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Wang Y, Li T, Xue W, Zheng Y, Wang Y, Zhang N, Zhao Y, Wang J, Li Y, Wang C, Hu W. Physicochemical and Biological Insights Into the Molecular Interactions Between Extracellular DNA and Exopolysaccharides in Myxococcus xanthus Biofilms. Front Microbiol 2022; 13:861865. [PMID: 35531272 PMCID: PMC9073016 DOI: 10.3389/fmicb.2022.861865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular DNA (eDNA) is a critical component in the extracellular matrix (ECM) of bacterial biofilms, while little is known about the mechanisms underlying how eDNA integrates into the ECM through potential macromolecular interactions. Myxococcus xanthus biofilm was employed as a suitable model for the investigation due to the co-distribution of eDNA and exopolysaccharides (EPS) owing to their direct interactions in the ECM. DNA is able to combine with M. xanthus EPS to form a macromolecular conjugate, which is dominated by the electrostatic forces participating in the polymer-polymer interactions. Without intercalation binding, DNA-EPS interactions exhibit a certain degree of reversibility. Acting as a strong extracellular framework during biofilm formation process, the eDNA-EPS complex not only facilitates the initial cell adhesion and subsequent establishment of ECM architecture, but also renders cells within biofilms stress resistances that are relevant to the survival of M. xanthus in some hostile environments. Furthermore, the EPS protects the conjugated DNA from the degradation by nucleic acid hydrolases, which leads to the continuous and stable existence of eDNA in the native ECM of M. xanthus biofilms. These results will shed light on developing prevention and treatment strategies against biofilm-related risks.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Tingyi Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Weiwei Xue
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yue Zheng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yipeng Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Ning Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yue Zhao
- College of Pharmaceutical Science, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jing Wang
- College of Pharmaceutical Science, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
- *Correspondence: Chuandong Wang,
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
- Wei Hu,
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Sochacka J, Pacholczyk M, Jeleń M, Morak-Młodawska B, Pluta K. Interaction of new tri-, tetra-, and pentacyclic azaphenothiazine derivatives with calf thymus DNA: Spectroscopic and molecular docking studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 262:120105. [PMID: 34245970 DOI: 10.1016/j.saa.2021.120105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Azaphenothiazines (AZA), modified phenothiazine derivatives, have been reported to exhibit a wide spectrum of biological activities, including anticancer activities, but the mechanisms of their interactions with biomolecules are not fully recognized. In this work, the mode of interaction of selected AZA with calf thymus DNA was investigated using UV-Vis absorption, fluorescence spectroscopy (competition experiment with ethidium bromide, quenching of fluorescence) and molecular docking. The investigated AZA represent dipyrido[3,4-b;3'4'-e][1,4]thiazine, quino[3,2-b]benzo[1,4]thiazine and diquino[3,2-b;2',3'-e][1,4]thiazine possessing tricyclic, tetracyclic and pentacyclic ring system with the additional N,N-dimethylaminopropyl group at the nitrogen atom in the 1,4 thiazine ring. The results obtained from spectroscopic studies showed that AZA bind to DNA by insertion of a fragment of the fused rings system between the base pair stack in the double helix of DNA. In addition, the number of rings in the AZA structures seemed to be related to the strength of the interaction, because pentacyclic AZA (binding constant Kb = 6.31 × 106 L/mol) demonstrated 10-fold higher affinity towards DNA than the tetracyclic AZA and about 100-fold higher affinity than that of tricyclic AZA. The molecular docking results showed that the binding mode of AZA to DNA helix was an intercalation mode with the partial insertion of one planar part of the AZA structure (the pyridine or quinoline ring) into the neighboring bases of one of the DNA chains with additional hydrogen bonding with the minor groove through the positively charged N,N-dimethylaminopropyl group. Chemical potential (μ), chemical hardness (ƞ), electronegativity (χ) and the value of electrons transferred from one system to another (ΔN) calculated from the HOMO and LUMO energies by the density functional theory method indicated that AZA acted as the electron acceptors to the DNA bases.
