Conformation Of DNA Molecules Research Articles

Rapid detection of trace Hg~(2+) in animal matrix by specific DNA electrochemical sensor

A highly specific electrochemical biosensor based on T-Hg~(2+)-T structure for fast screening trace Hg~(2+) in complex animal drug matrix was constructed by cyclic voltammetry(CV) and differential pulse voltammetry(DPV). In the presence of Hg~(2+), it can be specifically binded to the T base of DNA sequence on the surface of modified gold electrode, which changes the conformation of DNA molecule and the electrochemical signal. The concentration ratio of EDC/NHS, the concentration ratio of FC-DNA and the reaction time of the biosensor were optimized by the index of sensitivity and reproducibility in CV. The results showed that the stability of the biosensor was good within 3 days(RSD≤1.3%), the difference between batches was low(RSD=4.7%), and the specificity of the biosensor was high in the presence of interfering ions(As~(3+), Cd~(2+), Cu~(2+), Pb~(2+), Zn~(2+) and Fe~(3+)). DPV results showed that the peak current signal value has a linear relationship with the lgC_((Hg)) over a concentration range from 0.1 nmol·L~(-1) to 1.0 μmol·L~(-1) with a detection limit of 0.066 nmol·L~(-1). Finally, the recovery rate tested in the matrix of animal medicine was satisfactory as 99.17%-101.3%, which can meet the needs of the determination of trace Hg~(2+) in the matrix of Bombyx Batryticatus, and provide a new idea for the rapid screening of trace heavy metals in the matrix of other types of complex traditional Chinese medicine.

Study of the effect of argon glow discharge irradiation on the conformation of DNA molecules using laser spectroscopy methods

The aim of this work is to study the photochemical processes of hydrolysis of biomacromolecules, using the example of DNA in DNA and DNA-Polyethylene glycol (model of nucleoprotein) solutions. The processes induced by the line spectrum of an argon glow discharge lamp (AGDL) (700–1800 nm, 1.7–0.7 eV) have been studied by spectrophotometry, light scattering, turbidimetry, and spectrofluorimetry. It is shown that acridine orange (AO) intercalated in DNA is a good indicator of pH, i.e. of the presence of H3O+ ions in DNA solutions. H3O+ ions quench AO fluorescence and, in addition, eject it from the DNA in the solution. Using the methods of laser spectroscopy (light scattering, fluorescence, and resonance energy transfer) and spectrophotometry, we have observed hydrolysis of water solutions and of glycosidic and phosphodiester bonds in DNA and DNA-polyethylene glycol water solutions induced by near-infrared (700–1800 nm, (AGDL)) irradiation. The method is based on the difference between cancer and healthy cells because a normal cell has a perfect DNA repair system that makes near-infrared photo-irradiation non-invasive for them and lethal for a cancer cell. Using the turbidimetry method, the average size of the DNA aggregates from the calf thymus in a 150 mg ml−1 polyethylene glycol solution was determined and it is 250 nm in approximation that the aggregate has a spherical form. Aggregated DNA macromolecules are in B-form and the aggregate contains 12 · 106 b.p.

Fabrication of Graphene Nanopores and a Preliminary Study onλ-DNA Translocation

Nanopore sequencing is among the most promising technologies to achieve the goals of the "$1,000 Genome." Two major types of nanopores have been extensively investigated, protein and silicon-based solid-state nanopores. However, protein pores are short-lived and the length of solid-state nanopores is much larger than the distance between adjacent bases, resulting in incapability to discriminate individual bases along the single-stranded DNA molecules. In this paper, we report λ-DNA translocations through graphene nanopore. A large nanopore with diameter of about 30 nm on silicon nitride substrates were first fabricated using focused ion beam(FIB) system under the beam current of 2 pA, accelerating voltage of 30 kV and sculpting time of 1 s. Individual graphene membranes were suspended onto the substrates to cover the large pore, and nanopores with a diameter less than 10 nm are sculpted in the graphene sheet by focused electron beam(FEB) from a transmission electron microscope(TEM) under a 400 kx magnification times and 300 kV accelerating voltage at 1×105~5×105A/m2 current density for 2~3 min. The edges of these graphene nanopores became smoother and sharper when the temperature was increased to about 450 ℃, which might help to lower interactions between graphene nanopores and the analytes. The signals of DNA translocation through graphene nanopores had been recorded using a patch clamp amplifier at 10 kHz sampling frequency filtered at 5 kHz via an integrated four-pole low-pass Bessel filter. Analyses of the DNA translocation current traces indicated that different conformations of DNA molecules may exist during entrance into nanopores. In addition, our overall detection platform had a low noise amplitude of around 10 pA, which allowed more sensitive signal detection. Taken together, our observations demonstrate that graphene nanopores are feasible for DNA sensing, leading a forward step towards single-molecule DNA sequencing using monolayered graphene nanopores.

