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Farré-Gil D, Arcon JP, Laughton CA, Orozco M. CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes. Nucleic Acids Res 2024; 52:6791-6801. [PMID: 38813824 PMCID: PMC11229373 DOI: 10.1093/nar/gkae444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 05/01/2024] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
We present CGeNArate, a new model for molecular dynamics simulations of very long segments of B-DNA in the context of biotechnological or chromatin studies. The developed method uses a coarse-grained Hamiltonian with trajectories that are back-mapped to the atomistic resolution level with extreme accuracy by means of Machine Learning Approaches. The method is sequence-dependent and reproduces very well not only local, but also global physical properties of DNA. The efficiency of the method allows us to recover with a reduced computational effort high-quality atomic-resolution ensembles of segments containing many kilobases of DNA, entering into the gene range or even the entire DNA of certain cellular organelles.
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Affiliation(s)
- David Farré-Gil
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, E-08028 Barcelona, Spain
| | - Juan Pablo Arcon
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, E-08028 Barcelona, Spain
| | - Charles A Laughton
- School of Pharmacy and Biodiscovery Institute, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, E-08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, E-08028 Barcelona, Spain
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2
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Bennett ID, Burns JR, Ryadnov MG, Howorka S, Pyne ALB. Lipidated DNA Nanostructures Target and Rupture Bacterial Membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2207585. [PMID: 38840451 DOI: 10.1002/smll.202207585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/01/2024] [Indexed: 06/07/2024]
Abstract
Chemistry has the power to endow supramolecular nanostructures with new biomedically relevant functions. Here it is reported that DNA nanostructures modified with cholesterol tags disrupt bacterial membranes to cause microbial cell death. The lipidated DNA nanostructures bind more readily to cholesterol-free bacterial membranes than to cholesterol-rich, eukaryotic membranes. These highly negatively charged, lipidated DNA nanostructures cause bacterial cell death by rupturing membranes. Strikingly, killing is mediated by clusters of barrel-shaped nanostructures that adhere to the membrane without the involvement of expected bilayer-puncturing barrels. These DNA nanomaterials may inspire the development of polymeric or small-molecule antibacterial agents that mimic the principles of selective binding and rupturing to help combat antimicrobial resistance.
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Affiliation(s)
- Isabel D Bennett
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
- Division of Medicine, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory, Teddington, TW11 0LW, United Kingdom
- Department of Physics, King's College London, Strand Lane, London, WC2R 2LS, United Kingdom
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, United Kingdom
| | - Alice L B Pyne
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Sheffield, S1 3JD, United Kingdom
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3
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Rudnizky S, Murray PJ, Wolfe CH, Ha T. Single-Macromolecule Studies of Eukaryotic Genomic Maintenance. Annu Rev Phys Chem 2024; 75:209-230. [PMID: 38382570 DOI: 10.1146/annurev-physchem-090722-010601] [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] [Indexed: 02/23/2024]
Abstract
Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.
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Affiliation(s)
- Sergei Rudnizky
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter J Murray
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
| | - Clara H Wolfe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
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4
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Noh C, Kang Y, Heo S, Kim T, Kim H, Chang J, Sundharbaabu PR, Shim S, Lim KI, Lee JH, Jo K. Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal-Free Electro-Stain Composed of DNA-Binding Proteins and Synthetic Polymers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309702. [PMID: 38704672 DOI: 10.1002/advs.202309702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/19/2024] [Indexed: 05/06/2024]
Abstract
This paper presents the first scanning electron microscopy (SEM)-based DNA imaging in biological samples. This novel approach incorporates a metal-free electro-stain reagent, formulated by combining DNA-binding proteins and synthetic polymers to enhance the visibility of 2-nm-thick DNA under SEM. Notably, DNA molecules stain with proteins and polymers appear as dark lines under SEM. The resulting DNA images exhibit a thickness of 15.0±4.0 nm. As SEM is the primary platform, it integrates seamlessly with various chemically functionalized large surfaces with the aid of microfluidic devices. The approach allows high-resolution imaging of various DNA structures including linear, circular, single-stranded DNA and RNA, originating from nuclear and mitochondrial genomes. Furthermore, quantum dots are successfully visualized as bright labels that are sequence-specifically incorporated into DNA molecules, which highlights the potential for SEM-based optical DNA mapping. In conclusion, DNA imaging using SEM with the novel electro-stain offers electron microscopic resolution with the ease of optical microscopy.
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Affiliation(s)
- Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Yoonjung Kang
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Sujung Heo
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Taesoo Kim
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Hayeon Kim
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
| | - Junhyuck Chang
- School of Advanced Materials Science and Engineering, Department of MetaBioHealth Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
| | - Priyannth Ramasami Sundharbaabu
- School of Advanced Materials Science and Engineering, Department of MetaBioHealth Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
| | - Sanghee Shim
- Department of Chemistry, Korea University, Seoul, 02841, South Korea
| | - Kwang-Il Lim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, 04312, South Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Department of MetaBioHealth Sungkyunkwan University (SKKU), Suwon, 16419, South Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, South Korea
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Alebady MH, Hamama HH, Mahmoud SH. Effect of various surface coating methods on surface roughness, micromorphological analysis and fluoride release from contemporary glass ionomer restorations. BMC Oral Health 2024; 24:504. [PMID: 38685036 PMCID: PMC11057179 DOI: 10.1186/s12903-024-04234-5] [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: 09/01/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024] Open
Abstract
OBJECTIVE To evaluate the effect of various surface coating methods on surface roughness, micromorphological analysis and fluoride release from contemporary resin-modified and conventional glass ionomer restorations. MATERIALS & METHODS A total of 72 permanent human molars were used in this study. The teeth were randomly assigned into 2 groups according to type of restorative materials used; resin modified glass ionomer cement and conventional glass ionomer (SDI Limited. Bayswater Victoria, Australia). Each group was subdivided into 3 subgroups according to the application of coat material; Sub-group1: without application of coat; Sub-group2: manufacturer recommended coat was applied and sub-group3: customized (vaseline) coat was applied. Each group was then subdivided into two divisions according to the time of testing; immediate (after 24 h) and delayed (after 6 months of storage). Three specimens from each sub-group were selected for surface roughness test (AFM) and another 3 specimens for the micromorphological analysis using scanning electron microscope (SEM). For the fluoride release test, a total of 60 cylindrical discs were used (n = 60). The discs were randomly split into 2 groups according to type of restorative materials used (n = 30); resin modified glass ionomer cement and conventional glass ionomer. Each group was subdivided into 3 subgroups (n = 10) according to the application of the coat material; Sub-group1: without application of coat; Sub-group2: with the manufacturer recommended coat and sub-group3: with application of customized (vaseline) coat. Data for each test was then collected, tabulated, were collected, tabulated, and tested for the normality with Shapiro-Wilk test. Based on the outcome of normality test, the significant effects of variables were assessed using appropriate statistical analysis testing methods. RESULTS Regarding the data obtained from surface roughness test, Shapiro-Wilk test showed normal distribution pattern of all values (p > 0.05). Accordingly, Two-way ANOVA outcome showed that the 'type of restoration' or 'test time' had statistically significant effect on the AFM test (p < 0.05). Regarding Fluoride specific ion electrode test 2-way ANOVA followed by Least Significant Difference (LSD) Post-hoc test revealed significant difference among the groups (p < 0.05). It showed that SDI GIC group after 14 days of measurement had the highest mean of fluoride release (36.38 ± 3.16 PPM) and SDI RMGIC after 30 days of measurement had the second highest mean of fluoride release (43.28 ± 1.89 PPM). Finally, regarding the micromorphological analysis using SEM, a slight difference was observed between the studied groups. CONCLUSIONS Based on the results of this study, various coatings enhance surface roughness in the initial 24 h of restoration insertion. Different coat types seems that have no influence on fluoride release and the micromorphological features of the restoration/dentin interface.