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Affiliation(s)
- Jolanta Sochacka
- Department of General and Inorganic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland.
| | - Marcin Pacholczyk
- Silesian University of Technology, Department of Systems Biology and Engineering, Faculty of Automatic Control, Electronics and Computer Science, Akademicka 16, 44-100 Gliwice, Poland
| | - Małgorzata Jeleń
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland
| | - Beata Morak-Młodawska
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland
| | - Krystian Pluta
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland
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Galindo-Murillo R, Cheatham TE. Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations. Nucleic Acids Res 2021; 49:3735-3747. [PMID: 33764383 PMCID: PMC8053101 DOI: 10.1093/nar/gkab143] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/03/2021] [Accepted: 03/16/2021] [Indexed: 01/27/2023] Open
Abstract
Visualization of double stranded DNA in gels with the binding of the fluorescent dye ethidium bromide has been a basic experimental technique in any molecular biology laboratory for >40 years. The interaction between ethidium and double stranded DNA has been observed to be an intercalation between base pairs with strong experimental evidence. This presents a unique opportunity for computational chemistry and biomolecular simulation techniques to benchmark and assess their models in order to see if the theory can reproduce experiments and ultimately provide new insights. We present molecular dynamics simulations of the interaction of ethidium with two different double stranded DNA models. The first model system is the classic sequence d(CGCGAATTCGCG)2 also known as the Drew–Dickerson dodecamer. We found that the ethidium ligand binds mainly stacked on, or intercalated between, the terminal base pairs of the DNA with little to no interaction with the inner base pairs. As the intercalation at the terminal CpG steps is relatively rapid, the resultant DNA unwinding, rigidification, and increased stability of the internal base pair steps inhibits further intercalation. In order to reduce these interactions and to provide a larger groove space, a second 18-mer DNA duplex system with the sequence d(GCATGAACGAACGAACGC) was tested. We computed molecular dynamics simulations for 20 independent replicas with this sequence, each with ∼27 μs of sampling time. Results show several spontaneous intercalation and base-pair eversion events that are consistent with experimental observations. The present work suggests that extended MD simulations with modern DNA force fields and optimized simulation codes are allowing the ability to reproduce unbiased intercalation events that we were not able to previously reach due to limits in computing power and the lack of extensively tested force fields and analysis tools.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, UT 84112, USA
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, UT 84112, USA
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Vardevanyan PO, Antonyan AP, Parsadanyan MA, Shahinyan MA, Petrosyan NH. Study of interaction of methylene blue with DNA and albumin. J Biomol Struct Dyn 2021; 40:7779-7785. [PMID: 33729082 DOI: 10.1080/07391102.2021.1902397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The interaction of thiazine dye methylene blue (MB) with Calf thymus DNA and human blood serum albumin (HSA) has been studied. MB was revealed to stabilize the native structure of DNA and HSA, since the melting temperature of the complexes is shifted to higher values in relation to that of both macromolecules in pure state. It was also revealed that the absorption and fluorescence spectra of the MB-DNA complexes change significantly, while those of MB-albumin complexes do not change noticeably. Analysis of the obtained data allows to conclude that MB binds to DNA by two modes, including intercalation and electrostatic mechanisms. In the case of HSA, the main binding mode of MB, conditioning the stabilization of the protein native structure, is the electrostatic mechanism.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Poghos O Vardevanyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
| | - Ara P Antonyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
| | - Marine A Parsadanyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
| | - Mariam A Shahinyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
| | - Nara H Petrosyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
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Akulenkova EV, Demidov VN, Martynova AO, Paston SV. The Interaction of DNA with Phenanthroline and New Phenanthrocyanine Complexes of Zn(II). Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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6
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Grigoryan K, Zatikyan A, Shilajyan H. Effect of monovalent ions on the thermal stability of bovine serum albumin in dimethylsulfoxide aqueous solutions. Spectroscopic approach. J Biomol Struct Dyn 2020; 39:2284-2288. [PMID: 32178588 DOI: 10.1080/07391102.2020.1743759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Karine Grigoryan
