DNA In Aqueous Solution Research Articles

Effect of Ultrahigh Dose Rate on Biomolecular Radiation Damage.

Dose rate is one of the important parameters in radiation-induced biomolecular damage. The effects of dose rate have been known to modify radiation toxicity in biological systems. The rate and extent of sublethal DNA damage (e.g., base damage and single-strand breaks) repair and those of cell proliferation have been manifested by dose rate. However, the recent preclinical application of ultrahigh dose rate [(UHDR) ca. 40 Gy/s and higher] radiation modalities have been shown to lower the type and extent of radiation damage to biological systems. At these UHDR, radiation-induced physicochemical and chemical processes are expected to differ from those observed after irradiation at conventional dose rates (CONV). It is unclear whether these UHDR conditions can affect the quality (type) and quantity (extent) of biomolecular damage such as DNA lesions. Here, we comparatively study the influence of indirect effects of CONV and UHDR on the formation of DNA strand breaks and clustered damage including densely accumulated lesions in an aerated and an anoxic dilute aqueous solution of a plasmid DNA model under low and high hydroxyl radical (•OH) scavenging conditions. Aqueous solutions of purified supercoiled plasmid DNA (pUC19) were prepared in either air- or nitrogen-saturated conditions, with Tris buffer added as the radiation-produced •OH scavenger at low and high scavenging capacities. These DNA samples were irradiated using kV X-ray systems at CONV (0.1 Gy/s) and high dose rate (HDR, 25 Gy/s) as well as UHDR (55 and 125 Gy/s) under different scavenging and environmental conditions. DNA lesions including strand breaks and clustered damage including densely accumulated lesions were quantified by gel electrophoresis and the yields of these lesions were calculated from the dose-response curve. Non-DSB clustered damage including densely accumulated lesions were evaluated by treating DNAs using bacterial endonuclease enzymes (Fpg and Nth) prior to gel electrophoresis. UHDR of 55 and 125 Gy/s induced lower amounts of both isolated strand breaks and clustered DNA damage including densely accumulated lesions at doses >40 Gy in the presence of oxygen, compared to the abundance of these lesions induced by 0.1 and 25 Gy/s irradiation under the same dose conditions. Overall, the strand break and clustered damage including densely accumulated lesions yields decreased by factors of 1.3-3.5 after UHDR. We did not observe these differences either via •OH scavenging or by removing oxygen from the solution. In addition, our results point out that the inter-track recombination reactions did not contribute to the observed dose-rate effects on DNA damage. The effects of dose rate on DNA damage are highly dependent on the total dose, as expected, but also on the •OH scavenging capacity that is employed in the aqueous DNA solutions. These important variables may be relevant in biological systems as well. On a practical level, our in vitro plasmid DNA model, which permits to precisely vary the scavenging capacity and gassing conditions (air saturated vs. N2 saturated) can help to differentiate dose-rate effects on biomolecular damage. Our results indicate that the radical-radical reactions are important in understanding the dose-rate effect on DNA damage.

In silico study of DNA mononucleotide self-assembly.

Recent experiments have demonstrated the self-assembly and long-range ordering of concentrated aqueous solutions of DNA and RNA mononucleotides. These are found to form Watson-Crick pairs that stack into columns that become spatially organized into a columnar liquid-crystalline phase. In this work, we numerically investigate this phase behavior by adopting an extremely coarse-grained model in which nucleotides are represented as semi-disk-like polyhedra decorated with attractive (patchy) sites that mimic the stacking and pairing interactions. We carry out Monte Carlo simulations of these patchy polyhedra by adapting algorithms borrowed from computer graphics. This model reproduces the features of the experimental phase behavior, which essentially depends on the combination of pairing and stacking interactions.

Effects of low-dose gamma radiation on DNA measured using a quartz tuning fork sensor