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Affiliation(s)
- Mohanad H Alebady
- Conservative Dentistry Department, Faculty of Dentistry, Mansoura University, Mansoura, 35516, Egypt
| | - Hamdi H Hamama
- Conservative Dentistry Department, Faculty of Dentistry, Mansoura University, Mansoura, 35516, Egypt.
| | - Salah H Mahmoud
- Conservative Dentistry Department, Faculty of Dentistry, Mansoura University, Mansoura, 35516, Egypt
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6
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Deng E, Fan X. Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer. Biomolecules 2024; 14:488. [PMID: 38672504 PMCID: PMC11048305 DOI: 10.3390/biom14040488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a double-stranded circular DNA molecule found in multiple organisms, has garnered an increasing amount of attention in recent years due to its close association with the initiation, malignant progression, and heterogeneous evolution of cancer. The presence of eccDNA in serum assists in non-invasive tumor diagnosis as a biomarker that can be assessed via liquid biopsies. Furthermore, the specific expression patterns of eccDNA provide new insights into personalized cancer therapy. EccDNA plays a pivotal role in tumorigenesis, development, diagnosis, and treatment. In this review, we comprehensively outline the research trajectory of eccDNA, discuss its role as a diagnostic and prognostic biomarker, and elucidate its regulatory mechanisms in cancer. In particular, we emphasize the potential application value of eccDNA in cancer diagnosis and treatment and anticipate the development of novel tumor diagnosis strategies based on serum eccDNA in the future.
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Affiliation(s)
- Enze Deng
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Xiaoying Fan
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
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7
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Laeremans W, Segers M, Voorspoels A, Carlon E, Hooyberghs J. Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs cgDNA. J Chem Phys 2024; 160:144105. [PMID: 38591677 DOI: 10.1063/5.0197053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs all-atom models using stiffness matrices in Fourier space (q-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version, cgDNA+. Our analysis shows that while cgDNA+ closely follows the q-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables, which are rather strong in the q → 0 (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects that manifest themselves at longer length scales. In particular, cgDNA performs poorly on twist stiffness, with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist are strongly length scale dependent: DNA is torsionally soft at a few base pair distances but becomes more rigid at distances of a few dozen base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated.
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Affiliation(s)
- Wout Laeremans
- Soft Matter and Biological Physics, Department of Applied Physics, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, Netherlands
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
| | - Midas Segers
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Jef Hooyberghs
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
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8
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Vayssières M, Marechal N, Yun L, Lopez Duran B, Murugasamy NK, Fogg JM, Zechiedrich L, Nadal M, Lamour V. Structural basis of DNA crossover capture by Escherichia coli DNA gyrase. Science 2024; 384:227-232. [PMID: 38603484 PMCID: PMC11108255 DOI: 10.1126/science.adl5899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/14/2024] [Indexed: 04/13/2024]
Abstract
DNA supercoiling must be precisely regulated by topoisomerases to prevent DNA entanglement. The interaction of type IIA DNA topoisomerases with two DNA molecules, enabling the transport of one duplex through the transient double-stranded break of the other, remains elusive owing to structures derived solely from single linear duplex DNAs lacking topological constraints. Using cryo-electron microscopy, we solved the structure of Escherichia coli DNA gyrase bound to a negatively supercoiled minicircle DNA. We show how DNA gyrase captures a DNA crossover, revealing both conserved molecular grooves that accommodate the DNA helices. Together with molecular tweezer experiments, the structure shows that the DNA crossover is of positive chirality, reconciling the binding step of gyrase-mediated DNA relaxation and supercoiling in a single structure.
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Affiliation(s)
- Marlène Vayssières
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Nils Marechal
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Long Yun
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Brian Lopez Duran
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Naveen Kumar Murugasamy
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
| | - Jonathan M. Fogg
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Marc Nadal
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Life Sciences, Université Paris Cité, Paris, France
| | - Valérie Lamour
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut national de la Recherche Médicale (INSERM), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- Department of Integrated Structural Biology, IGBMC, Illkirch, France
- Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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9
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Shepherd JW, Guilbaud S, Zhou Z, Howard JAL, Burman M, Schaefer C, Kerrigan A, Steele-King C, Noy A, Leake MC. Correlating fluorescence microscopy, optical and magnetic tweezers to study single chiral biopolymers such as DNA. Nat Commun 2024; 15:2748. [PMID: 38553446 PMCID: PMC10980717 DOI: 10.1038/s41467-024-47126-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/21/2024] [Indexed: 04/02/2024] Open
Abstract
Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers.
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Affiliation(s)
- Jack W Shepherd
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
- Department of Biology, University of York, York, YO10 5DD, England
| | - Sebastien Guilbaud
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Zhaokun Zhou
- Guangdong Provincial Key Lab of Robotics and Intelligent System, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jamieson A L Howard
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Matthew Burman
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Charley Schaefer
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Adam Kerrigan
- The York-JEOL Nanocentre, University of York, York, YO10 5BR, England
| | - Clare Steele-King
- Bioscience Technology Facility, University of York, York, YO10 5DD, England
| | - Agnes Noy
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England
| | - Mark C Leake
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, England.
- Department of Biology, University of York, York, YO10 5DD, England.
