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Svidlov A, Drobotenko M, Basov A, Gerasimenko E, Malyshko V, Elkina A, Baryshev M, Dzhimak S. DNA Dynamics under Periodic Force Effects. Int J Mol Sci 2021; 22:7873. [PMID: 34360636 PMCID: PMC8345943 DOI: 10.3390/ijms22157873] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/22/2022] Open
Abstract
The sensitivity of DNA to electromagnetic radiation in different ranges differs depending on various factors. The aim of this study was to examine the molecular dynamics of DNA under the influence of external periodic influences with different frequencies. In the present paper, within the framework of a mechanical model without simplifications, we investigated the effect of various frequencies of external periodic action in the range from 1011 s-1 to 108 s-1 on the dynamics of a DNA molecule. It was shown that under the influence of an external periodic force, a DNA molecule can perform oscillatory movements with a specific frequency characteristic of this molecule, which differs from the frequency of the external influence ω. It was found that the frequency of such specific vibrations of a DNA molecule depends on the sequence of nucleotides. Using the developed mathematical model describing the rotational motion of the nitrogenous bases around the sugar-phosphate chain, it is possible to calculate the frequency and amplitude of the oscillations of an individual DNA area. Such calculations can find application in the field of molecular nanotechnology.
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Affiliation(s)
- Alexander Svidlov
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia;
| | - Mikhail Drobotenko
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
| | - Alexander Basov
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Eugeny Gerasimenko
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Vadim Malyshko
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia;
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Anna Elkina
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia;
| | - Mikhail Baryshev
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia;
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Stepan Dzhimak
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia;
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Globus T, Moskaluk C, Pramoonjago P, Gelmont B, Moyer A, Bykhovski A, Ferrance J. Sub-terahertz vibrational spectroscopy of ovarian cancer and normal control tissue for molecular diagnostic technology. Cancer Biomark 2019; 24:405-419. [DOI: 10.3233/cbm-182120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Tatiana Globus
- ECE Department, University of Virginia, Charlottesville, VA, 22904-4743, USA
- Vibratess LLC, Charlottesville, VA, 22902, USA
| | - Christopher Moskaluk
- Department of Pathology, University of Virginia, Charlottesville, VA, 22908-0712, USA
| | - Patcharin Pramoonjago
- Department of Pathology, University of Virginia, Charlottesville, VA, 22908-0712, USA
| | - Boris Gelmont
- ECE Department, University of Virginia, Charlottesville, VA, 22904-4743, USA
| | - Aaron Moyer
- Vibratess LLC, Charlottesville, VA, 22902, USA
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Globus T, Sizov I, Ferrance J, Jazaeri A, Bryant J, Moyer A, Gelmont B, Kester M, Bykhovski A. Sub-terahertz vibrational spectroscopy for microRNA based diagnostic of ovarian cancer. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2016. [DOI: 10.1088/2057-1739/2/4/045001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Yang X, Wei D, Yan S, Liu Y, Yu S, Zhang M, Yang Z, Zhu X, Huang Q, Cui HL, Fu W. Rapid and label-free detection and assessment of bacteria by terahertz time-domain spectroscopy. JOURNAL OF BIOPHOTONICS 2016; 9:1050-1058. [PMID: 26890249 DOI: 10.1002/jbio.201500270] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 12/08/2015] [Accepted: 01/29/2016] [Indexed: 05/27/2023]
Abstract
Here we demonstrated the potential and applicability of terahertz (THz) spectroscopy to detect four commonly found bacteria in the infectious diseases. Besides the different spectral characteristics between bacterial species, THz absorption differences for living bacteria, dead bacteria and bacterial powder of the same species were also investigated. Our results revealed that small differences in water contents between bacterial cells account for distinct discrepancies of the absorption coefficients, which can be used for bacterial species identification. Furthermore, living and dead bacteria showed different absorption coefficients as a result of their different hydration levels, suggesting that THz spectroscopy can be used to rapidly assess the living state of bacteria under test. Our results clearly demonstrated the ability of THz spectroscopy for time-saving and label-free detection of bacteria with minimal sample preparation, potentially to be utilized for point-of-care tests in the near future. Schematic representation of bacterial detection by THz spectroscopy. Different bacteria have distinctive absorption coefficients as a result of their different water contents.
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Affiliation(s)
- Xiang Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Dongshan Wei
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shihan Yan
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yueping Liu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Shu Yu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Mingkun Zhang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Zhongbo Yang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xiaoyan Zhu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Hong-Liang Cui
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China.
- College of Instrumentation Science and Electrical Engineering, Jilin University, Changchun, Jilin, 130061, China.
| | - Weiling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
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Terahertz spectroscopy for bacterial detection: opportunities and challenges. Appl Microbiol Biotechnol 2016; 100:5289-99. [DOI: 10.1007/s00253-016-7569-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/14/2016] [Accepted: 04/17/2016] [Indexed: 10/21/2022]
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Zhang M, Wei D, Tang M, Shi C, Cui HL, Du C. Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1059429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Globus T, Sizov I, Gelmont B. Sub-THz specific relaxation times of hydrogen bond oscillations in E.coli thioredoxin. Molecular dynamics and statistical analysis. Faraday Discuss 2014; 171:179-93. [PMID: 25415676 DOI: 10.1039/c4fd00029c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bonds (H-bonds) in biological macromolecules are important for the molecular structure and functions. Since interactions via hydrogen bonds are weaker than covalent bonds, it can be expected that atomic movements involving H-bonds have low frequency vibrational modes. Sub-Terahertz (sub-THz) vibrational spectroscopy that combines measurements with molecular dynamics (MD) computational prediction has been demonstrated as a promising approach for biological molecule characterization. Multiple resonance absorption lines have been reported. The knowledge of relaxation times of atomic oscillations is critical for the successful application of THz spectroscopy for hydrogen bond characterization. The purpose of this work is to use atomic oscillations in the 0.35-0.7 THz range, found from molecular dynamic (MD) simulations of E.coli thioredoxin (2TRX), to study relaxation dynamics of two intra-molecular H-bonds, OH-N and OH-C. Two different complimentary techniques are used in this study, one is the analysis of the statistical distribution of relaxation time and dissipation factor values relevant to low frequency oscillations, and the second is the analysis of the autocorrelation function of low frequency quasi-periodic movements. By studying hydrogen bond atomic displacements, it was found that the atoms are involved in a number of collective oscillations, which are characterized by different relaxation time scales ranging from 2-3 ps to more than 150 ps. The existence of long lasting relaxation processes opens the possibility to directly observe and study H-bond vibrational modes in sub-THz absorption spectra of bio-molecules if measured with an appropriate spectral resolution. The results of measurements using a recently developed frequency domain spectroscopic sensor with a spectral resolution of 1 GHz confirm the MD analysis.
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Affiliation(s)
- Tatiana Globus
- Department of Electrical and Computer Engineering, University of Virginia, 351 McCormick Road, P.O. Box 400743, Charlottesville, VA 22904-4743, USA.
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Sizov I, Rahman M, Gelmont B, Norton ML, Globus T. Sub-THz spectroscopic characterization of vibrational modes in artificially designed DNA monocrystal. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.08.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Bykhovski A, Woolard D. Terahertz Spectra of Biotin Based on First Principle, Molecular Mechanical, and Hybrid Simulations. IEEE J Biomed Health Inform 2013; 17:768-73. [DOI: 10.1109/jbhi.2013.2253786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Globus T, Sizov I, Gelmont B. Teraherz vibrational spectroscopy of <i>E. coli</i> and molecular constituents: Computational modeling and experiment. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.43a065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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