scholarly journals Hydration Shells of DNA from the Point of View of Terahertz Time-Domain Spectroscopy

2021 ◽  
Vol 22 (20) ◽  
pp. 11089
Author(s):  
Nadezda A. Penkova ◽  
Mars G. Sharapov ◽  
Nikita V. Penkov
Keyword(s):  
Time Domain ◽  
Hydration Shell ◽  
Bound Water ◽  
Free Water ◽  
Point Of View ◽  
Water Molecules ◽  
Terahertz Time Domain Spectroscopy ◽  
Time Domain Spectroscopy ◽  
Effective Medium Model ◽  
Hydration Shells

Hydration plays a fundamental role in DNA structure and functioning. However, the hydration shell has been studied only up to the scale of 10–20 water molecules per nucleotide. In the current work, hydration shells of DNA were studied in a solution by terahertz time-domain spectroscopy. The THz spectra of three DNA solutions (in water, 40mm MgCl2 and 150 mM KCl) were transformed using an effective medium model to obtain dielectric permittivities of the water phase of solutions. Then, the parameters of two relaxation bands related to bound and free water molecules, as well as to intermolecular oscillations, were calculated. The hydration shells of DNA differ from undisturbed water by the presence of strongly bound water molecules, a higher number of free molecules and an increased number of hydrogen bonds. The presence of 40 mM MgCl2 in the solution almost does not alter the hydration shell parameters. At the same time, 150 mM KCl significantly attenuates all the found effects of hydration. Different effects of salts on hydration cannot be explained by the difference in ionic strength of solutions, they should be attributed to the specific action of Mg2+ and K+ ions. The obtained results significantly expand the existing knowledge about DNA hydration and demonstrate a high potential for using the THz time-domain spectroscopy method.

Hydration Shells of DPPC Liposomes from the Point of View of Terahertz Time-Domain Spectroscopy

2020 ◽  
pp. 000370282094928
Author(s):  
Nikita V. Penkov ◽  
Valery A. Yashin ◽  
Konstantin N. Belosludtsev
Keyword(s):  
Time Domain ◽  
Liquid Crystalline ◽  
Dynamic Properties ◽  
Free Water ◽  
Point Of View ◽  
Terahertz Time Domain Spectroscopy ◽  
Hydration Properties ◽  
Water Binding ◽  
Time Domain Spectroscopy ◽  
Hydration Shells

Analysis of structural and dynamic properties of water in suspensions of liposomes composed from 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in three phase states (gel, rippled gel, liquid crystalline phase) by means of terahertz time-domain spectroscopy in 0.3–3.3 THz range was conducted in the current work. Fraction of free water molecules in DPPC liposome suspension was shown to decrease with temperature (compared to the analogous aqueous solution without liposomes), and intermolecular water binding was enhanced. The most crucial changes occur during gel-rippled gel phase transition (pretransition): at temperatures below pretransition point, liposomes alleviate water binding degree, while at temperatures above the transition point, they enhance water binding. This study has demonstrated the high information content of the terahertz time-domain spectroscopy method for exploring the hydration properties of phospholipids in water.

scholarly journals Relationships between Molecular Structure of Carbohydrates and their Dynamic Hydration Shells Revealed by Terahertz Time-Domain Spectroscopy

2021 ◽  
Vol 22 (21) ◽  
pp. 11969
Author(s):  
Nikita V. Penkov
Keyword(s):  
Aqueous Solutions ◽  
Time Domain ◽  
Water Structure ◽  
Free Water ◽  
Equatorial Orientation ◽  
Terahertz Time Domain Spectroscopy ◽  
Time Domain Spectroscopy ◽  
Glycosidic Bonds ◽  
Hydration Shells ◽  
Hydrogen Bond Energies

Despite more than a century of research on the hydration of biomolecules, the hydration of carbohydrates is insufficiently studied. An approach to studying dynamic hydration shells of carbohydrates in aqueous solutions based on terahertz time-domain spectroscopy assay is developed in the current work. Monosaccharides (glucose, galactose, galacturonic acid) and polysaccharides (dextran, amylopectin, polygalacturonic acid) solutions were studied. The contribution of the dissolved carbohydrates was subtracted from the measured dielectric permittivities of aqueous solutions based on the corresponding effective medium models. The obtained dielectric permittivities of the water phase were used to calculate the parameters describing intermolecular relaxation and oscillatory processes in water. It is established that all of the analyzed carbohydrates lead to the increase of the binding degree of water. Hydration shells of monosaccharides are characterized by elevated numbers of hydrogen bonds and their mean energies compared to undisturbed water, as well as by elevated numbers and the lifetime of free water molecules. The axial orientation of the OH(4) group of sugar facilitates a wider distribution of hydrogen bond energies in hydration shells compared to equatorial orientation. The presence of the carboxylic group affects water structure significantly. The hydration of polysaccharides is less apparent than that of monosaccharides, and it depends on the type of glycosidic bonds.