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10
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Pietruszka M, Marzec M. Proton-polarized states in DNA. Biosystems 2024; 237:105125. [PMID: 38331379 DOI: 10.1016/j.biosystems.2024.105125] [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: 12/08/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
Abstract
We observed signatures of a phase transition in the double-stranded DNA fragment of known length and sequences using a non-invasive semiconductor-electrolyte interface technique and statistical physics methods. Observations revealed a coherence peak in the electromotive force and a significant decline in calculated dynamic entropy at a critical temperature and pH. This behavior may arise from the dynamic interaction of proton (H+) pairs with opposite momentum and spin, carrying a charge q=2+ under critical conditions.
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Affiliation(s)
- Mariusz Pietruszka
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology, and Environmental Protection, 40-032 Katowice, Poland.
| | - Marek Marzec
- University of Silesia, Faculty of Natural Sciences, Institute of Biology, Biotechnology, and Environmental Protection, 40-032 Katowice, Poland
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11
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Sülzle J, Yang W, Shimoda Y, Ronceray N, Mayner E, Manley S, Radenovic A. Label-Free Imaging of DNA Interactions with 2D Materials. ACS PHOTONICS 2024; 11:737-744. [PMID: 38405387 PMCID: PMC10885193 DOI: 10.1021/acsphotonics.3c01604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 02/27/2024]
Abstract
Two-dimensional (2D) materials offer potential as substrates for biosensing devices, as their properties can be engineered to tune interactions between the surface and biomolecules. Yet, not many methods can measure these interactions in a liquid environment without introducing labeling agents such as fluorophores. In this work, we harness interferometric scattering (iSCAT) microscopy, a label-free imaging technique, to investigate the interactions of single molecules of long dsDNA with 2D materials. The millisecond temporal resolution of iSCAT allows us to capture the transient interactions and to observe the dynamics of unlabeled DNA binding to a hexagonal boron nitride (hBN) surface in solution for extended periods (including a fraction of 10%, of trajectories lasting longer than 110 ms). Using a focused ion beam technique to engineer defects, we find that DNA binding affinity is enhanced at defects; when exposed to long lanes, DNA binds preferentially at the lane edges. Overall, we demonstrate that iSCAT imaging is a useful tool to study how biomolecules interact with 2D materials, a key component in engineering future biosensors.
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Affiliation(s)
- Jenny Sülzle
- Institute
of Physics and Institute of Bioengineering, Laboratory of Experimental
Biophysics (LEB), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Wayne Yang
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Yuta Shimoda
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Nathan Ronceray
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Eveline Mayner
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Suliana Manley
- Institute
of Physics and Institute of Bioengineering, Laboratory of Experimental
Biophysics (LEB), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne, 1015, Switzerland
| | - Aleksandra Radenovic
- Institute
of Bioengineering, Laboratory of Nanoscale Biology (LBEN), École Polytechnique Fédérale
de Lausanne (EPFL), Lausanne, 1015, Switzerland
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12
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Vahid H, Scacchi A, Sammalkorpi M, Ala-Nissila T. Nonmonotonic electrophoretic mobility of rodlike polyelectrolytes by multivalent coions in added salt. Phys Rev E 2024; 109:014501. [PMID: 38366448 DOI: 10.1103/physreve.109.014501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/30/2023] [Indexed: 02/18/2024]
Abstract
It is well established that when multivalent counterions or salts are added to a solution of highly charged polyelectrolytes (PEs), correlation effects can cause charge inversion of the PE, leading to electrophoretic mobility (EM) reversal. In this work, we use coarse-grained molecular-dynamics simulations to unravel the less understood effect of coion valency on EM reversal for rigid DNA-like PEs. We find that EM reversal induced by multivalent counterions is suppressed with increasing coion valency in the salt added and eventually vanishes. Further, we find that EM is enhanced at fixed low salt concentrations for salts with monovalent counterions when multivalent coions with increasing valency are introduced. However, increasing the salt concentration causes a crossover that leads to EM reversal which is enhanced by increasing coion valency at high salt concentration. Remarkably, this multivalent coion-induced EM reversal persists even for low values of PE linear charge densities where multivalent counterions alone cannot induce EM reversal. These results facilitate tuning PE-PE interactions and self-assembly with both coion and counterion valencies.
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Affiliation(s)
- Hossein Vahid
- Department of Applied Physics, Aalto University, P.O. Box 11000, 00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Alberto Scacchi
- Department of Applied Physics, Aalto University, P.O. Box 11000, 00076 Aalto, Finland
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Tapio Ala-Nissila
- Department of Applied Physics, Aalto University, P.O. Box 11000, 00076 Aalto, Finland
- Quantum Technology Finland Center of Excellence, Department of Applied Physics, Aalto University, P.O. Box 11000, 00076 Aalto, Finland
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
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13
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Drobotenko MI, Svidlov AA, Dorohova АA, Baryshev MG, Dzhimak SS. Medium viscosity influence on the open states genesis in a DNA molecule. J Biomol Struct Dyn 2023:1-9. [PMID: 38102872 DOI: 10.1080/07391102.2023.2294178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
The studies were carried out by the mathematical modeling of DNA mechanical deformations. Numerical calculations done for the interferon alpha 17 gene, which consists of 980 base pairs. It has been established that the genesis and dynamics of open states in the DNA molecule depends on the magnitude of the external influence (torque) and on the viscosity of the environment. In addition, it is shown that the dynamics of open states zones can have a jump-like character with a small change in the magnitude of the torque. When torque is applied to all 980 base pairs of the gene, the following effect is observed: an increase in the viscosity of the medium leads to an increase in the value of the torque necessary for the occurrence of OS and DNA unwinding, i.e. viscosity plays an important stabilizing role in DNA dynamics. Under the influence of a localized torque on different (by the content of A-T and G-C pairs and location) regions of the interferon alpha 17 gene, it was found that the magnitude of the external torque necessary for the occurrence of open states at all calculated values of viscosity depends on the nucleotide composition. The dependence of the torque magnitude required for the open states occurrence on viscosity is observed when the torque is applied to areas close to the gene boundaries. At the same time, the significance of the end effect, which weakens DNA, decreased with increasing viscosity of the medium.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mikhail I Drobotenko
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
| | - Alexandr A Svidlov
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russia
| | - Аnna A Dorohova
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russia
| | - Mikhail G Baryshev
- Department of Safety and Productivity of agroecosystems, All-Russian Research Institute of Phytopathology, Russia
| | - Stepan S Dzhimak
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russia
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14
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Ibrahim M, Wenzel C, Lallemang M, Balzer BN, Schwierz N. Adsorbing DNA to Mica by Cations: Influence of Valency and Ion Type. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:15553-15562. [PMID: 37877163 DOI: 10.1021/acs.langmuir.3c01835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Ion-mediated attraction between DNA and mica plays a crucial role in biotechnological applications and molecular imaging. Here, we combine molecular dynamics simulations and single-molecule atomic force microscopy experiments to characterize the detachment forces of single-stranded DNA at mica surfaces mediated by the metal cations Li+, Na+, K+, Cs+, Mg2+, and Ca2+. Ion-specific adsorption at the mica/water interface compensates (Li+ and Na+) or overcompensates (K+, Cs+, Mg2+, and Ca2+) the bare negative surface charge of mica. In addition, direct and water-mediated contacts are formed between the ions, the phosphate oxygens of DNA, and mica. The different contact types give rise to low- and high-force pathways and a broad distribution of detachment forces. Weakly hydrated ions, such as Cs+ and water-mediated contacts, lead to low detachment forces and high mobility of the DNA on the surface. Direct ion-DNA or ion-surface contacts lead to significantly higher forces. The comprehensive view gained from our combined approach allows us to highlight the most promising cations for imaging in physiological conditions: K+, which overcompensates the negative mica charge and induces long-ranged attractions. Mg2+ and Ca2+, which form a few specific and long-lived contacts to bind DNA with high affinity.
