Dielectric relaxation measurements of 12 kbp plasmid DNA

Selective Manipulation of Biomolecules with Insulator-Based Dielectrophoretic Tweezers

Insulator-based dielectrophoretic (iDEP) trapping, separating, and concentrating nanoscale objects is carried out using a non-metal, unbiased, mobile tip acing as a tweezers. The spatial control and manipulation of fluorescently-labeled polystyrene particles and DNA were performed to demonstrate the feasibility of the iDEP tweezers. Frequency-dependent iDEP tweezers' strength and polarity were quantitatively determined using two theoretical approaches to DNA, which resulted in a factor of 2 ~ 40 differences between them. In either approach, the strength of iDEP was at least 4-order of magnitude stronger than the thermal force, indicating iDEP was a dominant force for trapping, holding, and separating DNA. The trapping strength and volume of the iDEP tweezers were also determined, which further supports direct capture and manipulation of DNA at the tip end.

Measuring Nanoparticle Polarizability Using Fluorescence Microscopy

Using a novel method developed to quantify the polarizability of photoluminescent nanoparticles in water, we present experimental observations of the extraordinary polarizability exhibited by nanoparticles of commensurate size with the Debye screening length, confirming previously reported theory. Semiconductor quantum dots (QDs) are ideal model nanoparticles to demonstrate this assay, due to their tunable size and bright photoluminescence. This assay is based upon microfluidic chambers with microelectrodes that generate trapping potentials that are weaker than thermal energy. By comparing the local electric field strength and variations in QD concentration, their polarizability was computed and found to agree with estimates based upon the hydrodynamic diameter found using light scattering. Strikingly, the polarizability of the nanoparticles increased 30-fold in low salt conditions compared to high salt conditions due to the increased thickness of the Debye layer relative to the particle radius. In addition to providing evidence that corroborates theoretical work studying direct solutions to the Poisson-Nernst-Planck equations, these observations provide an explanation for the previously observed conductivity dependence of biomolecule polarizability. As the polarizability of nanoparticles is of high importance to the electrically directed assembly of particles, as well as their interactions with other materials in complex environments, we anticipate that these results will be highly relevant to ongoing efforts in materials by design and nanomedicine.

Nanopore sensing at ultra-low concentrations using single-molecule dielectrophoretic trapping

Single-molecule techniques are being developed with the exciting prospect of revolutionizing the healthcare industry by generating vast amounts of genetic and proteomic data. One exceptionally promising route is in the use of nanopore sensors. However, a well-known complexity is that detection and capture is predominantly diffusion limited. This problem is compounded when taking into account the capture volume of a nanopore, typically 10⁸–10¹⁰ times smaller than the sample volume. To rectify this disproportionate ratio, we demonstrate a simple, yet powerful, method based on coupling single-molecule dielectrophoretic trapping to nanopore sensing. We show that DNA can be captured from a controllable, but typically much larger, volume and concentrated at the tip of a metallic nanopore. This enables the detection of single molecules at concentrations as low as 5 fM, which is approximately a 10³ reduction in the limit of detection compared with existing methods, while still maintaining efficient throughput.

Nanopore sensors have shown tremendous potential for biomolecule sensing, though the diffusion-controlled capture can limit the speed of analysis. Here, the authors report a dielectrophoretic method to concentrate DNA near the tip of a nanopore, reducing the limit of detection by three orders of magnitude.

Collapse of DNA under alternating electric fields

Recent studies have shown that double-stranded DNA can collapse in the presence of a strong electric field. Here we provide an in-depth study of the collapse of DNA under weak confinement in microchannels as a function of buffer strength, driving frequency, applied electric-field strength, and molecule size. We find that the critical electric field at which DNA molecules collapse (tens of kV/m) is strongly dependent on driving frequency (100-800 Hz) and molecular size (20-160 kbp), and weakly dependent on the ionic strength (8-60 mM). We argue that an apparent stretching at very high electric fields is an artifact of the finite frame time of video microscopy.

