Annular self-assembly of DNA molecular chains occurring in natural dry process of diluted solutions

The molecular orientation of DNA membranes, which were prepared by subjecting diluted solution of salmon sperm DNA to a natural drying process, was examined. X-ray diffraction and polarization microscopy revealed that the dried membranes have zonal structures. Each zone shows different features in molecular orientation. In the outer zones formed at the early stage in drying, DNA molecular chains were found to be aligned along the annular curve of the peripheral edge. Both the uneven thickness and disproportional molecular weight distribution in a membrane suggested that the radial flow transported DNA molecules to the edge and that they formed the accumulated phase. Above the critical concentration for the formation of liquid crystalline, the DNA chains would be aligned onto the preformed solid--liquid interface. The membranes with the highest birefringence were obtained from DNA samples with the relatively high molecular weight of around 29 kbp. In the innermost zone, on the other hand, the DNA molecules were radially oriented. This alignment can be attributed to the hydrodynamic effect caused by the rapid translation of the edge interface, which overcomes the Brownian motion of the chain segments. A transitive balance of physical effects was revealed in the dry process, which provided quite orthogonal molecular orientations in a single droplet.     

Molecular orientation of porphyrins accompanying the formation of chain-aligned DNA films

Porphyrin-containing DNA solid films with several binding orientations were successfully prepared by drying the aqueous solution of porphyrins and DNA in a magnetic field. By the measurement of linear dichroism absorption spectra from three identical spatial directions, the molecular orientations of porphyrins in chain-aligned DNA films were evaluated. Tetra(N-methylpyridinium-4-yl)-porphyrin was found to be bound at the surface of DNA chains like a patch. This orientation is different from the intercalative or groove binding manners observed in solutions. In contrast, tetra(4-sulfonatophenyl)-porphyrin exhibited an orientation perpendicular to the DNA axis, which may be attributed to H-aggregation of porphyrins along the direction parallel to DNA chains. Heme-protein with coiled coil backbone was also aligned along the DNA chains, orienting ferric protoporphyrin parallel to the magnetic field. The major effect for these molecular orientations would be the molecular packing of the rod-disk or the rod-rod systems.     

Orientation of DNA in agarose gels.

An orientation of the lambda DNA during the electrophoresis in agarose gels was measured by a microscopic linear dichroism technique. The method involved staining the DNA with the dye ethidium bromide and measuring under the microscope the polarization properties of the fluorescence field around the electrophoretic band containing the nucleic acid. It was first established that the fluorescence properties of the ethidium bromide-DNA complex were the same in agarose gel and in a solution. Then the linear dichroism method was used to measure the dichroism of the absorption dipole of EB dye bound to lambda DNA. In a typical experiment the orientation of two-tenth of a picogram (2 x 10(-13)g) of DNA was measured. When the electric field was turned on, the dichroism developed rapidly and assumed a steady state value which increased with the strength of the field and with the size of DNA. A linear dichroism equation related the measured dichroism of fluorescence to the mean orientation of the absorption dipole of ethidium bromide and to an extent to which the orientation of this dipole deviated from the mean. The observed development of dichroism in the presence of an electric field was interpreted as an alignment of DNA along the direction of the field. The increase in the steady state value of dichroism with the rise in the strength of the field and with the increase of the size of DNA was interpreted as a better alignment of DNA along the direction of the field and as a smaller deviation from its mean orientation.     

The orientation of DNA fragments in the agarose gels

A microscopic method of measuring the orientation of nucleic acids in the agarose gels is described. A nucleic acid undergoing electrophoresis is stained with the dye ethidium bromide and is viewed under high magnification with a polarization microscope. A high-numerical-aperture microscope objective is used to illuminate and to collect the fluorescence signal, and therefore the orientation of the minute quantities of nucleic-acid can be measured: in a typical experiment we can detect the orientation of one-tenth of a picogram (10(13)g) of DNA. Polarization properties of the fluorescent light emitted by the separate bands corresponding to different molecular weights of the DNA are examined. A linear dichroism equation relates the measured fluorescence to the mean orientation of the absorption dipole of the ethidium bromide (and therefore DNA) and to the extent to which it is disorganized. As an example, we measured the orientation of phi X174 DNA RF/HaeIII fragments undergoing electrophoresis in a field of 10 V/cm. Ethidium bromide bound to the fragments with an angle of the absorption dipole largely perpendicular to the direction of the electrophoretic current. The dichroism declined as the molecular weight of the fragments decreased which is interpreted as an increase in the degree of disorder for shorter DNA.     