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Affiliation(s)
- Mohd Ibrahim
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Christiane Wenzel
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Max Lallemang
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
| | - Bizan N Balzer
- Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, 79104 Freiburg, Germany
- Cluster of Excellence livMatS @ FIT-Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, 79104 Freiburg, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
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15
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Junier I, Ghobadpour E, Espeli O, Everaers R. DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling. Front Microbiol 2023; 14:1192831. [PMID: 37965550 PMCID: PMC10642903 DOI: 10.3389/fmicb.2023.1192831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/25/2023] [Indexed: 11/16/2023] Open
Abstract
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene transcription. Supercoiling affects all scales of the spatio-temporal organization of bacterial DNA, from the base pair to the large scale chromosome conformation. Highlighted in vitro and in vivo in the 1960s and 1970s, respectively, the first physical models were proposed concomitantly in order to predict the deformation properties of the double helix. About fifteen years later, polymer physics models demonstrated on larger scales the plectonemic nature and the tree-like organization of supercoiled DNA. Since then, many works have tried to establish a better understanding of the multiple structuring and physiological properties of bacterial DNA in thermodynamic equilibrium and far from equilibrium. The purpose of this essay is to address upcoming challenges by thoroughly exploring the relevance, predictive capacity, and limitations of current physical models, with a specific focus on structural properties beyond the scale of the double helix. We discuss more particularly the problem of DNA conformations, the interplay between DNA supercoiling with gene transcription and DNA replication, its role on nucleoid formation and, finally, the problem of scaling up models. Our primary objective is to foster increased collaboration between physicists and biologists. To achieve this, we have reduced the respective jargon to a minimum and we provide some explanatory background material for the two communities.
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Affiliation(s)
- Ivan Junier
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Université Grenoble Alpes, Grenoble, France
| | - Elham Ghobadpour
- CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Université Grenoble Alpes, Grenoble, France
- École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, Lyon, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Ralf Everaers
- École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, Lyon, France
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16
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Curuksu JD. Spectral analysis of DNA superhelical dynamics from molecular minicircle simulations. J Chem Phys 2023; 159:105101. [PMID: 37694753 DOI: 10.1063/5.0164440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023] Open
Abstract
Torsional and bending deformations of DNA molecules often occur in vivo and are important for biological functions. DNA "under stress" is a conformational state, which is by far the most frequent state during DNA-protein and gene regulation. In DNA minicircles of length <100 base pairs (bp), the combined effect of torsional and bending stresses can cause local unusual conformations, with certain base pair steps often absorbing most of the stress, leaving other steps close to their relaxed conformation. To better understand the superhelical dynamics of DNA under stress, molecular simulations of 94 bp minicircles with different torsional linking numbers were interpreted using Fourier analyses and principal component analyses. Sharp localized bends of nearly 90° in the helical axis were observed, which in turn decreased fluctuations of the rotational register and helped redistribute the torsional stress into writhe, i.e., superhelical turn up to 360°. In these kinked minicircles, only two-thirds of the DNA molecule bends and writhes and the remaining segment stays close to straight and preserves a conformational flexibility typical of canonical B-DNA (bending of 39° ± 17° distributed parsimoniously across 36 bp), which was confirmed and visualized by principal component analysis. These results confirm that stressed DNA molecules are highly heterogeneous along their sequence, with segments designed to locally store and release stress so that nearby segments can stay relaxed.
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Affiliation(s)
- Jeremy D Curuksu
- Amazon.com, Inc., New York, New York 10001, USA and Center for Data Science, New York University, New York, New York 10011, USA
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17
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Tessmer I. The roles of non-productive complexes of DNA repair proteins with DNA lesions. DNA Repair (Amst) 2023; 129:103542. [PMID: 37453245 DOI: 10.1016/j.dnarep.2023.103542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
A multitude of different types of lesions is continuously introduced into the DNA inside our cells, and their rapid and efficient repair is fundamentally important for the maintenance of genomic stability and cellular viability. This is achieved by a number of DNA repair systems that each involve different protein factors and employ versatile strategies to target different types of DNA lesions. Intriguingly, specialized DNA repair proteins have also evolved to form non-functional complexes with their target lesions. These proteins allow the marking of innocuous lesions to render them visible for DNA repair systems and can serve to directly recruit DNA repair cascades. Moreover, they also provide links between different DNA repair mechanisms or even between DNA lesions and transcription regulation. I will focus here in particular on recent findings from single molecule analyses on the alkyltransferase-like protein ATL, which is believed to initiate nucleotide excision repair (NER) of non-native NER target lesions, and the base excision repair (BER) enzyme hOGG1, which recruits the oncogene transcription factor Myc to gene promoters under oxidative stress.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef Schneider Str. 2, 97080 Würzburg, Germany
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18
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Pavlova AS, Ilyushchenko VV, Kupryushkin MS, Zharkov TD, Dyudeeva ES, Bauer IA, Chubarov AS, Pyshnyi DV, Pyshnaya IA. Complexes and Supramolecular Associates of Dodecyl-Containing Oligonucleotides with Serum Albumin. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1165-1180. [PMID: 37758315 DOI: 10.1134/s0006297923080102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/26/2023] [Accepted: 07/04/2023] [Indexed: 10/03/2023]
Abstract
Serum albumin is currently in the focus of biomedical research as a promising platform for the creation of multicomponent self-assembling systems due to the presence of several sites with high binding affinity of various compounds in its molecule, including lipophilic oligonucleotide conjugates. In this work, we investigated the stoichiometry of the dodecyl-containing oligonucleotides binding to bovine and human serum albumins using an electrophoretic mobility shift assay. The results indicate the formation of the albumin-oligonucleotide complexes with a stoichiometry of about 1 : (1.25 ± 0.25) under physiological-like conditions. Using atomic force microscopy, it was found that the interaction of human serum albumin with the duplex of complementary dodecyl-containing oligonucleotides resulted in the formation of circular associates with a diameter of 165.5 ± 94.3 nm and 28.9 ± 16.9 nm in height, and interaction with polydeoxyadenylic acid and dodecyl-containing oligothymidylate resulted in formation of supramolecular associates with the size of about 315.4 ± 70.9 and 188.3 ± 43.7 nm, respectively. The obtained data allow considering the dodecyl-containing oligonucleotides and albumin as potential components of the designed self-assembling systems for solving problems of molecular biology, biomedicine, and development of unique theranostics with targeted action.