Dielectrophoretic response of DNA shows different conduction mechanisms for poly(dG)-poly(dC) and poly(dA)-Poly(dT) in solution

Although the subject of some scrutiny over the years, the mechanism of conduction in DNA has not yet been resolved, with competing theories suggesting either electronic and ionic conduction mechanisms. In this paper we use dielectrophoresis to determine the electrical properties of poly(dG)-poly(dC) (GC) and poly(dA)-poly(dT) (AT) DNA in solution. The molecules show different conduction mechanisms; GC DNA exhibits conduction primarily through the molecule, whereas in AT DNA conduction through the counterion cloud surrounding the molecule in solution is more significant.

Localized modulated waves in microtubules

In the present paper, we study nonlinear dynamics of microtubules (MTs). As an analytical method, we use semi-discrete approximation and show that localized modulated solitonic waves move along MT. This is supported by numerical analysis. Both cases with and without viscosity effects are studied.

Dielectric relaxations of poly(acrylic acid)-graft-poly(ethylene oxide) aqueous solution: analysis coupled with scaling approach and hydrogen-bonding complex

Dielectric properties of poly(acrylic acid)-graft-poly(ethylene oxide) (PAA-g-PEO) aqueous solution were measured as a function of concentration and temperature over a frequency range of 40 Hz to 110 MHz. After subtracting the contribution of electrode polarization, three relaxation processes were observed at about 20 kHz, 220 kHz, and 4 MHz, and they are named low-, mid- and high-frequency relaxation, respectively. The relaxation parameters of these three relaxations (dielectric increment Δε and relaxation time τ) showed scaling relations with the polyelectrolyte concentration. The mechanisms of the three relaxations were concluded in light of the scaling theory: The relaxations of low- and mid frequency were attributed to the fluctuation of condensed counterions, while the high-frequency relaxation was ascribed to the fluctuation of free counterions. Based on the dielectric measurements of varying temperatures, the thermodynamic parameters (enthalpy change ΔH and entropy change ΔS) of the three relaxations were calculated and these relaxation processes were also discussed from the microscopic thermodynamical view. In addition, the impacts of PEO side chains on the conformation of PAA-g-PEO chains were discussed. PEO side chains greatly strengthen the hydrogen-bonding interactions between PAA-g-PEO chains, resulting in the chains overlapping at a very low concentration and the formation of a hydrogen-bonding complex. Some physicochemical parameters of PAA-g-PEO molecules were calculated, including the overlap concentration, the effective charge of the chain, the friction coefficient, and the diffusion coefficient of hydrogen counterions.

Role of hydrodynamic behavior of DNA molecules in dielectrophoretic polarization under the action of an electric field

A continuum model is developed to predict the dielectrophoretic polarizability of coiled DNA molecules under the action of an alternating current electric field. The model approximates the coiled DNA molecule as a charged porous spherical particle. The model explains the discrepancies among scaling laws of polarizability of different-sized DNA molecules with contour length and such discrepancies are attributed to different hydrodynamic behavior. With zero or one fitting parameter, theoretical predictions are in good agreement with various experimental data, even though in experiments there are some uncertainties in regard to certain parameters.

Dielectrophoretic manipulation of ribosomal RNA

The manipulation of ribosomal RNA (rRNA) extracted from E. coli cells by dielectrophoresis (DEP) has been demonstrated over the range of 3 kHz-50 MHz using interdigitated microelectrodes. Quantitative measurement using total internal reflection fluorescence microscopy of the time dependent collection indicated a positive DEP response characterized by a plateau between 3 kHz and 1 MHz followed by a decrease in response at higher frequencies. Negative DEP was observed above 9 MHz. The positive DEP response below 1 MHz is described by the Clausius-Mossotti model and corresponds to an induced dipole moment of 3300 D with a polarizability of 7.8×10(-32) F m(2). The negative DEP response above 9 MHz indicates that the rRNA molecules exhibit a net moment of -250 D, to give an effective permittivity value of 78.5 ε(0), close to that of the aqueous suspending medium, and a relatively small surface conductance value of ∼0.1 nS. This suggests that our rRNA samples have a fairly open structure accessible to the surrounding water molecules, with counterions strongly bound to the charged phosphate groups in the rRNA backbone. These results are the first demonstration of DEP for fast capture and release of rRNA units, opening new opportunities for rRNA-based biosensing devices.

