Deoxyribonucleic Acid Solutions Research Articles

Studies on the genotoxic effect of chromium oxide (Cr VI): Interaction with deoxyribonucleic acid in solution

Chromium is a toxic and carcinogenic compound widely distributed in environment. In the present study we have investigated the interaction of chromium oxide with DNA employing UV/vis and fluorescence spectroscopy as well as Circular dichroism, thermal denaturation, retardation polyacrylamide gel electrophoresis and DNA-cellulose affinity techniques. The results showed that the binding of chromium oxide to DNA is concentration dependent; at low concentration shows a little effect but ant higher concentrations (>100μg/ml) reduced the absorbance at 260 and 210nm producing hypochromicity. Also λmax of the metal at 210, 260 and 350nm was reduced. DNA chromophores quenched with the chromium oxide and decreased fluorescence emission intensity. Upon binding of the metal to DNA the elliplicity at positive extreme was decreased (275nm) and increased the ellipticity of the DNA at negative extreme 245nm. Thermal denaturation profile of DNA shifted to higher degrees upon chromium oxide binding which accompanied by hypochromicity. Also, affinity of chromium oxide to double stranded DNA was higher than single stranded DNA. From the result it is concluded that chromium oxide interacts with DNA via two modes of interaction inducing structural changes and DNA compaction evidence providing chromium oxide genotoxicity.

Application of terahertz spectroscopy to the characterization of biological samples using birefringence silicon grating

We present a device and method for performing vector transmission spectroscopy on biological specimens at terahertz (THz) frequencies. The device consists of artificial dielectric birefringence obtained from silicon microfluidic grating structures. The device can measure the complex dielectric function of a liquid, across a wide THz band of 2 to 5.5 THz, using a Fourier transform infrared spectrometer. Measurement data from a range of liquid specimens, including sucrose, salmon deoxyribonucleic acid (DNA), herring DNA, and bovine serum albumin protein solution in water are presented. The specimen handling is simple, using a microfluidic channel. The transmission through the device is improved significantly and thus the measurement accuracy and bandwidth are increased.

Formation of Complex Langmuir and Langmuir-Blodgett Films of DNA with a Dichain Cationic Surfactant

Formation of complex monolayers between a dichain cationic surfactant, namely, dihexadecyldimethylammonium bromide (DHDAB) and deoxyribonucleic acid (DNA) at the air-water interface was first time systematically investigated here. The adsorption of DNA onto DHDAB monolayer was monitored by observing the surface pressure vs. time graph. The polyion-complex monolayers formed in situ through the electrostatic attraction between cationic DHDAB and the phosphate groups of anionic DNA. The organization of the DNA-DHDAB complex at the air-water interface deduced from surface pressure-area (π-A) isotherms was compared with the spectroscopic data in Langmuir-Blodgett films. Study of UV-Vis absorption spectra of pure DNA solution and DNA adsorbed DHDAB complex Langmuir-Blodgett films confirms the successful transfer of the films onto quartz substrates.

Bio Organic-Based Gate Dielectric Materials for Thin Film Transistors

ABSTRACTThe potential of bio-dielectrics for thin film transistor applications was explored via the incorporation of titanium dioxide (TiO2) nanoparticles, rutile form, a high dielectric constant (ε) ceramic, in the deoxyribonucleic acid (DNA) bio-polymer. The DNA-ceramic hybrid films were fabricated from stable suspensions of the TiO2 nanoparticles in viscous, aqueous DNA solutions. Dielectric characterization revealed that the incorporation of TiO2 in DNA resulted in enhanced dielectric constant (14.3 at 1 kHz for 40 wt % TiO2) relative to that of DNA in the entire frequency range of 1 kHz-1 MHz. Variable temperature dielectric measurements, in the 20-80°C range, of the DNA-TiO2 films revealed that the ceramic additive stabilizes DNA against large temperature dependent variations in both ε and the dielectric loss factor tan δ. The bulk resistivity of the DNA-TiO2 hybrid films was measured to be two to three orders of magnitude higher than that of the control DNA films, indicating their potential for utilization as insulating dielectrics in transistor and capacitor applications.

