Transition Of DNA Molecules Research Articles

Manipulating and Visualizing Molecular Interactions in Customized Nanoscale Spaces.

We present a dynamically adjustable nanofluidic platform for formatting the conformations of and visualizing the interaction kinetics between biomolecules in solution, offering new time resolution and control of the reaction processes. This platform extends convex lens-induced confinement (CLiC), a technique for imaging molecules under confinement, by introducing a system for in situ modification of the chemical environment; this system uses a deep microchannel to diffusively exchange reagents within the nanoscale imaging region, whose height is fixed by a nanopost array. To illustrate, we visualize and manipulate salt-induced, surfactant-induced, and enzyme-induced reactions between small-molecule reagents and DNA molecules, where the conformations of the DNA molecules are formatted by the imposed nanoscale confinement. In response to dynamically modifying the local salt concentration, we report two salt-induced transitions in DNA molecules which occur on separate time scales: a rapid change in polymer extension due to modified local ionic screening and a gradual change in polymer brightness, reflecting release of intercalated YOYO-1 dye. Our time-resolved measurements provide new insights into the influence of YOYO-1 dye on polymer stiffness. In response to introducing cationic surfactants in solution, we temporally resolve single-molecule compaction trajectories of DNA polymers, guided by the confining nanogroove environment; this is in contrast to the uncontrolled collapse which would occur in free solution under similar conditions. In the presence of restriction enzymes, we directly visualize the cleavage of multiple DNA sites under adjustable nanoscale confinement. By using nanofabricated, nonabsorbing, low-background glass walls to confine biomolecules, our nanofluidic platform facilitates quantitative exploration of physiologically and biotechnologically relevant processes at the nanoscale. This device provides new kinetic information about dynamic chemical processes at the single-molecule level, using advancements in the CLiC design including a microchannel-based diffuser and postarray-based dialysis slit.

Hexagonal → cholesteric phase transition of DNA molecules in liquid-crystalline dispersion particles

To assess the character of packing of double-stranded (ds) DNA molecules in liquid-crystalline dispersion particles formed by phase exclusion of DNA molecules from aqueous salt solutions of poly(ethylene glycol), the circular dichroism spectra of these dispersions at different temperatures have been compared. It has been shown for the first time that heating dispersion particles with the hexagonal packing of ds-DNA molecules is accompanied by the hexagonal → cholesteric phase transition. This result can be described using the notion of quasi-nematic layers composed of orientationally ordered adjacent ds-DNA molecules in the structure of dispersion particles; these layers can be packed in two ways dictating their hexagonal or cholesteric spatial structure.

83 Application of differential scanning calorimetry to measure the differential binding of ions, water, and protons in the unfolding of DNA molecules

The overall stability of DNA molecules globally depends on base-pair stacking, base pairing, polyelectrolyte effect, and hydration contributions. In order to improve our understanding of the role of ions, water, and protons in the stability and melting behavior of DNA structures, we report an experimental approach to determine the differential binding of ions (Δn ion), water (Δn W), and protons (Δn H+) in the helix-coil transition of DNA molecules. A combination of differential scanning calorimetry (DSC) and temperature-dependent UV and CD spectroscopic techniques to investigate the unfolding of a variety of DNA molecules: S.T. DNA, two dodecamers, one undecamer, nine short hairpins as a function of the GC content of their stem, and two triplexes. We determine complete thermodynamic profiles, including all the three linking numbers, for the unfolding of each molecule. The CD spectra indicated that all molecules adopted the B-conformation at low temperatures. Thermodynamic profiles obtained from the DSC curves indicate that the favorable folding of each molecule results from the typical compensation of favorable enthalpy and unfavorable entropy contributions, and negligible heat capacity effects. UV and DSC melting curves as a function of salt, osmolyte, and proton concentrations yielded releases of ions, water, and protons (for the triplex with C+GC base triplets). Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of water and counterions. The thermodynamic data will be discussed in terms of the effects of DNA length, loop contributions and type of water molecules.