Effect of chain length on the conformation and friction behaviour of DNA

Four double-stranded DNA films with different chain lengths were prepared on 3-aminopropyltriethoxysilane (APS)-modified mica surfaces in the NaCl solution with concentration ranging from 0.001 to 0.1 M. By using an atomic force microscope, the force-distance curves and friction behaviour of each DNA film were studied in the NaCl solution that was used in the sample preparation. When adsorbed on mica as films in salt solution, the conformation of DNA molecules would be a combination of loops and “train-like”. As the chain length increased from 50 to 20000 bp, the extension rate of DNA film increased from 7.1 to 11.5 in 0.001 mol/L NaCl solution, which suggested that the DNA molecule with long chain likely resulted in more extended conformation. In addition, under low normal load, low NaCl concentration could increase the friction of DNA film and the chain length revealed insignificant effect on the friction force of DNA film. Therefore, long chain DNA with low salt concentration is more conducive to the nanopore sequencing process, since extended conformation can make DNA molecules easier to reach into nanopore and the high friction can reduce the translocation speed. These results may benefit the development of the third-generation sequencing technique based on nanopore.

Precision platform for convex lens-induced confinement microscopy

We present the conception, fabrication, and demonstration of a versatile, computer-controlled microscopy device which transforms a standard inverted fluorescence microscope into a precision single-molecule imaging station. The device uses the principle of convex lens-induced confinement [S. R. Leslie, A. P. Fields, and A. E. Cohen, Anal. Chem. 82, 6224 (2010)], which employs a tunable imaging chamber to enhance background rejection and extend diffusion-limited observation periods. Using nanopositioning stages, this device achieves repeatable and dynamic control over the geometry of the sample chamber on scales as small as the size of individual molecules, enabling regulation of their configurations and dynamics. Using microfluidics, this device enables serial insertion as well as sample recovery, facilitating temporally controlled, high-throughput measurements of multiple reagents. We report on the simulation and experimental characterization of this tunable chamber geometry, and its influence upon the diffusion and conformations of DNA molecules over extended observation periods. This new microscopy platform has the potential to capture, probe, and influence the configurations of single molecules, with dramatically improved imaging conditions in comparison to existing technologies. These capabilities are of immediate interest to a wide range of research and industry sectors in biotechnology, biophysics, materials, and chemistry.

Microwave-Assisted Synthesis of Arene Ruthenium(II) Complex as Apoptosis Inducer of A549 Cells

An arene ruthenium(ii) complex coordinated with 2-(2-chlorophenyl)-1H-imidazo[4,5-f][1,10]phenanthroline, [(η6-C6H6)Ru(o-ClPIP)Cl]Cl (1), has been prepared by using microwave-assisted synthesis technology. The anti-tumour activity of this complex against various tumour cells has been evaluated by MTT assay and the results show that complex 1 exhibits selective inhibitory activity against the growth of human lung adenocarcinoma A549 cells with IC50 = 31.58 μM. Further studies by flow cytometric analysis showed that apoptosis of A549 cells was observed when dealt with complex 1. Furthermore, complex 1 exhibits excellent binding affinity with DNA molecules which was confirmed by spectroscopy methods, as well viscosity and melting point experiments. As a result, the conformation of DNA molecules was disturbed by complex 1.

Molecular Imaging of Slip in Entangled DNA Solution

This work obtains the first molecular imaging of wall slip in entangled solutions. Using a combination of confocal fluorescence microscopy and rheometry, molecular images were captured in the nonlinear response regime of entangled DNA solutions. Conformations of DNA molecules were imaged during shear to correlate with the magnitude of wall slip. Interfacial chain disentanglement results in wall slip beyond the stress overshoot. Sufficient disentanglement can produce tumbling of individual DNA in the entangled solutions.

Hydrodynamic properties of DNA and DNA–lipid complex in an elongational flow field

The aim of this study was to determine the difference between hydrodynamic properties of DNA–cetyltrimethylammonium (CTA) complex and those of DNA, which may be related to the difference in fibre-forming ability of DNA–CTA from that of DNA. Responses of DNA and DNA–CTA complex to an elongational flow field were investigated. In both solution systems, results suggesting a coil–stretch transition were obtained. From a critical strain rate value, the radius of gyration of DNA–CTA molecules in ethanol–glycerol solution was revealed to be 0.3–0.5 times of that of DNA in aqueous NaCl solution. Shear viscosity of DNA–CTA solution was much smaller than that of DNA solution, also suggesting a smaller size of DNA–CTA in ethanol–glycerol solution than that of DNA in aqueous NaCl solution. The plateau birefringence value of the DNA–CTA system, a parameter that indicates the local molecular conformation and the molecular arrangement, was only about 1/10 of that of the DNA system. There is an empirically determined molecular model of DNA–CTA complex in which a DNA molecule is sheathed by a cylindrical crust made of CTA chains. This structure reduces the DNA molecular density in a pure elongational flow field region but cannot explain the observed reduction of birefringence intensity. The small plateau birefringence value of DNA–CTA compared with that of DNA was attributed to the reduced molecular polarizability by the particular conformation of DNA molecules and CTA chains in the DNA–CTA system such as that expected by the conformational models.

