Study of dielectric behavior of DNA in shear gradient

The dielectric behavior of the DNA molecule is investigated in the presence of mechanical force as well as the electrical field. In the present experiment, the direction of the electrical field is perpendicular to that of the mechanical force. The dipole moment of polar molecules manifest itself as dielectric increment at low frequencies or as the conductance increment at high frequencies. These two quantities are closely related to each other by Eq. (1) in the text. Because of the difficulty due to electrode polarization at low frequencies, no useful information was obtained by investigating the dielectric increment in the present system. Therefore, the effect of shear gradient was studied by measuring the conductance increment at high frequencies with various velocity gradients. The conductance increment decreased when the shear was applied perpendicular to the electrical field. The conductance change is converted into the unit of dielectric constant; it was found that the dielectric increment of DNA solution decreases by as much as 85 percent. From these observations, it is concluded that the direction of the dipole moment in DNA is longitudinal rather than transverse. The same experiment was repeated with the random coil DNA and no anisotropy in the dielectric increment was observed.     

Dielectric behavior of DNA solution at radio and microwave frequencies (at 20 degrees C).

The dielectric constant and conductivity of calf thymus DNA were investigated at frequencies between 0.1 MHz and 70 GHz. This work is to investigate the dielectric properties of DNA in low gigahertz region and also to study whether the dielectric behavior of the water is affected by the presence of highly charged DNA. The results of these measurements indicate the presence of two anomalous dispersions, the one between 1 MHz and 1 GHz and the second one above 1 GHZ. The dispersion at low frequencies is likely to arise from polar groups in the DNA molecule. The relaxation behavior of unbound water in DNA solution is only slightly affected by the presence of DNA at concentrations below 1%.     

Study of helix-coil transition of DNA by dielectric constant measurement

The thermal helix–coil transition of DNA was studied by means of dielectric constant measurements. The dielectric dispersion of native helical DNA is characterized by a large dielectric increment and a large relaxation time, whereas that of denatured coil DNA is characterized by a small dielectric increment and a small relaxation time. The dielectric dispersion of partially denatured DNA is of particular interest. At the intermediate stage of the helix–coil transition, dispersion curves which are different from either that of helix DNA or that of coil DNA appear. This is particularly pronounced for large DNA. This indicates the presence of an intermediate form of DNA. Flow birefringence measurements were carried out simultaneously. The negative birefringence of helical DNA diminishes as the helix–coil transition proceeds. However, the extinction angle remains constant, as long as it can be measured. These results indicate the absence of intermediate forms during the helix–coil transition. The discrepancy between dielectric and birefringence measurements can be resolved by assuming that the intermediate forms are not birefringent. The size distribution of native DNA and of the indicated intermediate form of DNA was studied. It is found that a logarithmic normal distribution function explains the distribution of size of DNA reasonably well.     

Dielectric behavior of aqueous solutions of plasmid DNA at microwave frequencies.

The relative permittivity and dielectric loss of aqueous solutions of plasmid (pUC8.c1 and pUC8.c2) DNA have been measured at 20 degrees C over the frequency range 100 MHz-10 GHz. The solutions had a concentration of 0.1% DNA, and were studied both in the relaxed and the supercoiled form. The dielectric measurements were made using a variety of techniques including frequency domain and time domain methods of operation. No evidence of any resonance absorption, nor of any other kind of enhanced absorption, was observed.     

Light-induced dielectrophoretic manipulation of DNA

Light-induced dielectrophoretic movement of polystyrene beads and lambda-DNA is studied using thin films of amorphous hydrogenated silicon as local photoaddressable electrodes with a diameter of 4 microm. Positive (high-field seeking) dielectrophoretic movement is observed for both types of objects. The absence of strong negative (low-field seeking) dielectrophoresis of DNA at high frequencies is in agreement with the similarity of the dielectric constants of DNA and water, the real part of the dielectric function. The corresponding imaginary part of the dielectric function governed by the conductivity of DNA can be determined from a comparison of the frequency dependence of the dielectrophoretic drift velocity with the Clausius-Mossotti relation.     

Dielectric behavior of DNA-proflavine complex

The dielectric relaxation of namtive DNA and DNA–proflavine complexes at different DNA phosphate (P) to dye (D) ratios, were investigated in the frequency range 100 c/sec to 100 Kc/sec. The proflavine molecules were found to have a profound effect on the static dielectric constant and the relaxation time of the polymers. The static dielectric constant was oberserved to decrese with increasing level of added proflavine. At P/D = 1, the variation of dielectric constant with frequency was small. Relaxation time (τ) was greater for the DNA–proflavine complexes compared to that for free DNA, Maximum value of the relaxation time was obtained at P/D = 10. The increase in the relaxation time and decrease in the static dielectric constant were attributed to the increase in length and meutralization of surface charges of the DNA molecules, respectively, as aresult of proflavine binding.     