- Department of Physical Chemistry, Faculty of Chemistry, Yerevan State University, Yerevan, Armenia
| | - Ashkhen Zatikyan
- Department of Physical Chemistry, Faculty of Chemistry, Yerevan State University, Yerevan, Armenia
| | - Hasmik Shilajyan
- Department of Physical Chemistry, Faculty of Chemistry, Yerevan State University, Yerevan, Armenia
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7
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Arakelyan VB, Mamasakhlisov AY, Kazaryan EM, Parsadanyan MA, Vardevanyan PO. Hybridization kinetics of DNA fragments in the presence of ligands intercalating into DNA-duplexes. J Biomol Struct Dyn 2020; 39:1907-1911. [PMID: 32141399 DOI: 10.1080/07391102.2020.1739559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
In this work the hybridization kinetics of DNA fragments on underlayer has been studied, when besides single-stranded DNA molecules there are also ligands in the medium that are able to intercalate into DNA-duplexes. A system of differential equations was obtained that describes the correlative change of the number of DNA-duplexes on the underlayer and the change of the number of ligands intercalating into DNA-duplexes. It was shown that the rate of underlayer filling by DNA-duplexes increases along with the enhancement of both equilibrium constant of formation reaction of DNA-duplexes and the concentration of DNA targets in the solution. It was also shown that the intercalation kinetics of ligands into DNA-duplexes relevantly depends on relation of dissociation rate constant of DNA-duplex to dissociation rate of the ligand complex with DNA-duplex.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Valeri B Arakelyan
- Faculty of Physics, Department of Molecular Physics, Yerevan State University, Yerevan, Armenia
| | - Aleksandr Y Mamasakhlisov
- Institute of Mathematics and High Technologies, Department of General Physics and Quantum Nano-structures, Russian-Armenian (Slavonic) University, Yerevan, Armenia
| | - Eduard M Kazaryan
- Institute of Mathematics and High Technologies, Department of General Physics and Quantum Nano-structures, Russian-Armenian (Slavonic) University, Yerevan, Armenia
| | - Marine A Parsadanyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
| | - Poghos O Vardevanyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
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Asatryan AL, Matinyan KS, Artsruni IG, Gevorgyan ES, Antonyan AP, Vardevanyan PO. Transient decondensation of chromatin in liver nuclei of rats treated with tannic acid. J Biomol Struct Dyn 2019; 38:3743-3749. [PMID: 31524078 DOI: 10.1080/07391102.2019.1664332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anush L Asatryan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Karine S Matinyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Irina G Artsruni
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Emil S Gevorgyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Ara P Antonyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Poghos O Vardevanyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
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Veselinovic J, Almashtoub S, Seker E. Anomalous Trends in Nucleic Acid-Based Electrochemical Biosensors with Nanoporous Gold Electrodes. Anal Chem 2019; 91:11923-11931. [PMID: 31429540 DOI: 10.1021/acs.analchem.9b02686] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular diagnostics have significantly advanced the early detection of diseases, where electrochemical sensing of biomarkers has shown considerable promise. For a nucleic acid-based electrochemical sensor with signal-off behavior, the performance is evaluated by percent signal suppression (% ss), which indicates the change in current after hybridization. The % ss is generally due to more redox molecules (e.g., methylene blue) associating with the probe DNA bases in the single-strand form than the double-strand form upon hybridization with the target nucleic acid. Nanostructured electrodes generally enhance electrochemical sensor performance via several mechanisms, including increased number of capture probes per electrode volume and unique nanoscale transport phenomena. Here, we employ nanoporous gold (np-Au) as a model electrode material to study the influence of probe immobilization solution concentration on sensor performance and the underlying mechanisms. Unlike planar gold (pl-Au) electrodes, where % ss reaches a steady state with increasing concentration of the grafting solution, the % ss displays peak performance at certain grafting solution concentrations followed by rapid deterioration and reversal of the % ss polarity, suggesting an unexpected case of increased charge transfer upon hybridization. Fluorometric assessments of electrochemically desorbed nucleic acids for different electrode morphologies reveal that a significant amount of DNA molecules (unhybridized and hybridized) remain within the nanopores posthybridization. Analysis of electrochemical signals (e.g., square wave voltammogram shape) suggests that the large unbound nucleic acid concentration may be altering the modes of methylene blue interaction with the nucleic acids and charge transfer to the electrode surfaces.