The acceleration of linear DNA during pulsed-field gel electrophoresis

The velocity and orientation of T4 and lambda DNA have been measured for the first 20 s during pulsed-field gel electrophoresis in order to clarify the DNA motions that occur. For a square pulse with field strength E = 10 V/cm, the velocity of lambda DNA increases gradually to 10.5 microns/s in 1.0 s, declines to 8.6 microns/s, and then rises to a plateau value of 9.3 microns/s after 4 s. T4 DNA behaves similarly, but more slowly. Parallel measurements of fluorescence-detected linear dichroism show that the DNA becomes substantially aligned with its chain axis parallel to the electrophoretic field E after the pulse is applied. The alignment also shows an overshoot, an undershoot, and a plateau comparable to those seen for velocity. When the field strength increases, both the velocity and the alignment reach their peaks more quickly. For all field strengths and both molecular weights, the velocity peak occurs when the molecular center of mass has moved 0.3 to 0.5 L, where L is the chain contour length. A qualitative model is provided.     

Transient orientation of linear DNA molecules during pulsed-field gel electrophoresis.

The transient orientation of lambda DNA and lambda-DNA oligomers has been measured during pulsed field gel electrophoresis. The DNA becomes substantially aligned parallel to the electric field E. In response to a single rectangular pulse, orientation shows an overshoot with a peak at 1 second, then a small undershoot, and finally a plateau. When the field is turned off, the orientation dissipates in two distinct exponential phases. Field inversion leads to periods of orientation with intervening periods of reduced orientation as the chains reverse direction. Field inversion pulses applied to linear oligomers of lambda-DNA show that orientation responses slow down but increase in amplitude as molecular weight increases, for a given field. Because DNA stretching and alignment parallel to E are expected to correlate with DNA velocity, the velocity in response to a pulsed field is also expected to exhibit an overshoot.     

Electric properties and structure of DNA-restriction fragments from measurements of the electric dichroism

The electric dichroism of 17 homogeneous DNA fragments, ranging in size from 43 to 4362 base-pairs, has been analyzed in high electric fields. The orientation of the small fragments can be described in terms of an induced dipole moment, whereas the large fragments are oriented according to a constant dipole mechanism. In the intermediate size range, DNA orients according to an induced dipole mechanism at low field strengths and according to a constant dipole mechanism at high field strengths. From these observations we propose an orientation mechanism with a saturating induced dipole. The induced dipole observed at low field strengths is saturated at a field strength Eo within a transition range Em to give a constant dipole moment at high field strengths. These parameters together with the polarizability and the limit reduced dichroism are evaluated by a least-squares analysis of the experimental data. Eo and Em are found to decrease with increasing chain length from Eo approximately 40 kV/cm (Em approximately 14 kV/cm) at 65 base-pairs to 10 kV/cm (6 kV/cm) at 194 base-pairs. The polarizability is found to increase with the square of the chain length, whereas the saturated dipole increases with chain length N at low N and goes to a limit value at high N. The temperature dependence of the orientation parameters is found to be very small. The values obtained for the limit dichroism are between -1.0 and -1.3 for chain lengths between 60 and 1000 base-pairs, whereas values around -1.4 are observed at chain lengths greater than 1000 base-pairs. These data indicate that electric fields extend the contour of DNA strands at high chain lengths from a weakly bent to a more linear form. The variations of the limit dichroism observed for short fragments suggest sequence-dependent differences in the secondary structure of the helix. The experimental results are compared with numerical calculations based on simple polyelectrolyte models. For short fragments the magnitude of several electrochemical parameters can be adequately explained by a polarization of the ion cloud around the DNA molecules. However, these polyelectrolyte models do not adequately describe the observed chain length dependence of the orientation phenomena.     

Electric dichroism of poly(riboadenylic acid)

Electric dichroism measurements on poly(A) in low-ionic-strength solution demonstrate that below a molecular weight of 130,000 the double-stranded polymer is hydrodynamically rigid and above that molecular weight becomes increasingly flexible. At 500,000 it is considerably more flexible than DNA of the same molecular weight, with a mean end-to-end distance of about 1150 Å compared to approximately 1600 Å for DNA. The fully extended length for both DNA and poly(A) of this molecular weight is about 2750 Å. It is further shown that the orientation of these polyelectrolytes in an electric field is consistent with theoretical treatments of the counter-ion distribution and a preliminary model based on the additivity of classical valence charge anisotropy and counter-ion polarization is postulated for the orientation mechanism. Single-stranded pol (A) is shown not only to retain its base stacking in the presence of the electric field but to extend the persistent regions of stacked bases so that it attains a rodlike structure very similar to the one in the double-stranded polymer is found to be less than that expected from consideration of the x-ray structure. An explanation for this result is sought in the electric asymmetry of the helical polymer.     

