51355
2018
2018
eng
25861
25874
14
40
20
article
Royal Society of Chemistry
Cambridge
1
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Influence of compatible solute ectoine on distinct DNA structures
In nature, the cellular environment of DNA includes not only water and ions, but also other components and co-solutes, which can exert both stabilizing and destabilizing effects on particular oligonucleotide conformations. Among them, ectoine, known as an important osmoprotectant organic co-solute in a broad range of pharmaceutical products, turns out to be of particular relevance. In this article, we study the influence of ectoine on a short single-stranded DNA fragment and on double-stranded helical B-DNA in aqueous solution by means of atomistic molecular dynamics (MD) simulations in combination with molecular theories of solution. Our results demonstrate a conformation-dependent binding behavior of ectoine, which favors the unfolded state of DNA by a combination of electrostatic and dispersion interactions. In conjunction with the Kirkwood-Buff theory, we introduce a simple framework to compute the influence of ectoine on the DNA melting temperature. Our findings reveal a significant linear decrease of the melting temperature with increasing ectoine concentration, which is found to be in qualitative agreement with results from denaturation experiments. The outcomes of our computer simulations provide a detailed mechanistic rationale for the surprising destabilizing influence of ectoine on distinct DNA structures.
Physical chemistry, chemical physics : a journal of European Chemical Societies
thermodynamic insights into molecular binding mechanisms and destabilization effects
10.1039/c8cp03543a
30288515
1463-9076
1463-9084
wos:2018
WOS:000448345800034
Smiatek, J (reprint author), Univ Stuttgart, Inst Computat Phys, Allmandring 3, D-70569 Stuttgart, Germany.; Smiatek, J (reprint author), Forschungszentrum Julich GmbH, Helmholtz Inst Munster Ion Energy Storage HI MS I, Corrensstr 46, D-48149 Munster, Germany., j.smiatek@fz-juelich.de
Deutsche Forschungsgemeinschaft (DFG)German Research Foundation (DFG) [Sonderforschungsbereich 716 (SFB 716)]
2021-07-22T12:57:00+00:00
sword
importub
filename=package.tar
957afef9cb1e187bf4da1223715950f3
Smiatek, Jens
false
true
Ewa Anna Oprzeska-Zingrebe
Susann Meyer
Alexander Roloff
Hans-Jörg Kunte
Jens Smiatek
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
46458
2017
2017
eng
10
7
article
Nature Publ. Group
London
1
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Ectoine can enhance structural changes in DNA in vitro
Strand breaks and conformational changes of DNA have consequences for the physiological role of DNA. The natural protecting molecule ectoine is beneficial to entire bacterial cells and biomolecules such as proteins by mitigating detrimental effects of environmental stresses. It was postulated that ectoine-like molecules bind to negatively charged spheres that mimic DNA surfaces. We investigated the effect of ectoine on DNA and whether ectoine is able to protect DNA from damages caused by ultraviolet radiation (UV-A). In order to determine different isoforms of DNA, agarose gel electrophoresis and atomic force microscopy experiments were carried out with plasmid pUC19 DNA. Our quantitative results revealed that a prolonged incubation of DNA with ectoine leads to an increase in transitions from supercoiled (undamaged) to open circular (single-strand break) conformation at pH 6.6. The effect is pH dependent and no significant changes were observed at physiological pH of 7.5. After UV-A irradiation in ectoine solution, changes in DNA conformation were even more pronounced and this effect was pH dependent. We hypothesize that ectoine is attracted to the negatively charge surface of DNA at lower pH and therefore fails to act as a stabilizing agent for DNA in our in vitro experiments.
Scientific reports
10.1038/s41598-017-07441-z
28775267
2045-2322
wos:2017
7170
WOS:000406889200001
Meyer, S (reprint author), Fed Inst Mat Res & Testing, D-12205 Berlin, Germany.; Meyer, S (reprint author), Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany., Susann.Meyer@bam.de
German Science Foundation (DFG) [STU 245/4-1]
importub
2020-04-20T01:38:01+00:00
filename=package.tar
1185029ba797bf10856f6030a18a19ca
Susann Meyer
M. -A. Schroeter
Marc B. Hahn
T. Solomun
Heinz Sturm
H. J. Kunte
Institut für Biochemie und Biologie
Referiert
Import
38378
2015
2015
eng
15212
15220
9
49
119
article
American Chemical Society
Washington
1
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Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA
Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-S-protein (G5P) to a single-stranded DNA (dT(25)). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonudeotide, which has important consequences for osmotic regulation mechanisms.
