Calculating Melting Temperature of Native and Modified Oligonucleotide Complexes at Various Cation Concentrations with the Use of Enhanced Counterion Condensation Model

2010 ◽  
Vol 3 (2) ◽  
pp. 61-75
Author(s):  
Aleksandr A. Lomzov ◽  
Dmitriy V. Pyshnyi
Keyword(s):  
Thermal Stability ◽  
Ionic Strength ◽  
Melting Temperature ◽  
Binding Constants ◽  
Data Sets ◽  
Dna Duplexes ◽  
Counterion Binding ◽  
Cation Concentration ◽  
Wide Range ◽  
Thermal Stability Of

A new model describing the influence of ionic strength on thermal stability of DNA comlexes of oligonucleotides is proposed. This model assumes that binding of cations with DNA polyanions influences solely the entropy of hybridization and has a saturating mode. The efficacy of counterion binding with single- and double-stranded DNA is different, and the number of cations which bind additionally with the oligonucleotide at duplex formation depends on bulk cation concentration. Analytical equations describing the influence of cation concentration on melting temperature of DNA-duplexes as function of the length of oligonucleotide, its GC-composition and presence of the modification (non-nucleotide insert) were obtained. The values of melting temperature (Tm ) and thermodynamic parameters ( o ∆H , o ∆S ) characterizing the hybridization of both native and «bridged» oligonucleotides (bearing non-nucleotide insert on the basis of diethylene glycol phosphodiester) with DNA in various concentrations of NaCl (0,01÷1 М) were obtained using the UV-melting technique. Based on both the data obtained and presented in literature the database (695 data sets) characterizing the influence of ionic strength on the thermal stability of oligonucleotide complexes of various structure is developed. The database analysis allows us to obtain the values of the equilibrium binding constants for condensation of caions on DNA and the number of ions required for saturation of a discrete binding site. The proposed enhanced model of cation condensation utilizing unified thermodynamic increments of dsDNA formation allows us to calculate melting temperatures of DNAduplexes in the wide range of ionic strength ([Na+] = 0,01÷1 М) with high accuracy.

A Comparative Study of the Influence of Aquaous 2,2,2-Trifluoroethanol And Ethanol on the Structural Organization, the Kinetic and Thermodynamic Properties of Oligodeoxyribonucleotides Intermolecular Complex Formation

2013 ◽  
Vol 8 (1) ◽  
pp. 115-124
Author(s):  
Aleksandr Lomzov ◽  
Kseniya Ivanova ◽  
Inna Pyshnaya ◽  
Elena Dmitrienko ◽  
Dmitriy Pyshnyi
Keyword(s):  
Thermal Stability ◽  
Aqueous Solution ◽  
Comparative Study ◽  
Melting Temperature ◽  
Structural Organization ◽  
Volume Fraction ◽  
Dna Duplexes ◽  
Intermolecular Complex ◽  
Linear Decrease ◽  
Thermal Stability Of

A comparative study of the structural organization, thermodynamic and kinetic properties of the oligodeoxynucleotides complexes formation in the presence of 2,2,2-trifluoroethanol and ethanol in aqueous solution (volume fraction of alcohol 0 to 50 %) was performed. No significant changes in the circular dichroism spectra of oligonucleotides and their complexes at the adding of 50 % v/v alcohol into a solution, was observed, and they retain the profile typical for B-form DNA. The study of the thermal stability of DNA duplexes showed that the increase in the volume fraction of ethanol in the aqueous solution up to 50 % results in a linear decrease in the melting temperature of the intermolecular DNA complexes. In the case of the 2,2,2-trifluoroethanol we observed atypical dependence of thermal stability of DNA duplexes on the fraction of the fluorine-containing co-solvent. Increasing the alcohol fraction from 0 to 20% v/v led to a linear decrease of the melting point of the complex. A further increase in the volume fraction of alcohol (up to 50 %) did not change the thermal stability of the duplexes. It was shown, that the destabilizing effect of the two co-solvents is due to the increase of the dissociation rate constant of the complex and has mainly entropic nature. On the example of oligonucleotides complexes of 8, 12, 15 and 20 base pairs length the possibility of prediction DNA duplexes thermal stability was shown. A model taking into account the change of a number solvent molecules interacting with nucleic acids at the duplex formation in aqueous ethanol (50 % v/v) or trifluoroethanol (20 % v/v) was applied. An accuracy of melting temperature prediction was 1.3 and 0.6 degrees. Using this model, we found that the addition of alcohols in solution leads to an increase in the number of water molecules that bind to a complementary pair of nucleotides at the formation of intermolecular complex (in the presence of ethanol or trifluoroethanol 0.51 ± 0.09 and 1.33 ± 0.12, respectively). At the same time, alcohols interacted with single-stranded oligonucleotides and double-stranded in the same way