Reinterpretation of linear dichroism of chromatin supports a perpendicular linker orientation in the folded state

We present a reinterpretation of linear dichroism data for the salt induced condensation of chromatin. A conflict between electric and flow linear dichroism data for identical chromatin samples, studied at varying degrees of Mg2+ induced folding, can be solved if the orientation in electric fields is mainly determined through the polarization of counter ions along the linker parts, whereas the orientation in flow is governed by the hydrodynamical response of the entire chromatin fiber. The orientation of a chromatin fiber in an electric field would then depend on the linker tilt angle so that at an angle larger than 55 degrees the fiber would tend to orient perpendicular to the applied field. The different orientation distributions obtained with the two methods of alignment may in this way provide extra information about the structure and folding of chromatin.     

Reinterpretation of Linear Dichroism of Chromatin Supports a Perpendicular Linker Orientation in the Folded State

Abstract

We present a reinterpretation of linear dichroism data for the salt induced condensation of chromatin. A conflict between electric and flow linear dichroism data for identical chromatin samples, studied at varying degrees of Mg²⁺ induced folding, can be solved if the orientation in electric fields is mainly determined through the polarization of counter ions along the linker parts, whereas the orientation in flow is governed by the hydrodynamical response of the entire chromatin fiber. The orientation of a chromatin fiber in an electric field would then depend on the linker tilt angle so that at an angle larger than 55° the fiber would tend to orient perpendicular to the applied field. The different orientation distributions obtained with the two methods of alignment may in this way provide extra information about the structure and folding of chromatin.     

Electric dichroism and bending amplitudes of DNA fragments according to a simple orientation function for weakly bent rods

The linear dichroism is calculated for DNA fragments in their thermal bending equilibrium. These calculations are given for relatively short fragments, where bent molecules can be described by an arc model. Using the measured value of 350 A for the persistence length, the limit dichroism (corresponding to complete alignment) decreases due to thermal bending, e.g., for a fragment with 100 base pairs to 80% of the value expected for straight molecules. Thermal bending should lead to a strong continuous decrease of the dichroism with increasing chain length, which is not observed, however, in electric dichroism experiments due to electric stretching. The influence of the electric field on the bending equilibrium is described by a contribution to the bending energy, which is calculated from the movement of charge equivalents against the potential gradient upon bending. The charge equivalents, which are assigned to the helix ends, are derived from the dipole moments causing the stationary degree of orientation. By this procedure the energy term inducing DNA stretching is given for induced, permanent, and saturating induced dipole models without introduction of any additional parameter. The stationary dichroism at a given electric field strength is then calculated according to an arc model by integration over all angles of orientation of helix axes or chords with respect to the field vector, and at each of these angles the contribution to the dichroism is calculated by integration over all helices with different degrees of bending. Orientation functions obtained by this procedure are fitted to dichroism data measured for various restriction fragments. Optimal fits are found for an induced dipole model with saturation of the polarizability. The difference between orientation functions with and without electric stretching is used to evaluate dichroism bending amplitudes. Both chain length and field strength dependence of bending amplitudes are consistent with experimental amplitudes derived from the dichroism decay in low salt buffers containing multivalent ions like Mg2+, spermine, or [CoNH3)6]3+. Bending amplitudes can be used to evaluate the persistence length from electrooptical data obtained for a single DNA restriction fragment. Bending and stretching effects are considerable already at relatively low chain length, and thus should not be neglected in any quantitative evaluation of experimental data.     