Despite the expected direct effects of radiation on DNA through its direct interaction with the biomolecule, research indicates that radiation also interacts with the DNA’s environment, resulting in indirect effects. Therefore, in this study, we explored the feasibility of using the quartz tuning fork (QTF) sensor system in biomedical applications, specifically in detecting DNA damage caused by low doses of gamma radiation, directly and indirectly. We differentiated between direct and indirect damage by analyzing the fork’s resonance frequency changes. This experiment was divided into three stages: before, during, and after irradiation. Each stage involved samples of pure DNA and DNA in a 60-µL aqueous solution, evaluated under identical conditions. Before irradiation, we measured frequency shifts (Δf) over a 20-min period, resulting in values of 19.34, 20.25, and 7.6 Hz for water, DNA, and DNA in water, respectively. Subsequently, the samples were irradiated with cesium-137 for the specified duration, resulting in frequency shifts of ∼ 39.21, 28.37, and 41.23 Hz for the same conditions. Our investigations showed an increase in Δf from 20.25 to 28.3 Hz at doses ranging from 7.5 to 30 µGy for pure DNA. Interestingly, DNA in aqueous solution exhibited hypersensitivity to radiation, with frequency shifts ranging from 7.6 to 41.23 Hz. Furthermore, we observed a significant difference in frequency shift after irradiation between pure DNA and DNA in water, with shifts of ∼ 70.75–98.45 Hz and 56.32–79.28 Hz for DNA and DNA in water, respectively. This result indicates a significant increase in DNA damage in aqueous environments, driven by the generation of active hydroxyl radicals (OH−), resulting in base damage and an associated increase in strand breaks. Consequently, our research indicates a lack of substantial direct impact on DNA repair owing to the absence of a conducive postirradiation environment. Therefore, QTF is a valuable biomarker for radiation sensitivity and is promising for future applications as a mass-sensitive biosensor.

Interactions of Co(II)- and Zn(II)porphyrin of 5,10,15,20-tetrakis(1-methyl-4-pyridinio)porphyrin with DNA in Aqueous Solution and Their Antimicrobial Activities.

Antibiotics are frequently used to treat, prevent, or control bacterial infections, but in recent years, infections resistant to all known classes of conventional antibiotics have significantly grown. The development of novel, nontoxic, and nonincursive antimicrobial methods that work more quickly and efficiently than the present antibiotics is required to combat this growing public health issue. Here, Co(II) and Zn(II) derivatives of tetrakis(1-methylpyridinium-4yl)porphyrin [H2TMPyP]4+ as a tetra(ρ-toluenesulfonate) were synthesized and purified to investigate their interactions with DNA (pH 7.40, 25 °C) using UV-vis, fluorescence techniques, and antimicrobial activity. UV-vis results showed that [H2TMPyP]4+ had a high hypochromicity (∼64%) and a substantial bathochromic shift (Δλ, 14 nm), while [Co(II)TMPyP]4+ and [Zn(II)TMPyP]4+ showed little hypochromicity (∼37%) and a small bathochromic shift (Δλ, 3-6 nm). Results reveal that [H2TMPyP]4+ interacts with DNA via intercalation, while Co(II)- and [Zn(II)TMPyP]4+ interact with DNA via outside self-stacking. Fluorescence results also confirmed the interaction of [H2TMPyP]4+ and the metalloporphyrins with DNA. Results of the antimicrobial activity assay revealed that the metalloporphyrins showed inhibitory effects on Gram-positive and Gram-negative bacteria and fungi, but that neither the counterions nor [H2TMPyP]4+ exhibited any inhibitory effects. Mechanism of antimicrobial activities of metalloporphyrins are discussed.

Induced chiroptical properties of helical Eu(iii) complex by electrostatic interaction with DNA

CPL activity was successfully induced from a helical Eu(iii) complex, EuLCOOH, by electrostatic interaction with DNA in aqueous solutions.

Deciphering the Role of Anions of Ionic Liquids in Modulating the Structure and Stability of ct-DNA in Aqueous Solutions.

Stabilizing biomolecules under ambient conditions can be extremely beneficial for various biological applications. In this context, the utilization of ionic liquids (ILs) in enhancing the stability and preservation of nucleic acids in aqueous solutions is found to be promising. While the role of the cationic moiety of ILs in the said event has been thoroughly explored, the importance of the anionic moiety in ILs, if any, is rather poorly understood. Herein, we examine the function of anions of ILs in nucleic acid stabilization by examining the stability and structure of calf thymus-DNA (ct-DNA) in the presence of various ILs composed of a common 1-ethyl-3-methylimidazolium cations (Emim+) and different anions, which includes Cl-, Br-, , and by employing various spectroscopic techniques as well as Molecular Dynamics (MD) simulation studies. Analysis of our data suggests that the chemical nature of anions including polarity, basicity, and hydrophilicity become an important factor in the overall DNA-IL interaction event. At lower concentrations, the interplay of intermolecular interaction between the IL anions with their respective cations and the solvent molecules becomes a very crucial factor in inducing their stabilizing effect on ct-DNA. However, at higher concentrations of ILs, the ct-DNA stabilization is additionally governed by specific-ion effect. MD simulation studies have also provided valuable insights into molecular-level understanding of the DNA-IL interaction event. Overall, the present study clearly demonstrated that along with the cationic moiety of ILs, the anions of ILs can play a significant role in deciding the stability of duplex DNA in aqueous solution. The findings of this study are expected to enhance our knowledge on understanding of IL-DNA interactions in a better manner and will be helpful in designing optimized IL systems for nucleic acid based applications.