scholarly journals Intracellular Ionic Strength Sensing Using NanoLuc

2021 ◽  
Vol 22 (2) ◽  
pp. 677
Author(s):  
Tausif Altamash ◽  
Wesam Ahmed ◽  
Saad Rasool ◽  
Kabir H. Biswas
Keyword(s):  
Thermal Stability ◽  
Phase Separation ◽  
Drug Discovery ◽  
Ionic Strength ◽  
Cellular Signaling ◽  
Live Cells ◽  
Protein Activity ◽  
Cellular Survival ◽  
Cellular Processes ◽  
Wide Range

Intracellular ionic strength regulates myriad cellular processes that are fundamental to cellular survival and proliferation, including protein activity, aggregation, phase separation, and cell volume. It could be altered by changes in the activity of cellular signaling pathways, such as those that impact the activity of membrane-localized ion channels or by alterations in the microenvironmental osmolarity. Therefore, there is a demand for the development of sensitive tools for real-time monitoring of intracellular ionic strength. Here, we developed a bioluminescence-based intracellular ionic strength sensing strategy using the Nano Luciferase (NanoLuc) protein that has gained tremendous utility due to its high, long-lived bioluminescence output and thermal stability. Biochemical experiments using a recombinantly purified protein showed that NanoLuc bioluminescence is dependent on the ionic strength of the reaction buffer for a wide range of ionic strength conditions. Importantly, the decrease in the NanoLuc activity observed at higher ionic strengths could be reversed by decreasing the ionic strength of the reaction, thus making it suitable for sensing intracellular ionic strength alterations. Finally, we used an mNeonGreen–NanoLuc fusion protein to successfully monitor ionic strength alterations in a ratiometric manner through independent fluorescence and bioluminescence measurements in cell lysates and live cells. We envisage that the biosensing strategy developed here for detecting alterations in intracellular ionic strength will be applicable in a wide range of experiments, including high throughput cellular signaling, ion channel functional genomics, and drug discovery.

Thermal stability of marks gold nanoparticles: A molecular dynamics simulation

2017 ◽  
Vol 31 (07) ◽  
pp. 1741001
Author(s):  
Yanlin Jia ◽  
Siqi Li ◽  
Weihong Qi ◽  
Mingpu Wang ◽  
Zhou Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Melting Temperature ◽  
Cohesive Energy ◽  
Au Nanoparticles ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Structure Variation ◽  
Deformation Parameters ◽  
Thermal Stability Of

Molecular dynamics (MDs) simulations were used to explore the thermal stability of Au nanoparticles (NPs) with decahedral, cuboctahedral, icosahedral and Marks NPs. According to the calculated cohesive energy and melting temperature, the Marks NPs have a higher cohesive energy and melting temperature compared to these other shapes. The Lindemann index, radial distribution function, deformation parameters, mean square displacement and self-diffusivity have been used to characterize the structure variation during heating. This work may inspire researchers to prepare Marks NPs and apply them in different fields.