The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces & biophysical chemistry
10.1021/acs.jpcb.5b09506
1520-6106
wos:2015
WOS:000366339700013
Solomun, T (reprint author), Fed Inst Mat Res & Testing, D-12205 Berlin, Germany., tihomir.solomun@bam.de; smiatek@icp.uni-stuttgart.de
Deutsche Forschungsgemeinschaft (DFG) [STU 245/4-1, BI 536/3-1]; cluster of excellence Simulation Technology [EXC 310]; [SFB 716]
Marc Benjamin Hahn
Tihomir Solomun
Robert Wellhausen
Sabrina Hermann
Harald Seitz
Susann Meyer
Hans-Jörg Kunte
Johannes Zeman
Frank Uhlig
Jens Smiatek
Heinz Sturm
Institut für Biochemie und Biologie
Referiert
55475
2017
2017
eng
1798
1805
8
3
19
article
RSC Publ.
Cambridge
1
2016-12-14
2016-12-14
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Direct electron irradiation of DNA in a fully aqueous environment
We report on a study in which plasmid DNA in water was irradiated with 30 keV electrons generated by a scanning electron microscope and passed through a 100 nm thick Si3N4 membrane. The corresponding Monte Carlo simulations suggest that the kinetic energy spectrum of the electrons throughout the water is dominated by low energy electrons (<100 eV). The DNA radiation damage, single-strand breaks (SSBs) and double-strand breaks (DSBs), was determined by gel electrophoresis. The median lethal dose of D-1/2 = 1.7 +/- 0.3 Gy was found to be much smaller as compared to partially or fully hydrated DNA irradiated under vacuum conditions. The ratio of the DSBs to SSBs was found to be 1 : 12 as compared to 1 : 88 found for hydrated DNA. Our method enables quantitative measurements of radiation damage to biomolecules (DNA, proteins) in solutions under varying conditions (pH, salinity, co-solutes) for an electron energy range which is difficult to probe by standard methods.
Physical chemistry, chemical physics : PCCP ; a journal of European chemical societies
Damage determination in combination with Monte Carlo simulations
10.1039/c6cp07707b
28059422
1463-9076
1463-9084
wos:2017
WOS:000394426400012
Hahn, MB (reprint author), Free Univ Berlin, Dept Phys, D-14195 Berlin, Germany.; Hahn, MB; Solomun, T (reprint author), Bundesanstalt Mat Forsch & Prufung, D-12205 Berlin, Germany., hahn@physik.fu-berlin.de; tihomir.solomun@bam.de
2022-07-06T11:25:59+00:00
sword
importub
filename=package.tar
af40902176e2278fdf9f0d0c4c06634e
Hahn, Marc Benjamin
Solomun, Tihomir
false
true
Marc Benjamin Hahn
Susann Meyer
Maria-Astrid Schröter
Harald Seitz
Hans-Jörg Kunte
Tihomir Solomun
Heinz Sturm
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
46643
2017
2017
eng
8
95
article
American Physical Society
College Park
1
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Measurements and simulations of microscopic damage to DNA in water by 30 keV electrons: A general approach applicable to other radiation sources and biological targets
The determination of the microscopic dose-damage relationship for DNA in an aqueous environment is of a fundamental interest for dosimetry and applications in radiation therapy and protection. We combine GEANT4 particle-scattering simulations in water with calculations concerning the movement of biomolecules to obtain the energy deposit in the biologically relevant nanoscopic volume. We juxtaposition these results to the experimentally determined damage to obtain the dose-damage relationship at a molecular level. This approach is tested for an experimentally challenging system concerning the direct irradiation of plasmid DNA (pUC19) in water with electrons as primary particles. Here a microscopic target model for the plasmid DNA based on the relation of lineal energy and radiation quality is used to calculate the effective target volume. It was found that on average fewer than two ionizations within a 7.5-nm radius around the sugar-phosphate backbone are sufficient to cause a single strand break, with a corresponding median lethal energy deposit being E-1/2 = 6 +/- 4 eV. The presented method is applicable for ionizing radiation (e.g.,.gamma rays, x rays, and electrons) and a variety of targets, such as DNA, proteins, or cells.
Physical review : E, Statistical, nonlinear and soft matter physics
10.1103/PhysRevE.95.052419
28618479
2470-0045
2470-0053
wos:2017
052419
WOS:000402477200012
Hahn, MB (reprint author), Free Univ Berlin, Inst Expt Phys, D-14195 Berlin, Germany.; Hahn, MB (reprint author), Bundesanstalt Mat Forsch Prufung, D-12205 Berlin, Germany., hahn@physik.fu-berlin.de; tihomir.solomun@bam.de
German Science Foundation (DFG) [STU 245/4-1]
importub
2020-04-20T03:11:01+00:00
filename=package.tar
0fa467eae5be0434d16385eff72d7907
Marc Benjamin Hahn
Susann Meyer
Hans-Jorg Kunte
Tihomir Solomun
Heinz Sturm
Institut für Biochemie und Biologie
Referiert
Import