Time-dependent DNA condensation induced by amyloid beta-peptide

The major protein component of the amyloid deposition in Alzheimer's disease is a 39-43 residue peptide, amyloid beta (A beta). A beta is toxic to neurons, although the mechanism of neurodegeneration is uncertain. Evidence exists for non-B DNA conformation in the hippocampus of Alzheimer's disease brains, and A beta was reportedly able to transform DNA conformation in vitro. In this study, we found that DNA conformation was altered in the presence of A beta, and A beta induced DNA condensation in a time-dependent manner. Furthermore, A beta sheets, serving as condensation nuclei, were crucial for DNA condensation, and Cu2+ and Zn2+ ions inhibited A beta sheet-induced DNA condensation. Our results suggest DNA condensation as a mechanism of A beta toxicity.

Surface-Relevant Regulable DNA Toroids Induced by Dopamine

Dopamine (2-(3,4-dihydroxyphenyl)ethylamine) is known as a natural chemical neurotransmitter and is also a cytotoxic and genotoxic molecule for cell apoptosis. In this work, the interaction of DNA with dopamine was investigated. Though the electrostatic interaction of DNA and dopamine was weak in aqueous solution, dopamine condensed circular pBR322 DNA into toroids on the mica surface cooperatively with ethanol. The formed DNA toroids came from the shrinking of DNA that was driven by ethanol-enhanced DNA-dopamine electrostatic interaction. The size of the DNA toroids could be modulated by varying the concentration of dopamine. This study offers useful information about the DNA condensation induced by monovalent cations and the sample preparation for AFM measurement and application.

The structural transition of DNA-Tris(1,10-phenanthroline) cobalt(III) complexes in ethanol-water solution

The interaction of DNA with Tris(1,10-phenanthroline) cobalt(III) was studied by means of atomic force microscopy. Changes in the morphologies of DNA complex in the presence of ethanol may well indicate the crucial role of electrostatic force in causing DNA condensation. With the increase of the concentration of ethanol, electrostatic interaction is enhanced corresponding to a lower dielectric constant. Counterions condense along the sugar phosphate backbone of DNA when e is lowered and the phosphate charge density can thus be neutralized to the level of DNA condensation. Electroanalytical measurement of DNA condensed with Co(phen)(3)(3+) in ethanol solution indicated that intercalating reaction remains existing. According to both the microscopic and spectroscopic results, it can be found that no secondary structure transition occurs upon DNA condensing. B-A conformation transition takes place at more than 60% ethanol solution.

Electrodissolution of Inorganic ions/DNA Multilayer Film for Tunable DNA Release

A layer-by-layer film composed of DNA and inorganic zirconium ion (Zr4+) was fabricated on the surface of gold thin film, and an electric field triggered disintegration of the multilayer film was studied by using electrochemical surface plasmon resonance (EC-SPR). EC-SPR results demonstrated that the film was disassembled upon the application of an electric field and the disassembly rate varied with the applied potential, leading to the controlled release of DNA. The electrodissolution could be switched off by removing the electric potential and reactivated by reapplying the potential.

DNA-Templated Gold Nanoparticles Formation

The interaction between HAuCl4 and DNA has enabled creation of DNA-templated gold nanoparticles without formation of large nanoparticles. It was found that spheral DNA-HAuCl4 hybrid of 8.7 nm in diameter, flower-like DNA-HAuCl4 hybrid, nanoparticles chains and nanoparticles network of DNA-HAuCl4 hybrid could be obtained by varying the reaction conditions, including DNA concentration and reaction temperature. The intermediate product was investigated by shortening the reaction time of DNA and HAuCl4, and the obtained nanoparticles preserved a small DNA segment, which indicated that the reaction between DNA and HAuCl4 had a process.

Effects of bridge ions, DNA species, and developing temperature on flat-lying DNA monolayers

Recently, we have successfully constructed flat-lying DNA monolayers on a mica surface (J. Phys. Chem. B 2006, 110, 10792-10798). In this work, the effects of various factors including bridge ions, DNA species, and developing temperature on the configuration of DNA monolayers have been investigated by atomic force microscopy (AFM) in detail. AFM results show that the species of bridge ions and developing temperature play a crucial role during the formation process. For example, the divalent cation Zn2+ resulted in many DNA chains stuck side by side in the monolayers due to the strong interactions between it and DNA's bases or the mica surface. Most DNA chain's conglutinations disappeared when the developing temperature was higher than 40 degrees C. Cd2+ and Ca2+ produced more compact DNA monolayers with some obvious aggregations, especially for the DNA monolayers constructed by using Ca2+ as the bridge ion. Co2+ produced well-ordered, flat-lying DNA monolayers similar to that of Mg2+. Furthermore, it was found that the flat-lying DNA monolayers could still form on a mica surface when plasmid DNA pBR 322 and linear DNA pBR 322/Pst I were used as the DNA source. Whereas, it was hard to form DNA monolayers on a (3-aminopropyl)triethoxysilane-mica surface because the strong interactions between DNA and substrate prevented the lateral movement of DNA molecules.

Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution

Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nano-device applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mechanism. We report here, for the first time, that DNA destabilization and conformational transition induced by SWNTs are sequence-dependent. Contrasting changes for SWNTs binding to poly[dGdC]:poly[dGdC] and poly[dAdT]:poly[dAdT] were observed. For GC homopolymer, DNA melting temperature was decreased 40 degrees C by SWNTs but no change for AT-DNA. SWNTs can induce B-A transition for GC-DNA but AT-DNA resisted the transition. Our circular dichroism, competitive binding assay and triplex destabilization studies provide direct evidence that SWNTs induce DNA B-A transition in solution and they bind to the DNA major groove with GC preference.