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Affiliation(s)
- Anna S Pavlova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Valeriya V Ilyushchenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Timofey D Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Evgeniya S Dyudeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Irina A Bauer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alexey S Chubarov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Inna A Pyshnaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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19
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Basov A, Dorohova A, Malyshko V, Moiseev A, Svidlov A, Bezhenar M, Nechipurenko Y, Dzhimak S. Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17. Int J Mol Sci 2023; 24:12137. [PMID: 37569512 PMCID: PMC10418495 DOI: 10.3390/ijms241512137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023] Open
Abstract
The influence of a single 2H/1H replacement on the frequency generation of different-size bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was studied by a developed algorithm and mathematical modeling without simplifications or averaging. This new approach showed the efficacy of researching DNA bubbles and open states both when all hydrogen bonds in nitrogenous base pairs are protium and after an 2H-substitution. After a single deuterium substitution under specific energies, it was demonstrated that the non-coding region of IFNA17 had a more significant regulatory role in bubble generation in the whole gene than the promoter had. It was revealed that a single deuterium substitution for protium has an influence on the frequency generation of DNA bubbles, which also depends on their size and is always higher for the smaller bubbles under the largest number of the studied energies. Wherein, compared to the natural condition under the same critical value of energy, the bigger raises of the bubble frequency occurrence (maximums) were found for 11-30 base pair (bp) bubbles (higher by 319%), 2-4 bp bubbles (higher by 300%), and 31 bp and over ones (higher by 220%); whereas the most significant reductions of the indicators (minimums) were observed for 11-30 bp bubbles (lower by 43%) and bubbles size over 30 bp (lower by 82%). In this study, we also analyzed the impact of several circumstances on the AT/GC ratio in the formation of DNA bubbles, both under natural conditions and after a single hydrogen isotope exchange. Moreover, based on the obtained data, substantial positive and inverse correlations were revealed between the AT/GC ratio and some factors (energy values, size of DNA bubbles). So, this modeling and variant of the modified algorithm, adapted for researching DNA bubbles, can be useful to study the regulation of replication and transcription in the genes under different isotopic substitutions in the nucleobases.
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Affiliation(s)
- Alexandr Basov
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, Krasnodar 350063, Russia; (A.B.); (V.M.)
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
| | - Anna Dorohova
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Vadim Malyshko
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, Krasnodar 350063, Russia; (A.B.); (V.M.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Arkadii Moiseev
- Scientific Department, Kuban State Agrarian University, Krasnodar 350004, Russia;
| | - Alexandr Svidlov
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Maria Bezhenar
- Department of Function Theory, Kuban State University, Krasnodar 350040, Russia;
| | - Yury Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Stepan Dzhimak
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
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20
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Ahmad K, Javed A, Lanphere C, Coveney PV, Orlova EV, Howorka S. Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Nat Commun 2023; 14:3630. [PMID: 37336895 DOI: 10.1038/s41467-023-38681-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/11/2023] [Indexed: 06/21/2023] Open
Abstract
DNA can be folded into rationally designed, unique, and functional materials. To fully realise the potential of these DNA materials, a fundamental understanding of their structure and dynamics is necessary, both in simple solvents as well as more complex and diverse anisotropic environments. Here we analyse an archetypal six-duplex DNA nanoarchitecture with single-particle cryo-electron microscopy and molecular dynamics simulations in solvents of tunable ionic strength and within the anisotropic environment of biological membranes. Outside lipid bilayers, the six-duplex bundle lacks the designed symmetrical barrel-type architecture. Rather, duplexes are arranged in non-hexagonal fashion and are disorted to form a wider, less elongated structure. Insertion into lipid membranes, however, restores the anticipated barrel shape due to lateral duplex compression by the bilayer. The salt concentration has a drastic impact on the stability of the inserted barrel-shaped DNA nanopore given the tunable electrostatic repulsion between the negatively charged duplexes. By synergistically combining experiments and simulations, we increase fundamental understanding into the environment-dependent structural dynamics of a widely used nanoarchitecture. This insight will pave the way for future engineering and biosensing applications.
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Affiliation(s)
- Katya Ahmad
- Centre for Computational Science, University College London, London, WC1H 0AJ, UK
| | - Abid Javed
- Department of Biological Sciences, Birkbeck, University of London, London, WC1E 7HX, UK
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Conor Lanphere
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, UK
| | - Peter V Coveney
- Centre for Computational Science, University College London, London, WC1H 0AJ, UK.
- Advanced Research Computing Centre, University College London, London, WC1H 0AJ, UK.
- Informatics Institute, University of Amsterdam, Amsterdam, 1090 GH, The Netherlands.
| | - Elena V Orlova
- Department of Biological Sciences, Birkbeck, University of London, London, WC1E 7HX, UK.
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, UK.
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21
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Balqis N, Mohamed Jan B, Simon Cornelis Metselaar H, Sidek A, Kenanakis G, Ikram R. An Overview of Recycling Wastes into Graphene Derivatives Using Microwave Synthesis; Trends and Prospects. MATERIALS (BASEL, SWITZERLAND) 2023; 16:ma16103726. [PMID: 37241354 DOI: 10.3390/ma16103726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023]
Abstract
It is no secret that graphene, a two-dimensional single-layered carbon atom crystal lattice, has drawn tremendous attention due to its distinct electronic, surface, mechanical, and optoelectronic properties. Graphene also has opened up new possibilities for future systems and devices due to its distinct structure and characteristics which has increased its demand in a variety of applications. However, scaling up graphene production is still a difficult, daunting, and challenging task. Although there is a vast body of literature reported on the synthesis of graphene through conventional and eco-friendly methods, viable processes for mass graphene production are still lacking. This review focuses on the variety of unwanted waste materials, such as biowastes, coal, and industrial wastes, for producing graphene and its potential derivatives. Among the synthetic routes, the main emphasis relies on microwave-assisted production of graphene derivatives. In addition, a detailed analysis of the characterization of graphene-based materials is presented. This paper also highlights the current advances and applications through the recycling of waste-derived graphene materials using microwave-assisted technology. In the end, it would alleviate the current challenges and forecast the specific direction of waste-derived graphene future prospects and developments.