Thermal Decomposition of Supersaturated Ti1-xAlxN Solid Solution Synthesized by High-Energy Milling

2016 ◽  
Vol 9 ◽  
pp. 82-89
Author(s):  
Maya Radune ◽  
Michael Zinigrad ◽  
David Fuks ◽  
S. Hayun ◽  
Nachum Frage
Keyword(s):  
Thermal Stability ◽  
Solid Solution ◽  
Spinodal Decomposition ◽  
Density Functional ◽  
Chemical Deposition ◽  
High Energy ◽  
Nucleation And Growth ◽  
Scanning Calorimetry ◽  
Wide Range ◽  
Thermal Stability Of

Supersaturated titanium-aluminum nitride (Ti1-xAlxN) is a very attractive material for a wide range of applications due to its high oxidation and wear resistance accompanied by high strength, hardness, thermal conductivity and thermal shock resistance. Currently, its applications are limited to coatings obtained by physical or chemical deposition. Bulk materials based on Ti1-xAlxN may be fabricated by powder metallurgy approach using powders synthesized by high-energy ball milling (HEBM), which composition corresponds to supersaturated Ti1-xAlxN solid solution. In the present study, thermal stability of the supersaturated Ti1-xAlxN solid solution was investigated. According to the quasi-binary TiN-AlN phase diagram, constructed using density functional theory (DFT) analysis, the concentration ranges, where decomposition takes place through spinodal decomposition or through nucleation and growth, were determined. Experimental study on thermal stability of solid Ti1-xAlxN solution powder was conducted by means of differential scanning calorimetry (DSC), Brunauer-Emmited-Teller (BET) and XRD. The results indicated that spinodal decomposition of Ti1-xAlxN starts at 800°C, while at temperature higher than 1300°C regular decomposition (nucleation and growth) is occur.

scholarly journals Study of the thermal stability of foam of different expansion ratio

2020 ◽  
Vol 29 (3) ◽  
pp. 103-110
Author(s):  
A. V. Koksharov ◽  
S. I. Osipenko ◽  
E. V. Gaynullina
Keyword(s):  
Thermal Stability ◽  
Thermal Exposure ◽  
Expansion Ratio ◽  
Heat Fluxes ◽  
Foam Layer ◽  
Destructive Effect ◽  
Foam Expansion ◽  
Destruction Rate ◽  
Wide Range ◽  
Thermal Stability Of

Introduction. Currently, the industry produces a wide range of foam generators to produce fire-extinguishing foams, and the foams they produce differ significantly in their expansion ratio and, consequently, fire resistance. Since heat fluxes have the main destructive effect on the foam, the purpose of this paper is to establish the patterns of destruction of foam of different expansion ratio when heated.Methods of research. The foam with expansion ratio from 7.5 to 80 was used for the tests. It was obtained by mechanical beating of 6 % solution of foaming agent PO-6RZ. The thermal stability of the foam was studied when the heat flow from the gas burner flame affects the foam layer. During the experiment, the change in the height of the foam column in time was recorded.Results and Discussion. The results of measurements, presented in the form of dependence of foam layer destruction rate on time, quantity of released liquid phase on 1 m2·s, dependence of foam layer destruction rate on its density allowed revealing a number of patterns. The destruction rate of foam with an expansion ratio of up to 30 remains constant throughout the entire duration of thermal exposure. As the foam expansion ratio increases, the rate of destruction at the initial stage of heat flux exposure increases. With a foam expansion ratio of more than 50, there is initially a sharp increase in the rate of destruction, which subsequently decreases as the foam column decreases. In the conditions of the experiment, the best characteristics were shown by the foam with an expansion ratio of 50, because in the foam with a smaller expansion ratio the syneresis makes a significant contribution to its destruction, and the foams with a larger expansion ratio are destroyed by the mechanical effect of convective flame flows.Conclusion. The study of the foam destruction patterns under thermal impact allowed establishing the fact that its destruction is limited by the rate of impoverishment of the upper layers with liquid.

scholarly journals Thermal stability of N-heterocycle-stabilized iodanes – a systematic investigation