Flow dichroism of DNA: a new apparatus and further studies

A new apparatus for the study of flow dichroism of macromolecules is described. The flow is down a long, narrow channel and an unpolarized light beam propagates along the flow direction. For a molecule such as DNA, in which the transition moments of the chromophores are perpendicular to the axis of orientation, an increase of absorbance is observed during flow. The apparatus is best suited for macromolecules which are readily orientable or at high shear gradients so that the extinction angle is close to 0°. The apparatus has the following advantages: dilute macromolecule solutions can be used; high shear gradients are easily obtained; only small volumes of solution are needed. The flow can be stopped rapidly so that relaxation times for disorientation can be studied. The flow dichorism of native, two-stranded DNA has been measured for the molecular weight range of 0.6 × 10⁶ to 125 × 10⁶, and for the shear gradient range (in aqueous solution at 25°C) from 200 sec^?1 to 21000 sec^?1. At a fixed gradient the dichroism increases with molecular weight, but the curve is concave downwards. At a given molecular weight the dichroism increases with increasing shear gradient, but the curve is concave downwards. When the solvent viscosity and temperature are varied, the dichroism is a function of η〈G〉/T showing that the orientation is due to hydro-dynamic shear stress and that the flexibility of DNA in a flow field is not due to local denaturation. The Zimm-Rouse theory with no parameters taken from flow optical data predicts the correct order of magnitude of the dichroism but the experimentally observed shear gradient and molecular weight dependence do not fit the theory. This is an expected result, since the theory is believed to be applicable only at small distortions and extensions of the macromolecule.     

Polarized fluorescence in an electric field: comparison with other electrooptical effects for rodlike fragments of DNA and the problem of the saturation of the induced moment in polyelectrolytes

Electrical birefringence, electrical dichroism and polarisation of fluorescence in an electric field experiments have been performed at high fields on sonicated fragments of DNA labelled with Acridine Orange. The latter electrooptical effect gives access to the field dependence of the fourth moment of the orientation function while the two former give access to the field dependence of the second moment. The origin of the large departure from an E2 dependence at rather low degrees of orientation is extensively discussed. Following a suggestion of Shirai on the calculation of orientational averages for a saturated induced moment, we can show that this model rationalizes the existence of a linear E dependence of the orientation factor at intermediate fields and explains very well our experimental results. When applied to previous dichroic data at higher fields it shows that the low value of the dichroism at saturation introduced to fit with other models, in contradiction with the absence of base tilting in the B form of DNA, is not required for a quantitative fit with this new orientation mechanism. The transition from an E2 dependence at low fields to an E dependence at intermediate fields gives an estimate of the field required for the saturation of the ionic polarisation E approximately 6 kV/cm.     

The dichroism of DNA in electric fields

We have studied the dichroism of various samples of calf thymus DNA (of molecular weight from 3 × 10⁵ to 7 × 10⁶) in pulsed electric fields. The results may be summarized as follows:

• 1 We find that calf thymus DNA behaves in electrical orientation as if it possessed a large permanent dipole moment. This apparent moment is sensitive to such effects as Mg⁺⁺ binding which lower the net charge on DNA.
• 2 The limiting dichroism at infinite field corresponds to an angle of at least 80% between the transition moments at 265 nm and the helix axis, and could be consistant with a number of known forms of DNA. This result is independent of DNA molecular weight. There is evidence that the conformation may be different in 80% ethanol.
• 3 The dichroism relaxation curves contain a component with a relaxation time of about 8 μsec, which is nearly independent of molecular weight, and a longest component which behaves either according to the Broersma theory for low-molecular-weight samples, or the Zimm-Rouse theory at high molecular weights.

     

Characterization of methylprednisolone esters of hyaluronan in aqueous solution: conformation and aggregation behavior

Methylprednisolone steroid esters of hyaluronan differing in degree of functionalization and molecular weight were investigated in aqueous solution. Conformation and aggregation phenomena were elucidated by means of circular dichroism, viscometry, rheology, and nuclear magnetic resonance, mainly by (1)H pulsed field gradient (PFG) NMR, which allows the determination of the diffusion coefficient of the species under investigation. The functionalization of hyaluronan with the steroid induces a reduction of the molecular volume, as a consequence of intramolecular hydrophobic interactions. For concentrated samples we have observed the coexistence of unimolecular collapsed chains and of aggregates, the latter disappearing upon dilution. The methylprednisolone ester of lower molecular weight hyaluronan has a larger molecular volume than its higher molecular weight analogue, even though still smaller than the underivatized polymer. This effect can be explained with the reduced flexibility of the polymer backbone probably impairing intramolecular interactions.     

Orientation of adsorbed cytochrome c as a function of the electrical potential of the interface studied by total internal reflection fluorescence.

A method for determination of the orientation of adsorbed structure-stable proteins using Total Internal Reflection Fluorescence is outlined. The theory has been elaborated for orientation studies on adsorbed free base cytochrome c, of which the prophyrin can be used as an intrinsic fluorescent label. The ratio of fluorescence intensities at two polarization modes of the incident light (the transverse magnetic and the transverse electric polarization mode, respectively) gives a relation between the orientation angles of the porphyrin relative to the interface. As an illustration of the theory, experimental results on the adsorption of cytochrome c at an optically transparent SnO2 film electrode are presented. It is concluded that the orientation of the molecules can only be affected by the interfacial potential during the process of adsorption, but, once adsorbed, the orientation cannot be changed anymore by variation of the potential.     