Dielectrophoretic investigation of plant virus particles: Cow Pea Mosaic Virus and Tobacco Mosaic Virus

This paper reports experimental results on the dielectrophoretic (DEP) behaviour on two nonenveloped plant viruses of different geometrical shapes, namely Cow Pea Mosaic Virus (CPMV) and Tobacco Mosaic Virus (TMV). The DEP properties of carboxy-modified latex beads of the same size are also reported. The DEP properties of single particles were obtained from measurement of the frequency at which the DEP force on a particle goes to zero (the crossover frequency). The DEP behaviour of particle ensembles was also measured using image processing. The dielectric properties of the particles were evaluated from the DEP data. The surface conductance was found to be 0.3 nS for CPMV, 0.38 nS for TMV, and 0.52 nS for 27 nm diameter carboxy-latex beads. Data analysis has shown that the optimal condition for separation of TMV and CPMV is a low-conductivity suspending medium - below 1 mS/m.

Dielectric properties of E. coli cell as simulated by the three-shell spheroidal model

Dielectric properties of E. coli cell have been re-studied by means of the three-shell spheroidal model, where the three shells correspond to the outer membrane, the periplasmic space and the inner membrane, respectively. With the model, a curve-fitting procedure has been developed to analyze the dielectric spectra. Although E. coli cell has been studied before, its special morphological structure was taken into account more comprehensively than any previous model in the present work. Dielectric properties of various cell components have been estimated from the observed dielectric spectra, especially the permittivity of the outer membrane, which was evaluated quantitatively for the first time. The values of epsilon(om) were 12 for kappa(om) of 0 to 10(-4) S/m and 34 for kappa(om) of 10(-3) S/m. The specific capacitance of the inner membrane was 0.6-0.70 microF/cm(2). The relative permittivity and the conductivity of the cytoplasm were about 100 and 0.22 S/m, respectively, and the conductivity of the periplasmic space was 2.2-3.2 S/m.

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 degrees 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 behavior of DNA in water–organic co-solvent mixtures

The radiowave dielectric dispersions of DNA in different water-organic co-solvent mixtures have been measured in the frequency range from 100 kHz to 100 MHz, where the polarization mechanism is generally attributed to the confinement of counterions within some specific lengths, either along tangential or perpendicular to the polyion chain. The dielectric dispersions have been analyzed on the basis of two partially different dielectric models, a continuum counterion fluctuation model proposed by Mandel and a discrete charged site model, proposed by Minakata. The influence of the quality of the solvent on the dielectric parameters has been investigated in water-methanol and water-glycerol mixtures at different composition, by varying the permittivity (m) and the viscosity eta of the solvent phase. The analysis of the dielectric spectra in solvents where electrostatic and hydrodynamic interactions vary with the solvent composition suggests that both the two models are able, in principle, to account for the observed high-frequency dielectric behavior. However, while some certain assumptions are necessary about the polyion structure within the Mandel model, no structural prerequisite is needed within the Minakata model, where the polarization mechanism invoked considers a radial counterion exchange with the outer medium, which is largely independent of the local polyion conformation.