8-Oxoguanine-DNA-Glycosylase Gene Polymorphism and the Effects of an Alternating Magnetic Field on the Sensitivity of Peripheral Blood.

The production of reactive oxygen species (ROS) in animals and cells often results from exposure to low-intensity factors, including magnetic fields. Much of the discussion about the initiation of oxidative stress and the role of ROS and radicals in the effects of magnetic fields has centered on radical-induced DNA damage. The DNA concentration in the final solution was determined spectrophotometrically. Typing of the polymorphic variant rs1052133 of the 8-oxoguanin DNA glycosylase (hOGG1) gene was performed by polymerase chain reaction. An enzyme immunoassay was performed to determine the level of 8-oxyguanine in DNA. To process samples exposed to an alternating magnetic field, the authors developed a device for the automated study of biological fluids in an alternating magnetic field. The content of hydrogen peroxide in aqueous solutions of DNA was determined using the spectrophotometric method. It was experimentally determined that an increase in the concentration of hydrogen peroxide in an aqueous medium by 3-5 times under the action of a low-frequency magnetic field reduces the resistance of the genomic material to oxidative modification and the accumulation of 8-oxyguanine in DNA. A model is proposed for the mechanism of action of a low-frequency magnetic field on aqueous solutions of nucleic acids and proteins, which satisfies the model of a chemical oscillator for the transformations of reactive oxygen species in an aqueous medium. The model illustrates the oscillating nature of the processes occurring in an aqueous solution of DNA and makes it possible to predict changes in the concentration of hydrogen peroxide in an aqueous solution of biopolymers, depending on the frequency of the acting low-intensity magnetic field. The key element in the mechanisms involved in the effects of low-intensity magnetic field on living systems is the occurrence of ROS generation in the aquatic environment of chemical oscillators, in which the competition of physical and chemical processes (electron transfers, reactions of decay and addition of radicals, spin magnetically induced conversion, synthesis, and decay of the longest-lived form-hydrogen peroxide) is controlled by a magnetic field.

Interactions of ammonium based ionic liquids with DNA in aqueous medium through Volumetric, acoustic and viscometric properties

Ionic liquids (ILs) have emerged as a promising alternative solvent for DNA based studies as most of the studied ILs enhance the stability of DNA and act as a media for extraction and storage. Investigation of IL-DNA interactions through spectroscopic and computational analysis have been carried out earlier and we here attempt to explore the interaction through physicochemical properties of IL-DNA mixture in water medium that provide fundamental knowledge of the solvation behaviour. Properties such as density, ρ, speed of sound, u and viscosity, η, of two ILs, Benzyltributylammonium chloride ([BTBA]Cl) and Tetrabutylammonium bromide ([TBA]Br) in water as well as in aqueous DNA solutions with varying concentrations were measured over a temperature range from 293.15 − 323.15 K and at atmospheric pressure. The derived volumetric properties were calculated to understand the strength and extent of the solute–solvent interactions prevail in the solution. The analysis of partial molar volume at infinite dilution, V2∞, helped in the comparison of the strength of the interactions in between the studied solutes. The second derivative of V2∞ with respect to temperature, (∂2V2∞/∂T2)P facilitated in identifying the influence of the solutes in water structure formation around the solute and it was interesting to note that, although both the ILs behaved similarly in water as structure makers, [TBA]Br showed variation in the presence of DNA by demonstrating water structure breaking effects. Similar results were obtained from the analysis of viscometric properties as well. Further, the capability of the ILs to stay solvated in the DNA aqueous solution was confirmed by the results from the solvation number calculations.

Optical Polymorphism of Liquid-Crystalline Dispersions of DNA at High Concentrations of Crowding Polymer.

