mobilized and become dispersed in the process water. In this water containing dissolved salts from natural deposits, U/F are capable of forming thixotropic gels. The consequence of this is the production of large volumes of mature fine tailings (MFT) with a high water holding capacity. For mine planning purposes, the objective of predicting and possibly mitigating MFT formation requires an understanding of the colloidal behaviour of U/F particles in salt solutions. In this work, photon correlation spectroscopy and the deuterium NMR method are used to provide an insight into the U/F floc formation process. These results are correlated with conventional analysis of settling data.NRC publication: Ye