Characterization of DNA degradation using direct current conductivity and dynamic dielectric relaxation techniques

The purpose of this study was to evaluate DNA degradation upon thermal heating using dielectric relaxation and direct current (DC) conductivity methods. Herring sperm DNA, human growth hormone (HgH) plasmid DNA, and secreted alkaline phosphatase (SEAP) plasmid DNA were used as the examples. DNA was heated at 80°C for 1 hour. The dielectric relaxation spectra as a function of the applied field frequency were measured for HgH DNA at 0.5 hours and at 1 hour. The frequency range covered was from 10 kHz to 100 kHz. The DC conductivity measurements were made for all 3 kinds of DNA at 4 time points: 0 hours, 0.5 hours, 0.75 hours, and 1 hour. At each time point the DC conductivity was measured for each sample as a function of concentration via water dilution. The results show that the dielectric relaxation method is less sensitive in characterizing heat-driven DNA degradation. Conversely, DC conductivity is very sensitive. The semiquantitative dependence of the conductivity upon heating suggests that DNA degradation involves more than plasmid DNA nicking. Double strand and single strand breaks may also occur. In addition, herring sperm DNA, HgH DNA, and SEAP DNA, though similar in their DC conductivity functional forms upon dilution, exhibit significant differences in their responses to sustained heating.     

Dielectric properties of aqueous solutions of sonicated DNA above 40 MHz

The dielectric properties of sonicated calf-thymus DNA sodium salt in aqueous solutions have been studied in the frequency range from 40 MHz to 2 GHz by time domain spectroscopy (TDS). A dielectric dispersion not previously reported was found, which has a characteristic frequency of about 150 MHz. All of the dielectric parameters are insensitive to the size of DNA fragments and to helix-to-coil transitions. The study of this dispersion as a function of DNA concentration and temperature allows us to conclude that it may be due to counterion fluctuation on short sections, probably in a direction transverse to the macromolecular axis.     

Hydration effects accompanying the formation of DNA complexes with some ligands

In the range of millimeter wavelengths the dielectric properties of aqueous solutions of some biologically active ligands (potential anticarcinogen chlorophyllin; pharmacological drug caffeine; polyamine putrescine; mutagens proflavine and ethidium bromide; actinocin derivative, an analogue of antitumor antibiotic actinomycin D) and DNA complexes with these substances were studied. It was shown that complex formation is accompanied by the change in dielectric properties of the solution. These changes during interaction of DNA with the first three compounds correspond to a decrease in hydration (compared with the total hydration of free components), and in other cases they cause an increase in hydration. The number of water molecules bound with both the ligand and DNA nucleotide in the complex was estimated. The results were compared with existing models of DNA interaction with the studied substances.     

Dielectric behaviour and conformational stability of collagen on interaction with DNA

Collagen-DNA interaction studies will aid in improving the stability of DNA against nucleases. In the present study, the effect of DNA on different physico-chemical properties of collagen like viscosity, conformation and dielectric behaviour has been studied. Increase of DNA concentration leads to the increment of viscosity of collagen at the pH 4 and 5, but the trend is reversed at the pH of 6 and 7 due to the formation of collagen fibrils. The temperature dependent CD spectroscopic studies for collagen-DNA conjugate showed that thermal stability of collagen is modulated with increasing molar concentration of DNA. It also shows that DNA interactions with collagen did not result in change in the triple helical structure of collagen. Impedance measurements show that the strength of ion pairs for different molar concentrations of collagen-DNA conjugates has changed. Nyquist plot for collagen-DNA conjugate posses higher Y″ at DNA concentration of 1:25 and 1:50 whereas at 1:1 and 1:10 lower Y″ than the native collagen have been observed. An understanding of this nature of the collagen-DNA interactions is helpful for gene delivery applications.     

Effect of ions on the dielectric relaxation of DNA

The dielectric relaxation of DNA solutions has been investigated with and without extraneous ions covering a wide frequency range. The effect of monovalent ions such as Na, K, and Li as well as divalent ions such as Mg, Ca, and Hg have been included in the study. These ions are found to have a profound effect on the dielectric increment and the relaxation time without affecting the molecular dimension drastically. This dielectric effect is interpreted as indicating the importance of counterion fluctuation on the low frequency dielectric constant of DNA in solution. The effect of an organic ion, tetra-methylammoniun bromide, has also been studied. This ion has no noticeable effect. A simple theory is derived on the basis of a microscopic model to account for the effect of external ions on the dielectric behavior of solutions of DNA.     