Optically active liquid-crystalline dispersions (LCD) of nucleic acids, obtained by polymer- and salt-induced (psi-) condensation, e.g., by mixing of aqueous saline solutions of low molecular weight DNA (≤106 Da) and polyethylene glycol (PEG), possess an outstanding circular dichroism (CD) signal (so-called psi-CD) and are of interest for sensor applications. Typically, such CD signals are observed in PEG content from ≈12.5% to ≈22%. However, in the literature, there are very conflicting data on the existence of psi-CD in DNA LCDs at a higher content of crowding polymer up to 30-40%. In the present work, we demonstrate that, in the range of PEG content in the system above ≈24%, optically polymorphic LCDs can be formed, characterized by both negative and positive psi-CD signals, as well as by ones rather slightly differing from the spectrum of isotropic DNA solution. Such a change in the CD signal is determined by the concentration of the stock solution of PEG used for the preparation of LCDs. We assume that various saturation of polymer chains with water molecules may affect the amount of active water, which in turn leads to a change in the hydration of DNA molecules and their transition from B-form to Z-form.

DNA-induced circularly polarized luminescence of helicene racemates.

Enantiopure helicenes have been extensively investigated due to their outstanding chiroptical properties, while helicene racemates are considered as chiroptically silent. Here, we describe a facile method to produce circularly polarized luminescence (CPL) from helicene racemates via supramolecular association with DNA in aqueous solution. Racemic cationic helicene derivatives are immobilized in the grooves of commercially available double-stranded right-handed DNA, and the discrimination of left- and right-handed helicenes by chiral DNA is monitored by single molecule force spectroscopy. This subsequently leads to the generation of prominent CPL with dissymmetric factor |glum | of close to 0.01, which is approximate to enantiopure helicenes. The strategy developed in this work avoids the tedious and expensive chiral resolution process and provides a distinctive insight into the fabrication of CPL-emitting systems.

Mesoporous aluminum impregnated rubber seed shell waste enriched with calcium as adsorbent material for the removal of microbial DNA in aqueous solution

Water contamination by pathogens and diseases induced by these pathogens is a major water quality issue all over the world. Poor public health has been linked to tap water polluted with DNA harboring antibiotic resistance genes sequence. According to HSAB concept, surface modification of rubber seed shell waste with alumina (AIRSS) as novel agro-waste adsorbent creates more active surface constituents for DNA adsorption. The proximate, ultimate and EDAX analysis provides the percentage levels of ash concentration, volatile, moisture and fixed carbon content, elemental composition present in the adsorbent. The structural features of AIRSS were determined using FT-IR, SEM and XRD. In order to improve reaction conditions, the effect of pH, temperature, adsorbent amount, and reaction time is also examined. The highest percent of DNA removal (92.5%) was achieved at the optimum conditions: 2 g/L at pH 4, contact time 120 minutes as compared to the conventional methods. The DNA adsorbs onto the surface of AIRSS through physical (vander Waals force) and chemical interactions, as demonstrated by kinetics and spectroscopic analyses. Changes in enthalpy (H), free energy (G), and entropy (S) indicate that adsorption is a spontaneous and exothermic process, according to thermodynamic parameters. The results of the experiments showed that the prepared AIRSP adsorbent could be used to remove DNA from water. The efficacy of AIRSS for the removal of DNA has decreased after nine months of storage and use. Low pH and the presence of AIRSS improved DNA-AIRSS adsorption, according to our findings.

Columnar liquid crystalline phases of surfactant-DNA complexes

ABSTRACT Cationic surfactants form complexes with DNA in aqueous solutions. In the case of single-chain surfactants that self-assemble into micelles, these complexes have a two-dimensional columnar structure. We have studied the structural polymorphism of such complexes by varying the chain length of the surfactant. A variety of columnar structures are observed, such as square, hexagonal and superhexagonal. Formation of these different structures can be qualitatively understood in terms of the interplay between entropic and electrostatic contributions to their free energy.

Broadband Passively Mode-Locked Fiber Laser with DNA Aqueous Solution as Saturable Absorber

We demonstrate a passively mode-locked fiber laser using aqueous DNA solution as a saturable absorber (SA), with broadband pulse laser emission from 1 to 1.5 µm. The mode-locked laser with erbium-doped fiber as the gain material has a center wavelength of 1563 nm, a 3 dB bandwidth of 3.9 nm, and a pulse width of 822 fs, whereas the laser with ytterbium-doped fiber as the gain material and an identical DNA aqueous SA has a center wavelength of 1037 nm, a 3 dB bandwidth of 5.04 nm, and a pulse width of 250 ps. The proposed laser, which is simple and cost effective to fabricate, exhibits excellent long-term stability as well as thermal stability during high-power operation. This mode-locked laser scheme with a liquid-phase DNA component has the potential to provide in-depth understanding of the optical nonlinearity and usefulness of DNA.