Electrostatic Accumulation and Release of DNA Using a Micromachined Lance

This paper investigates the accumulation and release of deoxyribonucleic acid (DNA) relative to a surface micromachined silicon lance. The lance is a critical element of nanoinjection, a proposed approach for injecting foreign DNA into living cells. The quantity of DNA accumulated on the nanoinjector lance and the speed at which it can be moved on and off the lance are essential to the proposed system's function. Prototype nanoinjector lances were fabricated using a multilayer surface micromachining process. DNA stained with the fluorescent dye 4', 6-diamidino-2-phenylidole dihydrochloride was visualized using fluorescent illumination as the DNA was accumulated on and released from the tips of microelectromechanical systems (MEMS) microlances using a 1.5-V dc source. In 5 min 46 s, the lance accumulated over 32 000 DNA molecules from a dilute DNA solution. The lance then released over 6200 DNA molecules within 6 s. Finally, the nanoinjector lance was used to inject a reporter gene encoding a red fluorescent protein into a mouse embryo, resulting in expression of the gene. The nanoinjector lance represents an important and significant step in the development of a self-contained MEMS-based DNA injection system.

Electrical Characteristics and Doping Mechanism of DNA Molecules Doped with Iodine Solutions

This study examined the electrical characteristics of deoxyribonucleic acid (DNA) molecules doped with iodine solution and their chemical state changes before and after doping. The experiments were progressed in each lambda (A), poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA under the same conditions. The authors prepared 20 nm gap Au/Ti electrodes fabricated by e-beam lithography. DNA solutions were dropped on the nano gap of the electrodes and DNA films were formed by drying in a vacuum. DNA films were doped with an iodine solution dissolved in methanol. The authors measured the electrical conductivity of DNA molecules as the number of iodine doping times in 10(-2) torr vacuum. As increase of the iodine solution doping number, the electrical conductivity of three sorts of DNA molecules was remarkably improved respectively. X-ray photoelectron spectroscopy (XPS) was performed to inspect the electrical conduction mechanism that holes on DNA nitrogen region were generated by transferring electrons to iodine molecules.

Microrheology study of semidiluted deoxyribonucleic acid solutions

Linear rheological behavior and Microrheology measurements of sodium salt calf-thymus DNA aqueous solutions as a function of concentration are reported here. The microrheological behavior was obtained by a combination of experimental techniques: mechanical Rheometry and Dynamic light scattering (DLS). The viscoelastic properties of DNA in water as a function of concentration were performed at 20 °C and rheological and microrhelogical curves were performed. The result indicated that for concentrations lower than the entanglement concentration (Ce) the system exhibits a predominantly viscous behavior, whereas for higher concentrations exhibits a predominantly elastic behavior. The plateau modulus (G0) and the zero complex viscosity () follow a power law concentration dependence of the form: and , respectively The microrheology results overlap perfectly in a single line with the mechanical rheology results, extending the time resolution to faster breathing modes

Dielectric and dielectrophoretic properties of DNA

The physical properties of DNA are quite important for molecular genetics as well as for its nanotechnological applications. Studying the interactions of alternating current (AC) electric fields with deoxyribonucleic acid (DNA) allows one to draw conclusions about these properties. These interactions are usually investigated in two different ways. In dielectric spectroscopy, a DNA solution is placed in a homogeneous AC field and electronic parameters are measured over several frequency decades in the Hz to GHz range. These electronic data are then interpreted on the basis of physico-chemical models as a result of certain phenomena on the molecular level. In dielectrophoretic studies, a DNA solution is exposed to an inhomogeneous AC field and the spatial response of few or single molecules is monitored by optical or scanning force microscopy. This response can involve translation, elongation and orientation of the molecular strings. In this review, a survey is given of the literature dealing with the dielectric and dielectrophoretic properties of DNA as well as with applications of DNA dielectrophoresis.

Metal-Insulator-Gap-Insulator-Semiconductor Structure for Sensing Devices

We report on the use of sensing devices that have a metal-insulator-gap-insulator-semiconductor structure. We have used capacitance-voltage measurements from a metal-insulator-gap-insulator-semiconductor sensing device to characterize different pH solutions and deoxyribonucleic acid (DNA) solutions. Hysteresis in the capacitance-voltage curves results from mobile ionic charges in the solutions and the influence of changes on the sensing surface condition. As the pH decreases in the pH range of 2.7 to 7.0, the flatband voltage shift toward the negative voltage increases. The differences in the flatband voltage shift in capacitance-voltage curves are related to the mobile ionic charge density in solutions with different pH values or DNA molecules.