DNA molecule dynamics in converging–diverging microchannels

The conformation and dynamics of double-stranded DNA molecules in a pressure-driven flow-through sharp/gradual converging (contraction half)-diverging (expansion half) square microchannels with a contraction/expansion ratio of 4:1/1:4 were examined using fluorescently labelled lambda-phage DNA at 2.2< or =De< or =30.7 (De is Deborah number, a dimensionless number used in rheology to characterize how fluid a material is). Both the diffusion and stretching of individual DNA molecules and their local flow velocity were visualized, recorded and measured with using MPIV (microparticle image velocimetry) and CLSM (confocal laser-scanning microscopy). The onset of the coil-stretch transition in DNA molecules and their time-dependent velocity in the elongational flow were determined at the micro scale. Velocity distribution was measured via MPIV through orange fluorescent particles and carboylate-modified microspheres of 1 mum diameter. The channel geometry effect in terms of the channel contraction/expansion angle, the mass flow rate and the solution viscosity on the conformation and diffusion were also studied and discussed.

Metal–insulator transition in DNA molecules induced by long-range correlations in the sequence of nucleotides

Abstract We propose an analytical approach for calculation of the electron localization length in the DNA molecules. In the fishbone model the localization length is directly related to the binary correlation function of the sequence of nucleotides. Application of the proposed method to some known DNA sequences shows sharp maxima in the energy dependence of the localization length. These maxima can be considered as mobility edges. Existence of the mobility edge is rather rare event and it requires that the correlation function apart from an inverse power law decay, also oscillates as a function of the distance between the nucleotides. Although many DNA sequences exhibit slow decay of correlations, only very few of them possess the mobility edge. It is not clear yet what is the biological role of the mobility edge.

Elongation flow studies of DNA as a function of temperature

The response of T4-phage DNA molecules to an elongational flow field was monitored by flow-induced birefringence as a function of temperature. The flow-induced birefringence observed in this study was localized in the pure elongational flow area with a critical strain rate, indicating that the birefringence was attributed to a coil–stretch transition of DNA molecules. The slight decrease in the birefringence intensity with increases in temperature to 40°C was explained by a thermal-activation process. At temperatures above 50°C, flow-induced birefringence decreased remarkably, and no birefringence was observed at temperatures above 60°C. After the flow experiments, ambient temperature was reduced back to room temperature, and flow experiments at room temperature were performed again. Flow-induced birefringence was recovered almost completely in samples for which the first flow measurements were made at temperatures below 53°C. Irreversible changes were observed for samples for which the first flow experiments were performed at temperatures above 55°C. The temperature dependence of UV-absorption spectra revealed that the double-strand DNA helix began to partially untwine at a temperature over 50°C, and duplexes became almost completely untwined at a temperature over 55°C. A comparison of electrophoresis patterns for untwined molecules showed that flow-induced scission of DNA molecules occurred in a sample solution in flow experiments performed at 65°C, while no molecular weight reduction was observed in the sample solution at 55°C. In this article, this difference between the untwined DNA molecules is discussed on the basis of the thermally activated bond scission (TABS) model. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 83: 1357–1365, 2002

Direct observation of the coil‐globule transition in dna molecules

Direct observation of the coil‐globule transition in dna molecules

A statistical model of cooperative reaction between weak polyelectrolytes

Cooperative reactions between polyelectrolytes are discussed on the basis of a definite statistical model, consisting of combined segments alternating with symmetrical loops of coiled units. Lifson's method was used for calculating the statistical sum for this model and this simplifies the mathematical apparatus. Theoretical relationships between θ and pH are compared with experimental results obtained for reactions between weak polyelectrolytes. The parameters of the degree of cooperative interaction in the polyelectrolyte systems lie within the limits of 0·33–0.·4, which is close to the value of the parameter for the helix-coil transition in DNA molecules. This shows that there is close analogy between the cooperative combination of the macromolecules of weak polyelectrolytes and the helix-coil transition in DNA molecules.

Theory of the Helix-Coil Transition of DNA Molecules

Taking into account the nearest neighbor frequencies of two kinds of base pairs, helix-coil transition in the thermal denaturation process of DNA molecules is investigated. The partition function of a helical part of the molecule is calculated by using the matrix formulation which leads to the algebraic mean of the partition function for various base-pair sequences. The melting curves, that is the fraction of the number of unbonded base pairs as a function of temperature, are evaluated. Thus we can find rather strong dependence of the melting curve on the nearest neighbor frequencies as well as on the base compositions. Actually, when the base sequence has large nearest neighbor frequencies for the same kind of base pairs, it is shown that the melting occurs by two steps of transitions.