A Study of the Effect of a Protein on the Structure of Water in Solution Using Terahertz Time-Domain Spectroscopy

2017 ◽  
Vol 72 (2) ◽  
pp. 257-267 ◽  
Author(s):  
Nikita Penkov ◽  
Valery Yashin ◽  
Eugeny Fesenko ◽  
Andrew Manokhin ◽  
Eugeny Fesenko
Keyword(s):  
Aqueous Solutions ◽  
Aqueous Phase ◽  
Time Domain ◽  
Relaxation Times ◽  
Free Water ◽  
Model Parameters ◽  
Biological Macromolecules ◽  
Terahertz Time Domain Spectroscopy ◽  
Time Domain Spectroscopy ◽  
Hydration Shells

Terahertz time-domain spectroscopy (THz-TDS) was used to determine the spectra (range = 1.2–120 cm−1) of aqueous solutions of bovine serum albumin (BSA) at pH range 2.5–10. Under each of the selected pH, BSA molecules exist in a different conformation, compared to other pH values. The spectra were used to calculate the functions of the dielectric permittivity of BSA solutions. Dielectric functions of the aqueous phase of BSA solutions were calculated based on the Bruggeman model, without the contribution of BSA itself. Fitting of the dielectric functions was performed using a model which includes three water spectral bands: two relaxation bands with relaxation times of about 8.28 and 0.3 ps and a vibrational band with a maximum of about 180 cm−1. The parameters of these bands were determined through fitting and physical interpretation at the molecular level can be provided for each of them. A comparison between the values of model parameters of solutions with BSA and without BSA allowed to conclude that the main effect of BSA is the formation of strongly bound hydration shells in the immediate proximity to the protein molecule. At the same time, the structure of more distant layers of the hydration shells is destroyed, with an increased formation of free water molecules. Some differences are observed in the effect of different BSA conformations on the aqueous phase of solution. The proposed approach can be generalized and applied for studying of a wide class of biological macromolecules in aqueous solutions.

scholarly journals The Hydration Shell of Monomeric and Dimeric Insulin Studied by Terahertz Time-Domain Spectroscopy

2019 ◽  
Vol 117 (3) ◽  
pp. 533-541 ◽  
Author(s):  
Pengfei Wang ◽  
Xiangchao Wang ◽  
Liyuan Liu ◽  
Hongwei Zhao ◽  
Wei Qi ◽  
...  
Keyword(s):  
Time Domain ◽  
Hydration Shell ◽  
Terahertz Time Domain Spectroscopy ◽  
Time Domain Spectroscopy

scholarly journals Development of Terahertz Time-Domain Spectroscopy for Properties Analysis of Highly Diluted Antibodies

2020 ◽  
Vol 10 (21) ◽  
pp. 7736
Author(s):  
Nikita Penkov ◽  
Eugeny Fesenko
Keyword(s):  
Energy Distribution ◽  
Time Domain ◽  
Water Molecules ◽  
Terahertz Time Domain Spectroscopy ◽  
Intermolecular Hydrogen Bonds ◽  
Control Solution ◽  
Debye Relaxation ◽  
Time Domain Spectroscopy ◽  
Direct Measurements ◽  
Vibrational Bands

This work represents the development of a three-band (Debye relaxation, intermolecular bending, and stretching vibrational bands) approach to the terahertz time-domain spectroscopy (THz-TDS) for the analysis of aqueous solutions of lactose saturated with highly diluted (HD) antibodies to interferon-gamma. Since THz-TDS is sensitive to a very slight changes in water properties, we aimed to assess its applicability for the analysis of HD antibodies. To evaluate water features in tested samples we also used Fourier transform infrared spectroscopy, considering the first overtone of intramolecular stretching vibrations of water molecules. We showed a broadening of the energy distribution of intermolecular bonds in the solution of HD substances in comparison to the control solution. This broadening corresponded to the presence of an active component even in HD samples. The results of both methods were similar; however, with the THz-TDS it was possible to analyze the changes in energy distribution of intermolecular (hydrogen) bonds in the solutions. Therefore, our approach to THz-TDS method is applicable for analyzing structural properties of the solutions containing HD antibodies and for the indirect investigation of altered aqueous properties in water solutions when direct measurements of a substance concentration are not available.

scholarly journals Detection of Microplastic in Salts Using Terahertz Time-Domain Spectroscopy

Sensors ◽  
2021 ◽  
Vol 21 (9) ◽  
pp. 3161
Author(s):  
Jaeseung Im ◽  
Taewon Goo ◽  
Jugyoung Kim ◽  
Soobong Choi ◽  
Sung Ju Hong ◽  
...  
Keyword(s):  
Dielectric Constant ◽  
Refractive Index ◽  
Optical Properties ◽  
Time Domain ◽  
High Density Polyethylene ◽  
Volume Ratio ◽  
Terahertz Time Domain Spectroscopy ◽  
Time Domain Spectroscopy ◽  
Practical Applications ◽  
Effective Medium Model

We report on a prototypical study of the detection of microplastic embedded in table salts by using terahertz time-domain spectroscopy. In the experiment, high-density polyethylene (HDPE) of sizes from 150 to 400 μm are used as a representative microplastic and mixed with table salts. Analyzing terahertz transmittance with an effective medium model, we extract various optical properties such as refractive index, absorption coefficient, and real/imaginary parts of the dielectric constant of the mixture. Consequently, the optical properties exhibit volume-ratio-dependence in 0.1–0.5 THz regimes. Especially, the refractive index and the real part of the dielectric constant possess monotonic frequency dependence, meaning that the quantities can be relevant indicators for the detection of the microplastic in terms of practical applications. Our work proves that terahertz time-domain spectroscopy can pave a way to recognize microplastic mixed with salts and be expanded for detecting various micro-sized particles.

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