Effect of ions on counterion fluctuation in low-molecular weight DNA dielectric dispersions

The dielectric permittivity of aqueous solutions of low-molecular weight DNA (Mr = 3.2 X 10(5) ) in the presence of MgCl2 and AgNO3 has been measured in the frequency range from 5 kHz to 30 MHz, at a temperature of 25 degrees C. The DNA concentration was 3.5 X 10(-4) M in terms of phosphate and the salt concentration was varied from 1 X 10(-5) to 2 X 10(-4) M. The dielectric results have been analyzed in terms of two contiguous dielectric dispersions, and characteristic parameters have been discussed on the basis of polyelectrolyte theories which deal with counterion fluctuation. Some molecular parameters of the DNA molecule in electrolyte solutions are estimated.     

The effect of a variable dielectric coefficient and finite ion size on Poisson-Boltzmann calculations of DNA-electrolyte systems.

The results of variable dielectric coefficient Poisson-Boltzmann calculations of the counter-ion concentration in the vicinity of an all-atom model of the B-form of DNA are presented with an emphasis on the importance of spatial variations in the dielectric properties of the solvent, particularly at the macro-ion-solvent interface. Calculations of the distribution of hard-sphere electrolyte ions of various dimensions are reported. The presence of a dielectric boundary significantly increases the magnitude of the electrostatic potential with a concomitant increase in the accumulation of small counter-ions in the groove regions of DNA. Because ions with radii greater than 2 A have restricted access to the minor groove, the effect there is less significant than it is within the major groove. Changes in the dielectric coefficient for the electrolyte solution, allowing variation from 10 to 25, 40, 60, and 78.5 within the first 7.4 A of the surface of DNA, substantially increases the calculated surface concentration of counter-ions of all sizes. A lower dielectric coefficient near the macro-ion surface also tends to increase the counter-ion density in regions where the electrostatic potential is more negative than -kT. Regardless of the choice of dielectric coefficient, the number of ions in regions where the electrostatic potential is less than -kT remains the same for 0.153 M added 1-1 monovalent electrolyte as for the case without added salt.(ABSTRACT TRUNCATED AT 250 WORDS)     

An electrostatic model for the dielectric effects,the adsorption of multivalent ions,and the bending of B-DNA

We have studied electrostatic properties of DNA with a discrete charge model consisting of a cylindrical dielectric core with a radius of 8 Å and a dielectric constant D_i = 4, surrounded by two helical strings of phosphate point charges at 10 Å from the axis, immersed in an aqueous medium with dielectric constant D_w = 78.54. Eliminating the dielectric core makes potentials in the phosphate surface less negative by about 0.5 kT/e. Salt effects are evaluated for the model without a dielectric core, using the shielded Coulomb potential. Smearing the phosphate charges increases their potential by about 2.5 kT/e, due mostly to the self-potential of the smeared charge. Potentials in the center of the minor and major grooves vary less than 0.02 kT/e along their helical path. The potential in the center of the minor groove is from 1.0 to 1.7 kT/e, more negative than in the center of the major groove, depending on dielectric core and salt concentration. So multivalent cations and also larger cationic ligands, such as some antibiotics, are likely to adsorb in the minor groove, in agreement with earlier computations by A. and B. Pullman. Dielectric effects on the surface potential and the local potential variations are found to be relatively small. Bending of DNA is studied by placing a multivalent cation, M^Z+, in the center of the minor or major groove, curving DNA around it for a certain length, and calculating the free energy difference between the bent and the straight configuration. Boltzmann averaged bending angles, 〈β〉, are found to be maximal in 0.03M monovalent salt, for a length of about 50 or 25 Å of curved DNA when an M^Z+ ion is adsorbed in the minor or the major groove, respectively. When the dielectric constant of water is used throughout the calculation, we find maximal bends of 〈β〉 = 11° for M²⁺ and 〈β〉 = 16° for M³⁺ in the minor groove, 〈β〉 = 13° for M³⁺ in the major groove. The absence of bends in DNA adsorbed to mica in the presence of Mg salts supports the role of Mg²⁺ in “ion bridging” between DNA and mica. The treatment of the effective dielectric constant between two points outside a dielectric cylinder in water is appended. © 1998 John Wiley & Sons, Inc. Biopoly 46: 503–516, 1998     