Detection of DNA Hybridization using Functionalized InN ISFETs

AbstractUltrathin (∼10 nm) InN ion sensitive field effect transistors (ISFETs) are functionalized by immobilized label-free oligonucleotide probes with 3-mercaptopropyltrimethoxysilane (MPTMS) through molecular vapor deposition (MVD) technique. This layer on the InN surface serves the function of selectively detecting the hybridization of complementary deoxyribonucleic acid (DNA). Using MVD technique to perform the gas-phase silanization of MPTMS provided a time-saving and simple method to reach 68° water contact angle after 1.5 h treatment. High resolution X-ray photoelectron spectroscopy (HRXPS) was employed to analyze the surface characteristics after functionalization. Modified probes DNA were covalently bonded to MPTMS-covered gate surface of InN ISFETs. And further hybridized with complementary DNA For a 12-mer oligonucleotide probe, a significant drain-source current decrease (∼ 6 μA) was observed for the hybridization with complementary DNA solution of 100 nM. In contrast, the noncomplementary DNA with single-base mismatch did not show obvious current changes. Functionalized ultrathin InN ISFETs for DNA sequence detection demonstrate the promise of biological sensing and genetic diagnosis applications.

Treatment of PAHs in contaminated soil by extraction with aqueous DNA followed by biodegradation with a pure culture of Sphingomonas sp.

The biodegradation of polycyclic aromatic hydrocarbons (PAHs) in aqueous deoxyribonucleic acid (DNA) solution from contaminated soil washing was investigated. Initial data with a model effluent consisting of anthracene, phenanthrene, pyrene and benzo[ a]pyrene that were individually dissolved in 1% aqueous DNA solution confirmed their positive degradation by Sphingomonas sp. at around 10 8 CFU mL −1 initial cell loading. For anthracene and phenanthrene, complete removal was achieved within 1 h treatment. Degradation of pyrene and benzo[ a]pyrene took a relatively longer time of a few days and weeks, respectively. DNA-dissolved PAHs were also degraded relatively faster than PAH crystals in aqueous medium to suggest that the binding of the PAHs in the polymer does not pose serious constraint to bacterial uptake. The DNA was stable against the PAH-degrading bacteria. Parallel experiments with actual DNA solutions obtained during pyrene extraction from an artificially spiked soil also showed similar results. Close to 100% pyrene degradation was achieved after 1 d treatment. With its chemical stability, the cell-treated DNA was re-used up to four cycles without a considerable decline in extraction performance.

Effect of Surfactant on FRET and Quenching in DNA Sequence Detection Using Conjugated Polymers

AbstractThe effect of a nonionic surfactant on various energy‐transfer and quenching processes in deoxyribonucleic acid (DNA) sequence detection using the cationic conjugated polymer (CCP) poly{[9,9‐bis(N,N,N‐trimethylammonium)hexylfluorene]‐co‐1,4‐phenylene diiodide} and peptide nucleic acid labeled with fluorescein (PNA‐Flu*) has been investigated. Steady‐state and time‐resolved measurements reveal that nonionic surfactant enhances both sensitivity and selectivity in targeted DNA sequence detection. The enhancement of the sensitivity is ascribed to an increase in the CCP quantum yield due to the surfactant breaking up polymer aggregates, increasing the isolated polymer chain concentration, and reducing interchain quenching. This also increases the polymer surface‐to‐volume ratio. The sensitivity is also improved as the surfactant reduces CCP quenching by DNA and buffer solution through incorporation of the CCP in micelles, which reduces charge‐transfer processes. Enhancement of the selectivity is achieved through the reduction of the hydrophobic interaction between the CCP and free PNA‐Flu*. Time‐resolved fluorescence lifetime analysis provides an effective way to differentiate these particular effects in the DNA‐PNA‐Flu assays. Comparing the decay profiles of the CCP, CCP/DNA, and CCP/complementary DNA:PNA‐Flu*, it was found that both surfactant and DNA do not alter dramatically the isolated polymer chain lifetime (the first increases the concentration of the single chains by breaking up the polymer aggregation and the latter reduces the concentration of the isolated polymer chain by static quenching), therefore the change in the isolated polymer chain fluorescence lifetime can predominantly reflect the quenching of the donor by FRET to the PNA fluorescent label. Here, surfactant increases Förster radius by enhancing the polymer fluorescence quantum yield. Furthermore, surfactant also increases the difference in the donor lifetimes between the complementary and noncomplementary cases. This difference reflects the increase in the energy‐transfer efficiency and hence higher selectivity. Fluorescein quenching is mediated by the CCP which causes Flu*‐Flu* self‐quenching via a PNA‐CCP hydrophobic interaction. Optimization or minimization of various interactions to achieve the best DNA detection sensor is discussed.