Interfacial electric polarizability of purple membranes in solution.

Chloroplasts in higher magnetic fields align with their equatorial plane perpendicular to the field. Because of the nonrandom orientation of the chromophores in the membrane the fluorescence radiation will be partially polarized. The chloroplast concentration, magnetic field, and temperature dependence of the fluorescence polarization has been investigated. The results are compared with a simplified model calculation. It is shown that the concentration dependence can be related to the linear dichroism of the fluorescence radiation and self-adsorption. Taking these effects into account results in the calculation of a higher fluorescence polarization (FP) ratio and higher inclination of chlorophyll dipoles to the membrane plane. Analyzing the magnetic field dependence of the FP ratio, we conclude that in a magnetic field not only will be chloroplasts be aligned, but the thylakoid stacks as well. A decrease in the FP ratio was observed around 20 degrees C. It is suggested that this decrease reflects a phase transition in the photosynthetic membrane.     

PM-SP-LB多层膜中BR分子的有序定向排列

用垂直转移法在石英片上制成的PM—SP—LB多层膜的可见区吸收谱表明吸收峰峰位与成膜液一致,均在574nm左右,比PM水悬浮液的吸收峰位略有红移;稳态线二色性表明,除PM碎片平躺在多层膜平面内外,在提拉时的竖直方向存在BR的取向优势,优势率约为0.51左右;同时还表明,25mN/m条件下制备的PM—SP—LB多层膜中BR分子的视黄醛生色团的跃迁矩与膜平面法向所成的角接近于天然紫膜中的值。     

Study of PE and iPP orientations on the surface of carbon nanotubes by using molecular dynamic simulations

In this study, the early stage of interfacial crystallisation behaviour of low molecular weight polyethylene (PE) and isotactic polypropylene (iPP) oligomer on the surface of carbon nanotubes (CNTs) with different diameters, chiralities and topography structures was studied using MD simulations. We started to simulate the effect of CNTs chirality and diameter on PE molecular chain orientation, and then the effect of CNTs topography structure on PE and iPP molecular chain orientation was investigated. Finally, some experiments were carried out to prove the simulated results. Our study shows that for CNTs with a diameter comparable with the radius of gyration (R_g) of a polymer chain, an easy orientation of PE chains along CNTs axis is observed for all the systems of the CNTs with different chiralities due to a geometric confinement effect. For CNTs with a much larger diameter, multiple orientation of PE chains is induced on its surface due to the lattice matching between graphite lattice and PE molecular chains. In this case, the chirality of CNTs dominates the orientation of graphite lattice, which determines the orientation of PE chains arrangement on CNTs surface. More importantly, it was found that the groove structure formed by CNT bundles is very useful for the stabilisation of polymer chain, and thus facilitates the orientation of molecular chain along the long axis of CNTs. As a result, a novel nanohybrid shish–kebab (NHSK) structure with CNTs acting as central shish while polymer lamellae as kebab can be successfully obtained for both PE with zigzag conformation and iPP with helical conformation. This simulation result was well supported by the experimental observation. Our study could provide not only a deep understanding of the origin of the polymer chain orientation on CNTs surface but also the guidance for the preparation of polymer/CNTs nanocomposites with novel NHSK structure.     

Induction of protein-like molecular architecture by self-assembly processes

One of the most intriguing self-assembly processes is the folding of peptide chains into native protein structures. We have developed a method for building protein-like structural motifs that incorporate sequences of biological interest. A lipophilic moiety is attached onto an N(alpha)-amino group of a peptide chain, resulting in a 'peptide-amphiphile'. The alignment of amphiphilic compounds at the lipid solvent interface is used to facilitate peptide alignment and structure initiation and propagation. Peptide-amphiphiles containing potentially triple-helical structural motifs have been synthesized. The resultant head group structures have been characterized by circular dichroism and NMR spectroscopies. Evidence for a self-assembly process of peptide-amphiphiles has been obtained from: (a) circular dichroism spectra and melting curves characteristic of triple-helices, (b) one- and two-dimensional NMR spectra indicative of stable triple-helical structure at low temperatures and melted triple-helices at high temperatures, and (c) pulsed-field gradient NMR experiments demonstrating different self-diffusion coefficients between proposed triple-helical and non-triple-helical species. The peptide-amphiphiles described here provide a simple approach for building stable protein structural motifs using peptide head groups.