Theoretical evaluation of dielectric absorption of microwave energy at the scale of nucleic acids

A theoretical model is proposed for the evaluation of dielectric properties of the cell nucleus between 0.3 and 3 GHz, as a function of its nucleic acids (NA) concentration (CNA). It is based on literature data on dielectric properties of DNA solutions and nucleoplasm. In skeletal muscle cells, the specific absorption rate (SAR) ratio between nucleoplasm and cytoplasm is found to be larger than one for CNA above 30 mg/ml. A nearly linear relationship is found between CNA and this nucleocytoplasmic SAR ratio. Considering the nanoscale of the layer of condensed counterions and bound water molecules at the NA-solution interface, the power absorption per unit volume is evaluated at this precise location. It is found to be between one and two orders of magnitude above that in muscle tissue as a whole. Under realistic microwave (MW) exposure conditions, however, these SAR inhomogeneities do not generate any significant thermal gradient at the scale considered here. Nevertheless, the question arises of a possible biological relevance of nonnegligible and preferential heat production at the location of the cell nucleus and of the NA molecules.

Frequency and voltage dependence of the dielectrophoretic trapping of short lengths of DNA and dCTP in a nanopipette

The study of the properties of DNA under high electric fields is of both fundamental and practical interest. We have exploited the high electric fields produced locally in the tip of a nanopipette to probe the motion of double- and single-stranded 40-mer DNA, a 1-kb single-stranded DNA, and a single-nucleotide triphosphate (dCTP) just inside and outside the pipette tip at different frequencies and amplitudes of applied voltages. We used dual laser excitation and dual color detection to simultaneously follow two fluorophore-labeled DNA sequences with millisecond time resolution, significantly faster than studies to date. A strong trapping effect was observed during the negative half cycle for all DNA samples and also the dCTP. This effect was maximum below 1 Hz and decreased with higher frequency. We assign this trapping to strong dielectrophoresis due to the high electric field and electric field gradient in the pipette tip. Dielectrophoresis in electrodeless tapered nanostructures has potential applications for controlled mixing and manipulation of short lengths of DNA and other biomolecules, opening new possibilities in miniaturized biological analysis.

Oriented and vectorial immobilization of linear M13 dsDNA between interdigitated electrodes--towards single molecule DNA nanostructures

The ability to control molecules at a resolution well below that offered by photolithography has gained much interest recently. DNA is a promising candidate for this task since it offers excellent specificity in base-pairing combined with addressability at the nanometer scale. New applications in biosensing, e.g. interaction analysis at the single molecule level, or nanobiotechnology, e.g. ultradense DNA microarrays, have been devised that rely on stretched DNA bridges. The basic technology required is the ability to deposit spatially defined, stretched DNA-bridges between anchoring structures on surfaces. In this paper we present two techniques for spanning 2 microm long dsDNA bridges between neighboring interdigitated electrodes (IDEs). The extended DNA used was linearized M13 dsDNA (M13mp18 7231 bp, ca. 2.5 microm length), either unmodified, or with chemical modifications at both ends. The first approach is based on the dielectrophoretic (DEP) concentration and alignment of linearized wild-type dsDNA. IDEs with 1.7 microm spacing are driven with an AC voltage around 1 MHz leading to field strengths in the order of 1 MV m(-1). The dsDNA is polarized and linearized by the force field and accumulates in the gap between two neighboring electrodes. This process is reversible and was visualized by fluorescence staining of M13 DNA using PicoGreen, as intercalating dye. The resulting dsDNA bridges and their orientation are discernible under the fluorescence microscope using fluorescent particles of different color. The particles are tagged with sequence specific peptide nucleic acid (PNA) probes that bind to the DNA double strand at specific sites. The second approach is based on asymmetric electrochemical modification of a gold IDE with 2.0 microm spacings followed by spontaneous or stimulated deposition of a chemically modified M13-DNA. One side of the IDE was selectively coated with streptavidin by electropolymerization of a novel hydrophilic conductive polymer in the presence of the binding protein. The second side was modified with gold nanoparticles by reductive plating from aqueous gold chloride solution. An asymmetric double stranded (ds) M13 DNA carrying a 5'-thiol group at one end and a 5'-biotin at the other end was obtained by polymerase chain reaction (PCR) using two differently labeled primers. For DNA bridges to form spontaneously the modified IDE was incubated over night with a 50 nM solution of the modified M13 DNA. Potential applications of DNA-bridge formation in biosensing and biotechnology are discussed.