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Affiliation(s)
- Nuralmeera Balqis
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Badrul Mohamed Jan
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | | | - Akhmal Sidek
- Petroleum Engineering Department, School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Malaysia
| | - George Kenanakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, N. Plastira 100, Vasilika Vouton, GR-700 13 Heraklion, Crete, Greece
| | - Rabia Ikram
- Department of Chemical Engineering, Faculty of Engineering, Universiti Malaya, Kuala Lumpur 50603, Malaysia
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22
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Lu W, Onuchic JN, Di Pierro M. An associative memory Hamiltonian model for DNA and nucleosomes. PLoS Comput Biol 2023; 19:e1011013. [PMID: 36972316 PMCID: PMC10079229 DOI: 10.1371/journal.pcbi.1011013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 04/06/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
A model for DNA and nucleosomes is introduced with the goal of studying chromosomes from a single base level all the way to higher-order chromatin structures. This model, dubbed the Widely Editable Chromatin Model (WEChroM), reproduces the complex mechanics of the double helix including its bending persistence length and twisting persistence length, and their respective temperature dependence. The WEChroM Hamiltonian is composed of chain connectivity, steric interactions, and associative memory terms representing all remaining interactions leading to the structure, dynamics, and mechanical characteristics of the B-DNA. Several applications of this model are discussed to demonstrate its applicability. WEChroM is used to investigate the behavior of circular DNA in the presence of positive and negative supercoiling. We show that it recapitulates the formation of plectonemes and of structural defects that relax mechanical stress. The model spontaneously manifests an asymmetric behavior with respect to positive or negative supercoiling, similar to what was previously observed in experiments. Additionally, we show that the associative memory Hamiltonian is also capable of reproducing the free energy of partial DNA unwrapping from nucleosomes. WEChroM is designed to emulate the continuously variable mechanical properties of the 10nm fiber and, by virtue of its simplicity, is ready to be scaled up to molecular systems large enough to investigate the structural ensembles of genes. WEChroM is implemented in the OpenMM simulation toolkits and is freely available for public use.
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Affiliation(s)
- Weiqi Lu
- Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America
| | - José N. Onuchic
- Center for Theoretical Biological Physics, & Department of Physics and Astronomy, Rice University, Houston, Texas, United States of America
- Department of Chemistry, & Department of Biosciences, Rice University, Houston, Texas, United States of America
- * E-mail: (JNO); (MDP)
| | - Michele Di Pierro
- Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
- Center for Theoretical Biological Physics, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail: (JNO); (MDP)
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23
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Kolbeck P, Dass M, Martynenko IV, van Dijk-Moes RJA, Brouwer KJH, van Blaaderen A, Vanderlinden W, Liedl T, Lipfert J. DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging. NANO LETTERS 2023; 23:1236-1243. [PMID: 36745573 PMCID: PMC9951250 DOI: 10.1021/acs.nanolett.2c04299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/25/2022] [Indexed: 06/01/2023]
Abstract
Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.
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Affiliation(s)
- Pauline
J. Kolbeck
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Mihir Dass
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
| | - Irina V. Martynenko
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
| | - Relinde J. A. van Dijk-Moes
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Kelly J. H. Brouwer
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Alfons van Blaaderen
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Willem Vanderlinden
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Tim Liedl
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
| | - Jan Lipfert
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
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24
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Waszkiewicz R, Ranasinghe M, Fogg JM, Catanese DJ, Ekiel-Jeżewska ML, Lisicki M, Demeler B, Zechiedrich L, Szymczak P. DNA supercoiling-induced shapes alter minicircle hydrodynamic properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522747. [PMID: 36711572 PMCID: PMC9881935 DOI: 10.1101/2023.01.04.522747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DNA in cells is organized in negatively supercoiled loops. The resulting torsional and bending strain allows DNA to adopt a surprisingly wide variety of 3-D shapes. This interplay between negative supercoiling, looping, and shape influences how DNA is stored, replicated, transcribed, repaired, and likely every other aspect of DNA activity. To understand the consequences of negative supercoiling and curvature on the hydrodynamic properties of DNA, we submitted 336 bp and 672 bp DNA minicircles to analytical ultracentrifugation (AUC). We found that the diffusion coefficient, sedimentation coefficient, and the DNA hydrodynamic radius strongly depended on circularity, loop length, and degree of negative supercoiling. Because AUC cannot ascertain shape beyond degree of non-globularity, we applied linear elasticity theory to predict DNA shapes, and combined these with hydrodynamic calculations to interpret the AUC data, with reasonable agreement between theory and experiment. These complementary approaches, together with earlier electron cryotomography data, provide a framework for understanding and predicting the effects of supercoiling on the shape and hydrodynamic properties of DNA.
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Affiliation(s)
- Radost Waszkiewicz
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Maduni Ranasinghe
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Alberta, T1K3M4, Canada
| | - Jonathan M. Fogg
- Department of Molecular Virology and Microbiology, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Daniel J. Catanese
- Department of Biosciences, Rice University, 6100 Main St., Houston, TX 77005-1827, USA
| | - Maria L. Ekiel-Jeżewska
- Institute of Fundamental Technological Research, Polish Academy of Sciences, A. Pawińskiego 5B, 02-106 Warsaw, Poland,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Maciej Lisicki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Borries Demeler
- University of Lethbridge, Dept. of Chemistry and Biochemistry, Alberta, T1K3M4, Canada,University of Montana, Dept. of Chemistry and Biochemistry, Missoula, MT 59812, USA,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Lynn Zechiedrich
- Department of Molecular Virology and Microbiology, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Pharmacology and Chemical Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland,Co-contributing authors: MLE-J: , ML: , BD: , LZ: , PS:
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25
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Li C, Zhou Z, Ren C, Deng Y, Peng F, Wang Q, Zhang H, Jiang Y. Triplex-forming oligonucleotides as an anti-gene technique for cancer therapy. Front Pharmacol 2022; 13:1007723. [PMID: 36618947 PMCID: PMC9811266 DOI: 10.3389/fphar.2022.1007723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Triplex-forming oligonucleotides (TFOs) can bind to the major groove of double-stranded DNA with high specificity and affinity and inhibit gene expression. Triplex-forming oligonucleotides have gained prominence because of their potential applications in antigene therapy. In particular, the target specificity of triplex-forming oligonucleotides combined with their ability to suppress oncogene expression has driven their development as anti-cancer agents. So far, triplex-forming oligonucleotides have not been used for clinical treatment and seem to be gradually snubbed in recent years. But triplex-forming oligonucleotides still represent an approach to down-regulate the expression of the target gene and a carrier of active substances. Therefore, in the present review, we will introduce the characteristics of triplex-forming oligonucleotides and their anti-cancer research progress. Then, we will discuss the challenges in their application.