Double-strand breaks in genome-sized DNA caused by megahertz ultrasound

Double-strand breaks (DSBs) of giant DNA molecules after exposure to 1.0 MHz pulsed-wave ultrasound were quantitatively evaluated by single-molecule observation of giant DNA (T4 GT7 DNA; 166 kbp) through fluorescence microscopy. Aqueous solutions of DNA were exposed to ultrasonic waves with different sound pressures, repetition periods (1, 2, 5 ms), and pulse durations (5, 10, 50 μs). Below a threshold value of sound pressure, almost no double-strand breaks were generated, and above the threshold, the degree of damage increased in an accelerated manner as the pressure increased. DNA damage was much more severe for exposure to ultrasound with a shorter pulse duration. In addition, a longer pulse repetition period caused worse damage in DNA molecules. The effect of microbubbles on the damage induced by exposure to ultrasound had also been studied. While a result showed that a very small amount of microbubbles increased DSBs of DNA, this effect of microbubbles only weakly depended on their concentrations.

Solvent Effect to the Uniformity of Surfactant-Free Salmon-DNA Thin Films.

Fabrication of surfactant-modified DNA thin films with high uniformity, specifically DNA–CTMA, has been well considered via drop-casting and spin-coating techniques. However, the fabrication of thin films with pure DNA has not been sufficiently studied. We characterize the uniformity of thin films from aqueous salmon DNA solutions mixed with ethanol, methanol, isopropanol, and acetone. Measurements of thickness and macroscopic uniformity are made via a focused-beam ellipsometer. We discuss important parameters for optimum uniformity and note what the effects of solvent modifications are. We find that methanol- and ethanol-added solutions provide optimal fabrication methods, which more consistently produce high degrees of uniformity with film thickness ranging from 20 to 200 nm adjusted by DNA concentration and the physical parameters of spin-coating methods.

Buffered λ-DNA solutions at high shear rates

We study buffered aqueous solutions of deoxyribonucleic acid isolated from bacteriophage lambda (λ-DNA) at shear rates up to 105 s−1. The shear rates are accessed with a narrow-gap rheometer at gap widths down to 20 μm. At lower shear rates, our data merge with the literature values. At high shear rates, the viscosity levels off into an infinite-shear viscosity plateau. Hence, the viscosity functions of buffered aqueous DNA solutions are now available for the entire shear-rate range from the first Newtonian plateau to that of infinite-shear viscosity. The latter hardly differs from the solvent viscosity. For the normal-stress differences, we observe a power-law dependence on the shear rate close to previous findings up to shear rates of about 104 s−1. Beyond this shear-rate range, we observe a stepwise change with the shear rate. By means of agarose gel electrophoresis, we confirm that the λ-DNA is not fragmented during our rheometric study at high shear rates. Yet, at the highest shear rates studied, shear-induced changes in the DNA to structures not being able to travel through the gel appear.

Liquid Crystal Peptide/DNA Coacervates in the Context of Prebiotic Molecular Evolution

Liquid–liquid phase separation (LLPS) phenomena are ubiquitous in biological systems, as various cellular LLPS structures control important biological processes. Due to their ease of in vitro assembly into membraneless compartments and their presence within modern cells, LLPS systems have been postulated to be one potential form that the first cells on Earth took on. Recently, liquid crystal (LC)-coacervate droplets assembled from aqueous solutions of short double-stranded DNA (s-dsDNA) and poly-L-lysine (PLL) have been reported. Such LC-coacervates conjugate the advantages of an associative LLPS with the relevant long-range ordering and fluidity properties typical of LC, which reflect and propagate the physico-chemical properties of their molecular constituents. Here, we investigate the structure, assembly, and function of DNA LC-coacervates in the context of prebiotic molecular evolution and the emergence of functional protocells on early Earth. We observe through polarization microscopy that LC-coacervate systems can be dynamically assembled and disassembled based on prebiotically available environmental factors including temperature, salinity, and dehydration/rehydration cycles. Based on these observations, we discuss how LC-coacervates can in principle provide selective pressures effecting and sustaining chemical evolution within partially ordered compartments. Finally, we speculate about the potential for LC-coacervates to perform various biologically relevant properties, such as segregation and concentration of biomolecules, catalysis, and scaffolding, potentially providing additional structural complexity, such as linearization of nucleic acids and peptides within the LC ordered matrix, that could have promoted more efficient polymerization. While there are still a number of remaining open questions regarding coacervates, as protocell models, including how modern biologies acquired such membraneless organelles, further elucidation of the structure and function of different LLPS systems in the context of origins of life and prebiotic chemistry could provide new insights for understanding new pathways of molecular evolution possibly leading to the emergence of the first cells on Earth.