Elongation/compaction of giant DNA caused by depletion interaction with a flexible polymer

Structural changes in giant DNA induced by the addition of the flexible polymer Polyethylene Glycol (PEG) were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule transition, whereas in concentrated solution, DNA molecules exhibit an extended conformation via macroscopic phase segregation. The long-axis length of the stretched state in DNA is about 10(3) times larger than that of the compact state. Phase segregation at high DNA concentrations occurs at lower PEG concentrations than the compaction at low DNA concentrations. These opposite changes in the conformation of DNA molecule are interpreted in terms of the free energy, including depletion interaction.

Conformational changes of DNA molecules in interactions with bioactive compounds. I. Influence of metal ions on the conformation of DNA molecules in solution

The influence of metal ions of different valence on the conformation of DNA molecule in solution has been studied. The influence of concentration and charge of counterions on the volume, persistent length and secondary structure of the macromolecules was analyzed. An assessment of the permeability of DNA coil for the solvent at different values of ionic strength of the solution was made. The state of the DNA molecule in solutions with high ionic strengths, when the presence of certain ions causes sharp changes in optical anisotropy of the macromolecule, is considered in detail.

Dielectrophoresis of nanoscale double-stranded DNA and humidity effects on its electrical conductivity

The dielectrophoresis method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. The method gives a high yield of trapping single or a few molecules only which enables transport measurements at the single molecule level. Electrical conductivity of individual 140-nm-long DNA molecules was measured, showing insulating behavior in dry conditions. In contrast, clear enhancement of conductivity was observed in moist conditions, relating to the interplay between the conformation of DNA molecules and their conductivity.

Effect of Flow on Complex Biological Macromolecules in Microfluidic Devices

Understanding the transport, orientation, and deformation of biological macromolecules by flow is important in designing microfluidic devices. In this study, epi-fluorescence microscopy was used to characterize the behavior of macromolecules in flow in a microfluidic device, particularly how the flow affects the conformation of the molecules. The microfluidic flow path consists of a large, inlet reservoir connected to a long, rectangular channel followed by a large downstream reservoir. The flow contains both regions of high elongation (along the centerline as the fluid converges from the upstream reservoir into the channel) and shear (in the channel near the walls). Solutions of λ-DNA labeled with a fluorescent probe were first characterized rheologically to determine fluid relaxation times, then introduced into the microfluidic device. Images of the DNA conformation in the device were captured through an epi-fluorescent microscope. The conformation of DNA molecules under flow showed tremendous heterogeneity, as observed by Chu [7,12] and co-workers in pure shear and pure elongational flows. Histograms of the distribution of conformations were measured along the channel centerline as a function of axial position and revealed dramatic stretching of the molecules due to the converging flow followed by an eventual return to equilibrium coil size far downstream of the channel entry. The importance of shear was probed via a series of measurements near the channel centerline and near the channel wall. High shear rates near the channel wall also resulted in dramatic stretching of the molecules, and may result in chain scission of the macromolecules.

Elongational flow studies of the conformation of DNA molecules in the globular state

Elongational flow studies of the conformation of DNA molecules in the globular state

Applications for atomic force microscopy of DNA

Tapping mode atomic force microscopy (AFM) of DNA in propanol, dry helium, and aqueous buffer each have specific applications. Resolution is best in propanol, which precipitates and immobilizes the DNA and provides a fluid imaging environment where adhesive forces are minimized. Resolution on exceptional images of DNA appears to be approximately 2 nm, sufficient to see helix turns in detail, but the smallest substructures typically seen on DNA in propanol are approximately 6-10 nm in size. Tapping AFM in dry helium provides a convenient way of imaging such things as conformations of DNA molecules and positions of proteins on DNA. Images of single-stranded DNA and RecA-DNA complexes are presented. In aqueous buffer DNA molecules as small as 300 bp have been imaged even when in motion. Images are presented of the changes in shape and position of circular plasmid DNA molecules.

The Effect of Metal Ions of Differentvalences on Conformation of DNA Molecules

The Effect of Metal Ions of Differentvalences on Conformation of DNA Molecules

π-Electronic Contribution to the Conformation of DNA

The contribution from π-electrons in base pairs to the conformation of DNA molecule is studied. As model substances, homo-oligomers of stacked purine and pyrimidine base pairs are considered. By the perturbation method in the LCAO MO scheme assuming the zero-differential overlap between monomers, the intermonomer interaction energy is calculated as a function of the helical angle θ between monomers and the monomer-to-monomer distance p along the helix axis. The effect of the overlap is taken into account by the short range repulsion term estimated by a semiempirical formula. The minimum in the interaction energy occurs at p =3.7A and θ=80° for the pentamer of guanine-cytosine pairs, and at p =3.4A and θ=58.5° for that of adenine-uracil. It is discussed why calculated θ-value differs from the experimental one 36°.