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Affiliation(s)
- Chun Li
- Department of Rehabilitation Medicine, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, China
| | - Zunzhen Zhou
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Chao Ren
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Yi Deng
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Feng Peng
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Qiongfen Wang
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Hong Zhang
- Department of Rehabilitation Medicine, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China,*Correspondence: Hong Zhang, ; Yuan Jiang,
| | - Yuan Jiang
- Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, China,*Correspondence: Hong Zhang, ; Yuan Jiang,
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26
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Souli MP, Nikitaki Z, Puchalska M, Brabcová KP, Spyratou E, Kote P, Efstathopoulos EP, Hada M, Georgakilas AG, Sihver L. Clustered DNA Damage Patterns after Proton Therapy Beam Irradiation Using Plasmid DNA. Int J Mol Sci 2022; 23:ijms232415606. [PMID: 36555249 PMCID: PMC9779025 DOI: 10.3390/ijms232415606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Modeling ionizing radiation interaction with biological matter is a major scientific challenge, especially for protons that are nowadays widely used in cancer treatment. That presupposes a sound understanding of the mechanisms that take place from the early events of the induction of DNA damage. Herein, we present results of irradiation-induced complex DNA damage measurements using plasmid pBR322 along a typical Proton Treatment Plan at the MedAustron proton and carbon beam therapy facility (energy 137-198 MeV and Linear Energy Transfer (LET) range 1-9 keV/μm), by means of Agarose Gel Electrophoresis and DNA fragmentation using Atomic Force Microscopy (AFM). The induction rate Mbp-1 Gy-1 for each type of damage, single strand breaks (SSBs), double-strand breaks (DSBs), base lesions and non-DSB clusters was measured after irradiations in solutions with varying scavenging capacity containing 2-amino-2-(hydroxymethyl)propane-1,3-diol (Tris) and coumarin-3-carboxylic acid (C3CA) as scavengers. Our combined results reveal the determining role of LET and Reactive Oxygen Species (ROS) in DNA fragmentation. Furthermore, AFM used to measure apparent DNA lengths provided us with insights into the role of increasing LET in the induction of highly complex DNA damage.
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Affiliation(s)
- Maria P Souli
- Atominstitut, Technische Universität Wien, 1020 Vienna, Austria
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | - Zacharenia Nikitaki
- Atominstitut, Technische Universität Wien, 1020 Vienna, Austria
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | | | | | - Ellas Spyratou
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 11517 Athens, Greece
| | - Panagiotis Kote
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | - Efstathios P Efstathopoulos
- 2nd Department of Radiology, Medical School, National and Kapodistrian University of Athens, 11517 Athens, Greece
| | - Megumi Hada
- Radiation Institute for Science & Engineering, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, 15780 Athens, Greece
| | - Lembit Sihver
- Atominstitut, Technische Universität Wien, 1020 Vienna, Austria
- Nuclear Physics Institute, Czech Academy of Sciences, Na Truhlářce 39/64, 180 86 Prague, Czech Republic
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27
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Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range. Int J Mol Sci 2022; 23:ijms232415487. [PMID: 36555136 PMCID: PMC9778762 DOI: 10.3390/ijms232415487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
The effect of single substitutions of protium for deuterium in hydrogen bonds between pairs of nitrogenous bases on the open states occurrence probability at high critical breaking energies of these bonds has been studied. The study was carried out using numerical methods based on the angular mathematical model of DNA. The IFNA17 gene was divided into three approximately equal parts. A comparison of the open states occurrence probability in these parts of the gene was done. To improve the accuracy of the results, a special data processing algorithm was developed. The developed methods have shown their suitability for taking into account the occurrence of open states in the entire range of high critical energies. It has been established that single 2H/1H substitutions in certain nitrogenous bases can be a mechanism for maintaining the vital activity of IFNA17 under critical conditions. In general, the developed method of the mathematical modeling provide unprecedented insight into the DNA behavior under the highest critical energy range, which greatly expands scientific understanding of nucleobases interaction.
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28
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Bezhenar MV, Elkina AA, Caceres JLH, Baryshev MG, Sulima AO, Dzhimak SS, Isaev VA. Review of Mathematical Models Describing the Mechanical Motion in a DNA Molecule. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922060021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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29
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Tanaka H, Seki Y, Ueno S, Shibutani Y. Conformational deformation of a multi-jointed elastic loop. Sci Rep 2022; 12:19984. [PMID: 36411324 PMCID: PMC9678883 DOI: 10.1038/s41598-022-24355-7] [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: 06/21/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022] Open
Abstract
A new class of deformation is presented for a planar loop structure made up of slender elastic bodies and joints. In demonstrating the circumferential shortening of the multi-jointed elastic loop, diverse three-dimensional (3D) deformations emerge through piecewise deflections and discrete rotations. These 3D morphologies correspond to conformations of molecular ring systems. Through image processing, the 3D reconstructions of the deformed structures are characterized by number, geometry, and initial imperfections of the body segments. We elucidate from measurements that the conformational deformation without self-stress results from a cyclical assembly of compressive bending of elastic bodies with high shear rigidity. The mechanical insights gained may apply in controlling the polymorphism exhibited by the cyclical structures across scales.
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Affiliation(s)
- Hiro Tanaka
- grid.136593.b0000 0004 0373 3971Department of Mechanical Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Yuji Seki
- grid.136593.b0000 0004 0373 3971Department of Mechanical Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Shohei Ueno
- grid.136593.b0000 0004 0373 3971Department of Mechanical Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Yoji Shibutani
- grid.136593.b0000 0004 0373 3971Department of Mechanical Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 Japan ,grid.267852.c0000 0004 0637 2083Nanotechnology Program, VNU Vietnam Japan University, Luu Huu Phuoc Street, My Dinh 1 Ward, Nam Tu Liem District, Hanoi, Vietnam
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30
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Extrachromosomal circular DNA: biogenesis, structure, functions and diseases. Signal Transduct Target Ther 2022; 7:342. [PMID: 36184613 PMCID: PMC9527254 DOI: 10.1038/s41392-022-01176-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to genomic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. In addition, the origin of eccDNA is considered to be associated with essential chromatin-related events, including the formation of super-enhancers and DNA repair machineries. Moreover, our understanding of the properties and functions of eccDNA has continuously and greatly expanded. Emerging investigations demonstrate that eccDNAs serve as multifunctional molecules in various organisms during diversified biological processes, such as epigenetic remodeling, telomere trimming, and the regulation of canonical signaling pathways. Importantly, its special distribution potentiates eccDNA as a measurable biomarker in many diseases, especially cancers. The loss of eccDNA homeostasis facilitates tumor initiation, malignant progression, and heterogeneous evolution in many cancers. An in-depth understanding of eccDNA provides novel insights for precision cancer treatment. In this review, we summarized the discovery history of eccDNA, discussed the biogenesis, characteristics, and functions of eccDNA. Moreover, we emphasized the role of eccDNA during tumor pathogenesis and malignant evolution. Therapeutically, we summarized potential clinical applications that target aberrant eccDNA in multiple diseases.