Dielectric relaxation of DNA solutions. III. Effects of DNA concentration, protein contamination, and mixed solvents

As a continuation of previous papers [Biopolymers (1976) 15 , 879; (1978) 17 , 1508], the low-frequency dielectric relaxation of DNA solutions was studied with a four-electrode cell and the simultaneous two-frequency measurement. Below a critical concentration, the dielectric relaxation time agrees with the rotational relaxation time estimated from the reduced viscosity and is almost independent of DNA concentration C_p, and the dielectric increment is proportional to C_p. The critical concentration is approximately 0.02% of DNA for molecular weight M_r 2 × 10⁶ and 0.2% for M_r 4.5 × 10⁵ in 1 mM NaCl. Dielectric relaxations are compared for samples before and after deproteinization, and the protein contamination is found to have a minor effect on the dipole moment of DNA. The effect of a mixed solvent of water and ethanol on the dielectric relaxation of DNA is well interpreted in terms of changes in viscosity and the dielectric constant of the solvent, assuming that the relaxation arises from rotation of the molecule with a quasi-permanent dipole due to counterion fluctuation.     

Dielectric study of the interaction between DNA and an oligopeptide (lysine-tyrosine-lysine).

Interaction between Na-DNA and the oligopeptide lysine-tyrosine-lysine (LTL) is studied by a dielectric method. The comparison between conductivities (at the frequence of 5MHz) of LTL alone and of the complex LTL-DNA allows us to show up an electrostatic interaction between LTL and phosphates sites of DNA. During the formation of the complex LTL-DNA, a certain fraction of Na+ counter-ions is ejected from the phosphates sites.     

Molecular-weight dependence of the low-frequency dielectric properties of aqueous solutions of gel-fractionated DNA

Combined three- and four-terminal AC bridge measurements have been made at frequencies from 10 Hz to 100 KHz on samples of DNA with different molecular weight in aqueous solution under varying conditions of DNA concentrations and added salt. A method is described for the separation of large quantities of DNA fractionated according to size. A complicated pattern of dependence of the specific dielectric increment on concentration is found, and the difficulties of comparing the results from sample to sample are discussed. The dielectric properties of the fractionated samples of DNA in aqueous solution are reported for solutions sufficiently dilute that specific dielectric increment is independent of concentration. The specific dielectric increment of the solutions (with concentration measured in moles of DNA molecules/liter) is found to increase as the square of the molecular weight. The results are compared with results of polyelectrolyte theories which deal explicitly with counterion fluctuations and interactions. The frequency dependence of the dispersion is much broader than for simple Debye relaxation. It is satisfactorily fitted by the empirical Cole–Cole circular are function and the breadth of the dispersion is found to be, if anything, less for the fractionated samples than for native DNA in solution.     

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 epsilon 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.     

Dielectric control of counterion-induced single-chain folding transition of DNA

In the presence of condensing agents, single chains of giant double-stranded DNA undergo a first-order phase transition between an elongated coil state and a folded compact state. To connect this like-charged attraction phenomenon to counterion condensation, we performed a series of single-chain experiments on aqueous solutions of DNA, where we varied the extent of counterion condensation by varying the relative dielectric constant epsilon(r) from 80 to 170. Single-chain observations of changes in the conformation of giant DNA were performed by transmission electron microscopy and fluorescence microscopy, with tetravalent spermine (SPM(4+)) as a condensing agent. At a fixed dielectric constant, single DNA chains fold into a compact state upon the addition of spermine, whereas at a constant spermine concentration single DNA chains unfold with an increase in epsilon(r). In both cases, the transition is largely discrete at the level of single chains. We found that the critical concentration of spermine necessary to induce the single-chain folding transition increases exponentially as the dielectric constant increases, corresponding to 87-88% of the DNA charge neutralized at the onset of the transition. We also observed that the toroidal morphology of compact DNA partially unfolds when epsilon(r) is increased.     

On the electric polarization of DNA

Dielectric dispersion of DNA was studied in the frequency range 100 Hz–100 kHz at four different temperatures (6–30°C). The dielectric increment ε₀–ε_∞ increased with the rise of temperature. The relaxation time, on the other hand, decreased. Both the increase in dielectric increment and the decrease in relaxation time could not be explained on the basis of the counterion polarization theory. Dipole moment was estimated from Kirkwood theory. It was found to decrease systematically with temperature. Even at 0°C there was a dipole moment of 10⁴D.