DNA-templated gold nanowires

We have developed simple methods of reproducibly creating deoxyribonucleic acid (DNA)-templated gold nanowires on silicon. First DNA nanowires were aligned on silicon surfaces. Briefly, modified silicon wafer was soaked in the DNA solution, and then the solution was removed using micropipettes; the surface tension at the moving air–solution interface is sufficient to align the DNA nanowires on the silicon wafer. In another attempt, an aqueous dispersion of sodium azide-stabilized gold nanoparticles was prepared. The nanoparticles aligned double-stranded λ-DNA to form a linear nanoparticle array. Continuous gold nanowires were obtained. The above nanowires were structurally characterized using scanning electron microscopy. The results of the characterizations show the wires to be 57–323 nm wide, to be continuous with a length of 2.8–9.5 μm. The use of DNA as a template for the self-assembly of conducting nanowires represents a potentially important approach in the fabrication of nanoscale interconnects.

DNA purification silicon chip

A silicon microchip has been developed for purification of deoxyribonucleic acid (DNA) from human blood based on the known affinity of DNA to silica under high chaotropic salt conditions. The chip comprises several components which include a micromixer, microfilter, microbinder and two microvalves to perform the functions of the mixing, filtering, purification and fluidic control; and yet it can be accomplished by a simple mask process flow process. Original human blood sample which is a mixture of many components, including white blood cells (WBC), red blood cells (RBC), platelets, plasma, etc., can be used directly as the input sample. After cell sorting, cell lysing, DNA binding, eluting and cleaning processes, pure DNA has been extracted for the white blood cells. An average of 10 ng DNA/μl blood was able to be extracted from this fully integrated DNA extraction chip. The purity of the eluted DNA was evaluated by optical density at wavelengths of 260 nm and 280 nm. Tests results showed that the most DNA solution eluted was free from RNA and protein contamination.

Dynamics of Deoxyribonucleic Acid Solutions As Studied by Dielectric Relaxation Spectroscopy and Dynamic Mechanical Spectroscopy

An investigation was carried out by dielectric relaxation spectroscopy (DRS) and dynamic mechanical spectroscopy (DMS) on the dynamics of aqueous solutions of deoxyribonucleic acid (DNA). Novel information is generated and presented through our use of wide temperature and frequency range in DRS and DMS measurements. Two relaxation processes were detected at temperatures below 273 K. The higher frequency, Debye-like process has an activation energy of 27 kJ/mol and is assigned to the bound water around DNA molecules. The lower frequency process is of the Cole−Cole type and has an activation energy of 55 kJ/mol, the same as that of pure ice. In the higher temperature range, encompassing the physiological condition, conductivity dominates the dielectric response. A pronounced peak in the dielectric modulus spectrum is observed, and its molecular origin is found to lie in the migration of counterions along the DNA surface. Using Manning's model, it was calculated that the subunit length over which counterions...

Electrical Transport Properties of Au-Doped Deoxyribonucleic Acid Molecules

Deoxyribonucleic acid (DNA) molecules were doped with Au atoms and their electrical transport properties were measured. The Au doping was carried out by incubating a mixture of HAuCl4·3H2O and DNA solutions. The binding of Au atoms to DNA bases was identified using Fourier transform infrared spectroscopy and X-ray photoemission spectroscopy. The Au-doped DNA molecules were deposited on nanoelectrodes and the presence of the molecules between the electrodes was determined by both scanning electron microscopy and atomic force microscopy. Measurement of the current-voltage characteristics showed that the Au-doped DNA molecules exhibited a higher conductivity than undoped DNA molecules. Detailed analysis of the chemical composition shows that there is a strong possibility of reliably controlling the conductivity of DNA molecules using this method.