A novel strategy to construct a flat-lying DNA monolayer on a mica surface

Flat-lying, densely packed DNA monolayers in which DNA chains are well organized have been successfully constructed on a mica surface by dropping a droplet of a DNA solution on a freshly cleaved mica surface and subsequently transferring the mica to ultrapure water for developing. The formation kinetics of such monolayers was studied by tapping mode atomic force microscopy (TMAFM) technique. A series of TMAFM images of DNA films obtained at various developing times show that before the sample was immersed into water for developing the DNA chains always seriously aggregated by contacting, crossing, or overlapping and formed large-scale networks on the mica surface. During developing, the fibers of DNA networks gradually dispersed into many smaller fibers up to single DNA chains. At the same time, the fibers or DNA chains also experienced rearrangement to decrease electrostatic repulsion and interfacial Gibbs free energy. Finally, a flat-lying, densely packed DNA monolayer was formed. A formation mechanism of the DNA monolayers was proposed that consists of aggregation, dispersion, and rearrangement. The effects of both DNA and Mg2+ concentration in the formation solution on DNA monolayer formation were also investigated in detail.

Liposome-mediated conformation transition of DNA detected by molecular probe: methyl green

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper, we take methyl green (MG) as a probe molecule to detect the conformational change of DNA molecule induced by dimethyldioctadecylammonium bromide (DDAB) liposomes before the condensation process of DNA begins. DDAB-induced DNA topology changes were investigated by cyclic voltammetry (CV), circular dichroism (CD) and UV-VIS spectrometry. We find that upon binding to DNA, positively charged liposomes induce a conformational transition of DNA molecules from the native B-form to the C motif. Conformational transition in DNA results in the binding modes of MG to DNA, changing and being isolated from DNA to the solution. More stable complexes are formed between DNA and DDAB. That is also proved by the melting study of DNA.

Conformational transition of DNA induced by cationic lipid vesicle in acidic solution: spectroscopy investigation

The conformational transition of DNA induced by the interaction between DNA and a cationic lipid vesicle, didodecyidimethylammonium bromide (DDAB), had been investigated by circular dichroism (CD) and UV spectroscopy methods. We used singular value decomposition least squares method (SVDLS) to analyze the experimental CD spectra. Although pH value influenced the conformation of DNA in solution, the results showed that upon binding to double helical DNA, positively charged liposomes induced a conformational transition of DNA molecules from the native B-form to more compact conformations. At the same time, no obvious conformational changes occurred at single-strand DNA (ssDNA). While the cationic lipid vesicles and double-strand DNA (dsDNA) were mixed at a high molar ratio of DDAB vesicles to dsDNA, the conformation of dsDNA transformed from the B-form to the C-form resulting in an increase in duplex stability (DeltaT(m) = 8 +/- 0.4 degreesC). An increasing in T-m was also observed while the cationic lipid vesicles interacted with ssDNA.

Voltammetric and spectroscopic studies on methyl green and cationic lipid bound to calf thymus DNA

DNA interaction with cationic lipids promises to be a versatile and effective synthetic transfection agent. This paper presents the study on binding of a simple artifical cationic lipid, cetyltrimethylammonium bromide (CTAB), to calf thymus DNA (CT DNA) prior to the condensation process, taking methyl green (MG) as a probe. The results show that the CTAB binds to DNA through electrostatic interaction forming a hydrophobic complex, thus changing the micro-environment of duplex of DNA, so the binding state of MG and DNA is changed, and a complex CTAB-CT DNA-MG is formed. This fact suggests a new way to mediate the conformation of molecular assemblies of DNA and lipids. (C) 2000 Elsevier Science B.V. All rights reserved.

Molecular Dynamics Simulation of Peeling a DNA Molecule on Substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

Metric representation of DNA sequences

A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.

Recurrence plot analysis of DNA sequences

Recurrence plot technique of DNA sequences is established on metric representation and employed to analyze correlation structure of nucleotide strings. It is found that, in the transference of nucleotide strings, a human DNA fragment has a major correlation distance, but a yeast chromosome's correlation distance has a constant increasing. (C) 2004 Elsevier B.V All rights reserved.

Numerical simulation of condensation of bubbles under microgravity conditions by moving mesh method in the double-staggered grid

A numerical 2D method for simulation of two-phase flows including phase change under microgravity conditions is presented in this paper, with a level set method being coupled with the moving mesh method in the double-staggered grid systems. When the grid lines bend very much in a curvilinear grid, great errors may be generated by using the collocated grid or the staggered grid. So the double-staggered grid was adopted in this paper. The level set method is used to track the liquid-vapor interface. The numerical analysis is fulfilled by solving the Navier-Stokes equations using the SIMPLER method, and the surface tension force is modeled by a continuum surface force approximation. A comparison of the numerical results obtained with different numerical strategies shows that the double-staggered grid moving-mesh method presented in this paper is more accurate than that used previously in the collocated grid system. Based on the method presented in this paper, the condensation of a single bubble in the cold water under different level of gravity is simulated. The results show that the condensation process under the normal gravity condition is different from the condensation process under microgravity conditions. The whole condensation time is much longer under the normal gravity than under the microgravity conditions.