Poly(2‐[dimethylamino]ethyl methacrylate)‐b‐poly(hydroxypropyl methacrylate)/DNA polyplexes in aqueous solutions

AbstractThis study involves the investigation of the complexation ability of poly(2‐[dimethylamino]ethyl methacrylate)‐b‐poly(hydroxypropyl methacrylate) (PDMAEMA‐b‐PHPMA) amphiphilic pH and thermoresponsive block copolymers, and their quaternized counterparts QPDMAEMA‐b‐PHPMA, toward short DNA in aqueous solutions. The PDMAEMA‐b‐PHPMA amphiphilic block copolymers present various self‐assembly characteristics when inserted into aqueous media, depending on the composition, the solubilization protocol, the acidity and the temperature of the aqueous media. Copolymer aggregates‐DNA interactions and nanostructure formation after complexation are investigated by dynamic light scattering and intensity measurements in aqueous solutions in a fixed temperature range, utilizing two different solubilization protocols for the copolymers. Ethidium bromide assays by fluorescence spectroscopy and ζ‐potential measurements were also utilized to investigate the structure and properties of the DNA/copolymer polyplexes. The interpretation of such physicochemical characterization provides extra comprehension of the novel (Q)PDMAEMA‐b‐PHPMA copolymers self‐assembly characteristics and assesses their ability for DNA complexation, stabilization, and delivery.

Combining particle tracking microrheology and viscometry for the study of DNA aqueous solutions.

We use video particle tracking microrheology (VPTMR) in order to investigate the viscoelasticity of salmon DNA and correlate it to its steady-flow shear-thinning viscosity. Aqueous solutions of DNA are tested in a wide concentration range from the dilute to the semidilute unentangled concentration regime. The observed mean squared displacement shows power-law scaling with lag-time which is equivalent to power-law behavior of the complex modulus as a function of frequency that is, |G* (ω)| = S ∙ ω α . The relaxation exponent α changes abruptly with concentration in the semidilute regime from about 1 to about 0.5 which is the exponent predicted by the Rouse model. The quasi-property S follows the scaling of viscosity for uncharged polymers near θ-conditions in the semidilute regime that is, with νeff = 0.50 - 0.51. The shear-thinning exponent observed by viscometry increases gradually towards the value of 0.5 which has been predicted for Rouse chains under flow. Our findings are in agreement with recent studies of DNA solutions where DNA is treated as a model polymer and addresses the low-molar mass regime of DNA viscoelasticity. This work demonstrates that the combination of passive particle tracking with viscometry can provide a complete picture on the viscoelasticity of DNA-based biopolymer materials.

DNA Sequencing Modified Method through Effective Regulation of Its Translocation Speed in Aqueous Solution

Solid-state nanopore DNA sequencing modified method is developed. Method is based on the tunnel current investigation through the nanogap made on lateral gold electrodes in the form of nanowires or nanoribbons. The movement of DNA in aqueous solution is regulated by the potential applied to reference electrode. The potential applied to the lateral metal electrodes helps to the creation of the molecular junctions. They consist of the nucleosides passing through the pores. Taking into account that DNA moves under gravity, electrophoretic and drag forces, the analytic expression for the DNA translocation speed is calculated and analyzed. The conditions for decreasing the DNA translocation speed or increasing the nucleosides reading time are received. It is shown that one can control value of the DNA molecules bases reading time and the frequency of the bases passes by the choice of magnitude of the potential applied to reference electrode. Our results, therefore potentially suggest a realistic, inherently design-specific, high-throughput nanopore DNA sequencing device/cell as a de-novo alternative to the existing methods.