Applicability of the Quantification of Genetically Modified Organisms to Foods Processed from Maize and Soy

The applicability of quantifying genetically modified (GM) maize and soy to processed foods was investigated using heat treatment processing models. The detection methods were based on real-time quantitative polymerase chain reaction (PCR) analysis. Ground seeds of insect resistant GM maize (MON810) and glyphosate tolerant Roundup Ready (RR) soy were dissolved in water and were heat treated by autoclaving for various time intervals. The calculated copy numbers of the recombinant and taxon specific deoxyribonucleic acid (DNA) sequences in the extracted DNA solution were found to decrease with time. This decrease was influenced by the PCR-amplified size. The conversion factor (Cf), which is the ratio of the recombinant DNA sequence to the taxon specific DNA sequence and is used as a constant number for calculating GM% at each event, tended to be stable when the sizes of PCR products of two DNA sequences were nearly equal. The results suggested that the size of the PCR product plays a key role in the quantification of GM organisms in processed foods. It is believed that the Cf of the endosperm (3n) is influenced by whether the GM originated from a paternal or maternal source. The embryos and endosperms were separated from the F1 generation seeds of five GM maize events, and their Cf values were measured. Both paternal and maternal GM events were identified. In these, the endosperm Cf was lower than that of the embryo, and the embryo Cf was lower than that of the endosperm. These results demonstrate the difficulties encountered in the determination of GM% in maize grains (F2 generation) and in processed foods from maize and soy.

Selective Adsorption of DNA onto SiO2 Surface in SiO2/SiH Pattern

Deoxyribonucleic acid (DNA) molecules can be selectively adsorbed onto a SiO2 surface in SiO2/SiH pattern, fabricated using photolithography, by adding MgCl2 to a DNA solution. Since DNA molecules can be adsorbed onto a Si substrate through Mg2+, the adsorption of DNA molecules in a SiO2/SiH pattern is influenced by the concentration of MgCl2 and the difference in chemical property between a SiO2 surface and a SiH surface. The optimum concentration of MgCl2 at which DNA molecules are selectively adsorbed onto a SiO2 surface was 0.1 mM.

Self-organization of histone-jointed three-dimensional DNA network

A three-dimensional deoxyribonucleic acid (DNA) network was self-organized in a space between two cover slips, which was filled with an aqueous solution of lambda DNA mixed with multivalent cations such as Ca 2+ and histone; the former behaves as a DNA fixation factor on the cover-slip surface and the latter as a junction and pillar construction factor for the network. The geometry and the components of the three-dimensional DNA network thus formed were observed by fluorescence microscopy. It is revealed that (1) the three-dimensional network is based on two-dimensional networks formed on the inner surfaces of the two cover slips, (2) the three-dimensional network is composed of junctions for forming the two-dimensional networks, chains for connecting two adjacent junctions, and pillars connecting the two-dimensional network on one cover-slip surface to the other, and (3) the chains are made of bundles of stretched lambda DNA molecules, and the junctions and the pillars are made of the aggregates of DNA–histone complexes.

Controlled deposition of single DNA molecules on bare gold electrodes

We report a new approach to a directly controlled deposition of long deoxyribonucleic acid (DNA) molecules on a bare gold electrode array predefined on a positively charged substrate surface by electrostatic interaction without modification of gold electrodes and DNA molecules. The method involves depositing amino-terminated self-assembled monolayer on a specific region on a SiO 2/Si substrate, and subsequently defining gold electrode array on the modified region by mask pattern transfer technique, as well as transferring a droplet of DNA solution onto the patterned substrate. Atomic force microscopy observations demonstrate that DNA molecules are significantly less stable on the bare gold surface than that on the aminothiolated gold surface. However, DNA can stably immobilize on the bare gold electrode array predefined on the positively charged substrate surface. The noncovalent binding of DNA onto the bare gold electrodes was shown to be robust enough to withstand ultrasonically washing. The approach represents a simple route to positioning of single DNA molecules on predefined structures, and can be potentially applied to other charged one-dimensional nanostructures.