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Affiliation(s)
- Jovana Veselinovic
- Department of Chemical Engineering , University of California, Davis , Davis , California 95616 , United States
| | - Suzan Almashtoub
- Department of Chemical Engineering , University of California, Davis , Davis , California 95616 , United States
| | - Erkin Seker
- Department of Electrical and Computer Engineering , University of California, Davis , Davis , California 95616 , United States
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Vardevanyan PO, Antonyan AP, Parsadanyan MA, Shahinyan MA. Study of the influence of the ionic strength on complex-formation of ethidium bromide with poly(rA)-poly(rU). J Biomol Struct Dyn 2019; 38:2493-2498. [PMID: 31204613 DOI: 10.1080/07391102.2019.1630006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Poghos O Vardevanyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Ara P Antonyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Marine A Parsadanyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
| | - Mariam A Shahinyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Yerevan, Armenia
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Jia T, Chen ZH, Guo P, Yu J. An insight into DNA binding properties of newly designed cationic δ,δ'‑diazacarbazoles: Spectroscopy, AFM imaging and living cells staining studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 211:260-271. [PMID: 30557843 DOI: 10.1016/j.saa.2018.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/19/2018] [Accepted: 12/08/2018] [Indexed: 06/09/2023]
Abstract
Two cationic δ,δ'‑diazacarbazoles, 1‑Methyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (MPDPI) and 1,5‑Dimethyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (DPDPI), were devised and synthesized. Through characterizations of the interactions between DNA and the two δ,δ'‑diazacarbazoles by various spectroscopy means, the strong interactions between the two compounds and double-strand DNA have been observed and the interaction types and mechanisms were explored. UV-Vis and fluorescent data have shown the big changes of DNA in the presence of either of the two compounds, demonstrating that both of the δ,δ'‑diazacarbazoles can bind to DNA tightly, and high ionic strength decreased the intercalative interactions. The UV-Vis and fluorescence of dsDNA in the presence of DPDPI showed more profound changes than those in the presence of MPDPI, due to CH3 (in the structure of DPDPI) taking place of H (in the structure of MPDPI) at the position of 5‑NH. And the circular dichroism (CD) spectra of CT-DNA and atomic force microscopy (AFM) results indicated more compacted conformation of DNA in the presence of DPDPI than MPDPI, implying that DPDPI has a more significant effect on DNA conformations than MPDPI. Most interestingly, fluorescence enhancement of cationic δ,δ'‑diazacarbazoles occurred in the presence of DNA. With ionic strength increasing, the intercalative interactions between δ,δ'‑diazacarbazoles and DNA were weakened, but δ,δ'‑diazacarbazoles-DNA complexes showed enhanced fluorescence, which indicated that there are other interactions present at high ionic strength. Furthermore, laser confocal fluorescence microscopy results proved that DPDPI was membrane-permeable and stained living cells.
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Affiliation(s)
- Tao Jia
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Zhi-Hang Chen
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Peng Guo
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430072, PR China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, PR China.
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Oh YS, Park JH, Han SW, Kim SK, Lee YA. Retained binding mode of various DNA-binding molecules under molecular crowding condition. J Biomol Struct Dyn 2017; 36:3035-3046. [DOI: 10.1080/07391102.2017.1375992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Ye Sol Oh
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Jin Ha Park
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Sung Wook Han
- Department of Health & Biotechnology, Kyungwoon University, Kumi City, Gyeong-buk 39253, Republic of Korea
| | - Seog K. Kim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Young-Ae Lee
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
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