2019 ◽  
Vol 15 ◽  
pp. 2311-2318 ◽  
Author(s):  
Andreas Boelke ◽  
Yulia A Vlasenko ◽  
Mekhman S Yusubov ◽  
Boris J Nachtsheim ◽  
Pavel S Postnikov
Keyword(s):  
Thermal Stability ◽  
Differential Scanning Calorimetry ◽  
Thermogravimetric Analysis ◽  
Systematic Investigation ◽  
Scanning Calorimetry ◽  
Wide Range ◽  
C Decomposition ◽  
Thermal Stability Of ◽  
Peak Decomposition

The thermal stability of pseudocyclic and cyclic N-heterocycle-stabilized (hydroxy)aryl- and mesityl(aryl)-λ3-iodanes (NHIs) through thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) is investigated. Peak decomposition temperatures (T peak) were observed within a wide range between 120 and 270 °C. Decomposition enthalpies (ΔH dec) varied from −29.81 to 141.13 kJ/mol. A direct comparison between pseudocyclic and cyclic NHIs revealed high T peak but also higher ΔH dec values for the latter ones. NHIs bearing N-heterocycles with a high N/C-ratio such as triazoles show among the lowest T peak and the highest ΔH dec values. A comparison of NHIs with known (pseudo)cyclic benziodoxolones is made and we further correlated their thermal stability with reactivity in a model oxygenation.

Thermal Stability of NiAl-Base Coatings for High Temperature Application

2005 ◽  
Vol 237-240 ◽  
pp. 709-714
Author(s):  
Robert Filipek ◽  
Marek Danielewski ◽  
E. Tyliszczak ◽  
M. Pawełkiewicz ◽  
S. Datta
Keyword(s):  
Thermal Stability ◽  
Gas Turbines ◽  
Inverse Method ◽  
Critical Role ◽  
Diffusion Coatings ◽  
Aluminide Coatings ◽  
Wide Range ◽  
Industrial Energy ◽  
Temperature Application ◽  
Thermal Stability Of

Aluminide diffusion coatings act as a remedy against the aggressive environments in which modern aero-gas turbines operate. Platinum addition to basic aluminide coatings significantly improves the oxidation resistance of these coatings. The increase in operating temperatures of industrial energy systems and gas turbines, has led to the extensive use of coatings capable of providing improved service life. Interdiffusion plays a critical role in understanding the integrity of such coatings. The Danielewski-Holly model of interdiffusion which allows for the description of a wide range of processes (including processes stimulated by reactions at interfaces) is employed for studying of interdiffusion in the Pt-modified β-NiAl coatings. Using the inverse method the intrinsic diffusivities of Ni, Al and Pt were calculated. Such obtained diffusivities were subsequently used for modelling of thermal stability of Pt-modified aluminide coatings in air and in argon atmosphere.

Conductivity and Thermal-Stability of 5-Sulfosalicylic Acid Sodium Doped Polypyrrole

2010 ◽  
Vol 428-429 ◽  
pp. 579-582 ◽  
Author(s):  
Fu Fang Zhou ◽  
Bao Gai Zhai ◽  
Chun Xu Pan ◽  
Yuan Ming Huang
Keyword(s):  
Thermal Stability ◽  
Particle Size ◽  
Laser Light ◽  
Dopant Concentration ◽  
Laser Light Scattering ◽  
Probe Laser ◽  
Sulfosalicylic Acid ◽  
Wide Range ◽  
Thermal Stability Of

By varying the dopant-to-pyrrole ratio in a wide range from 0 to 60% a series of 5-sulfosalicylic acid sodium doped polypyrrole was synthesized in situ in aqueous solution with ferric chloride as the oxidant. The resulting polypyrroles were characterized with the four-probe, laser light scattering and thermo-gravimetry analysis, differential thermal analysis, respectively. Our results indicate that the particle size plays a determinative role to tune the conductivity in the studied range of dopant concentration; and this series of polypyrrole with size-tuned-conductivity exhibits little less thermal-stability although its size and conductivity changes simultaneously and acutely with the dopant concentration. The association of the conductivity with particle size was interpreted in terms of a theoretical model proposed by Baughman and Shacklelette.

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