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Sosorev AY, Parashchuk OD, Chicherin IV, Trubitsyn AA, Trukhanov VA, Baleva MV, Piunova UE, Kharlanov OG, Kamenski P, Paraschuk DY. Probing of nucleic acid compaction using low-frequency Raman spectroscopy. Phys Chem Chem Phys 2024; 26:17467-17475. [PMID: 38864440 DOI: 10.1039/d3cp05857c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Compaction of nucleic acids, namely DNA and RNA, determines their functions and involvement in vital cell processes including transcription, replication, DNA repair and translation. However, experimental probing of the compaction of nucleic acids is not straightforward. In this study, we suggest an approach for this probing using low-frequency Raman spectroscopy. Specifically, we show theoretically, computationally and experimentally the quantifiable correlation between the low-frequency Raman intensity from nucleic acids, magnitude of thermal fluctuations of atomic positions, and the compaction state of biomolecules. Noteworthily, we highlight that the LF Raman intensity differs by an order of magnitude for different samples of DNA, and even for the same sample in the course of long-term storage. The feasibility of the approach is further shown by assessment of the DNA compaction in the nuclei of plant cells. We anticipate that the suggested approach will enlighten compaction of nucleic acids and their dynamics during the key processes of the cell life cycle and under various factors, facilitating advancement of molecular biology and medicine.
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Affiliation(s)
- Andrey Yu Sosorev
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
- Enikolopov Institute of Synthetic Polymeric Materials, Russian Academy of Sciences, Profsoyuznaya 70, Moscow 117393, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Ulitsa Miklukho-Maklaya, 16/10, Moscow 117997, Russia
| | - Olga D Parashchuk
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
| | - Ivan V Chicherin
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow 119234, Russia
| | - Artem A Trubitsyn
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
| | - Vasiliy A Trukhanov
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
| | - Maria V Baleva
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow 119234, Russia
| | - Ulyana E Piunova
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow 119234, Russia
| | - Oleg G Kharlanov
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
| | - Piotr Kamenski
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, Moscow 119234, Russia
| | - Dmitry Yu Paraschuk
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1/62, Moscow 119991, Russia.
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Zhang L, Xiao K, Kong L. A computational method for small molecule-RNA binding sites identification by utilizing position specificity and complex network information. Biosystems 2024; 235:105094. [PMID: 38056591 DOI: 10.1016/j.biosystems.2023.105094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Some computational methods have been given for small molecule-RNA binding site identification due to that it plays a significant role in revealing biology function researches. However, it is still challenging to design an accurate model, especially for MCC. We designed a feature extraction technology from two aspects (position specificity and complex network information). Specifically, complex network was employed to express the space topological structure and sequence position information for improving prediction effect. Then, the features fused position specificity and complex network information were input into random forest classifier for model construction. The AUC of 88.22%, 77.92% and 81.46% were obtained on three independent datasets (RB19, CS71, RB78). Compared with the existing method, the best MCC were obtained on three datasets, which were 8.19%, 0.59% and 4.35% higher than the state-of-the-art prediction methods, respectively. The outstanding performances show that our method is a powerful tool to identify RNA binding sites, helping to the design RNA-targeting small molecule drugs. The data and resource codes are available at https://github.com/Kangxiaoneuq/PCN_RNAsite.
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Affiliation(s)
- Lichao Zhang
- School of Mathematics and Statistics, Northeastern University at Qinhuangdao, Qinhuangdao, 066000, PR China; Hebei Innovation Center for Smart Perception and Applied Technology of Agricultural Data, Qinhuangdao, 066000, PR China.
| | - Kang Xiao
- School of Mathematics and Statistics, Northeastern University at Qinhuangdao, Qinhuangdao, 066000, PR China.
| | - Liang Kong
- Hebei Innovation Center for Smart Perception and Applied Technology of Agricultural Data, Qinhuangdao, 066000, PR China; School of Mathematics and Information Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, 066000, PR China.
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Aggarwal A, Naskar S, Maiti PK. Molecular Rectifiers with a Very High Rectification Ratio Enabled by Oxidative Damage in Double-Stranded DNA. J Phys Chem B 2022; 126:4636-4646. [PMID: 35729785 DOI: 10.1021/acs.jpcb.2c01371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we report a novel strategy to construct highly efficient molecular diodes using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA suffers from constant oxidative damage, leading to the oxidation of guanine to 8-oxoguanine (8oxoG). Here, we study the charge migration properties of native and oxidatively damaged DNA using a multiscale multiconfigurational methodology comprising molecular dynamics, density functional theory, and kinetic Monte Carlo simulations. We perform a comprehensive study to understand the effect of different concentrations and locations of 8oxoG in a dsDNA sequence on its charge-transport properties and find tunable rectifier properties having potential applications in molecular electronics such as molecular switches and molecular rectifiers. We also discover the negative differential resistance properties of the fully oxidized Drew-Dickerson sequence. The presence of 8oxoG guanine leads to the trapping of charge, thus operating as a charge sink, which reveals how oxidized guanine saves the rest of the genome from further oxidative damage.
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Affiliation(s)
- Abhishek Aggarwal
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India
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Sosorev AY. Modeling of Electron Hole Transport within a Small Ribosomal Subunit. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022020224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract—
Synchronized operation of various parts of the ribosome during protein synthesis implies the presence of a coordinating pathway, however, this is still unknown. We have recently suggested that such a pathway can be based on charge transport along the transfer and ribosomal RNA molecules and localization of the charges in functionally important areas of the ribosome. In the current study, using density functional theory calculations, we show that charge carriers (electron holes) can efficiently migrate within the central element of the small ribosomal subunit—the h44 helix. Monte-Carlo modeling revealed that electron holes tend to localize in the functionally important areas of the h44 helix, near the decoding center and intersubunit bridges. On the basis of the results obtained, we suggest that charge transport and localization within the h44 helix could coordinate intersubunit ratcheting with other processes occurring during protein synthesis.
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Walking around Ribosomal Small Subunit: A Possible "Tourist Map" for Electron Holes. Molecules 2021; 26:molecules26185479. [PMID: 34576950 PMCID: PMC8467113 DOI: 10.3390/molecules26185479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/27/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
Despite several decades of research, the physics underlying translation-protein synthesis at the ribosome-remains poorly studied. For instance, the mechanism coordinating various events occurring in distant parts of the ribosome is unknown. Very recently, we suggested that this allosteric mechanism could be based on the transport of electric charges (electron holes) along RNA molecules and localization of these charges in the functionally important areas; this assumption was justified using tRNA as an example. In this study, we turn to the ribosome and show computationally that holes can also efficiently migrate within the whole ribosomal small subunit (SSU). The potential sites of charge localization in SSU are revealed, and it is shown that most of them are located in the functionally important areas of the ribosome-intersubunit bridges, Fe4S4 cluster, and the pivot linking the SSU head to its body. As a result, we suppose that hole localization within the SSU can affect intersubunit rotation (ratcheting) and SSU head swiveling, in agreement with the scenario of electronic coordination of ribosome operation. We anticipate that our findings will improve the understanding of the translation process and advance molecular biology and medicine.
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