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31
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Ouyang Q, Xie Z, Liu J, Gong M, Yu H. Application of Atomic Force Microscopy as Advanced Asphalt Testing Technology: A Comprehensive Review. Polymers (Basel) 2022; 14:polym14142851. [PMID: 35890627 PMCID: PMC9316586 DOI: 10.3390/polym14142851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/16/2022] Open
Abstract
In the past three decades, researchers have engaged in the relationship between the composition, macro performance, and microstructure of asphalt. There are many research results in the use of atomic force microscopy (AFM) to study the microstructure and related mechanisms of asphalt. Based on previous studies, the performance of asphalt from its microstructure has been observed and analyzed, and different evaluation indices and modification methods have been proposed, providing guidance toward improving the performance of asphalt materials and benefiting potential applications. This review focuses on the typical application and analysis of AFM in the study of the aging regeneration and modification properties of asphalt. Additionally, this review introduces the history of the rheological and chemical testing of asphalt materials and the history of using AFM to investigate asphalt. Furthermore, this review introduces the basic principles of various modes of application of AFM in the microstructure of asphalt, providing a research direction for the further popularization and application of AFM in asphalt or other materials in the future. This review aims to provide a reference and direction for researchers to further popularize the application of AFM in asphalt and standardize the testing methods of AFM. This paper is also helpful in further exploring the relationship between the microstructure and macro performance of asphalt.
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Affiliation(s)
- Qijian Ouyang
- School of Civil Engineering and Transportation, South China University of Technology, Guangzhou 510641, China; (Q.O.); (Z.X.); (J.L.)
| | - Zhiwei Xie
- School of Civil Engineering and Transportation, South China University of Technology, Guangzhou 510641, China; (Q.O.); (Z.X.); (J.L.)
| | - Jinhai Liu
- School of Civil Engineering and Transportation, South China University of Technology, Guangzhou 510641, China; (Q.O.); (Z.X.); (J.L.)
| | - Minghui Gong
- State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210096, China;
| | - Huayang Yu
- School of Civil Engineering and Transportation, South China University of Technology, Guangzhou 510641, China; (Q.O.); (Z.X.); (J.L.)
- State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210096, China;
- Guangdong Provincial Key Laboratory of Modern Civil Engineering Technology, Guangzhou 510641, China
- Correspondence:
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32
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Kaufhold WT, Pfeifer W, Castro CE, Di Michele L. Probing the Mechanical Properties of DNA Nanostructures with Metadynamics. ACS NANO 2022; 16:8784-8797. [PMID: 35580231 PMCID: PMC9245350 DOI: 10.1021/acsnano.1c08999] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, the convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecular conformational distributions by flattening free energy landscapes. Here we leveraged this approach to sample the free energy landscapes of DNA nanostructures whose unbiased dynamics are nonergodic, including bistable Holliday junctions and part of a bistable DNA origami structure. Taking a DNA origami-compliant joint as a case study, we further demonstrate that metadynamics can predict the mechanical response of a full DNA origami device to an applied force, showing good agreement with experiments. Our results exemplify the efficient computation of free energy landscapes and force response in DNA nanodevices, which could be applied for rapid feedback in iterative design workflows and generally facilitate the integration of simulation and experiments. Metadynamics will be particularly useful to guide the design of dynamic devices for nanorobotics, biosensing, or nanomanufacturing applications.
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Affiliation(s)
- Will T. Kaufhold
- Department
of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
- Department
of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Wolfgang Pfeifer
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Carlos E. Castro
- Department
of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Lorenzo Di Michele
- Department
of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
- Department
of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
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33
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Kaufhold WT, Pfeifer W, Castro CE, Di Michele L. Probing the Mechanical Properties of DNA Nanostructures with Metadynamics. ACS NANO 2022; 16:8784-8797. [PMID: 35580231 DOI: 10.48550/arxiv.2110.01477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, the convergence of distributions from unbiased simulation is slow, limiting applications to equilibrium structural properties. Given the increasing interest in dynamic, reconfigurable, and deformable devices, methods that enable efficient quantification of large ranges of motion, conformational transitions, and mechanical deformation are critically needed. Metadynamics is an automated biasing technique that enables the rapid acquisition of molecular conformational distributions by flattening free energy landscapes. Here we leveraged this approach to sample the free energy landscapes of DNA nanostructures whose unbiased dynamics are nonergodic, including bistable Holliday junctions and part of a bistable DNA origami structure. Taking a DNA origami-compliant joint as a case study, we further demonstrate that metadynamics can predict the mechanical response of a full DNA origami device to an applied force, showing good agreement with experiments. Our results exemplify the efficient computation of free energy landscapes and force response in DNA nanodevices, which could be applied for rapid feedback in iterative design workflows and generally facilitate the integration of simulation and experiments. Metadynamics will be particularly useful to guide the design of dynamic devices for nanorobotics, biosensing, or nanomanufacturing applications.
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Affiliation(s)
- Will T Kaufhold
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
- Department of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
| | - Wolfgang Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus 43210, Ohio, United States
| | - Lorenzo Di Michele
- Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
- Department of Chemistry and fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K
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34
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Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
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35
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Abstract
Atomic force microscopy (AFM) is a microscopy technique that uses a sharp probe to trace a sample surface at nanometer resolution. For biological applications, one of its key advantages is its ability to visualize the substructure of single molecules and molecular complexes in an aqueous environment. Here, we describe the application of AFM to determine the secondary and tertiary structure of surface-bound DNA, and its interactions with proteins.
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Affiliation(s)
- Philip J Haynes
- London Centre for Nanotechnology, University College London, London, UK
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Kavit H S Main
- London Centre for Nanotechnology, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | - Bernice Akpinar
- London Centre for Nanotechnology, University College London, London, UK
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, London, UK
| | - Alice L B Pyne
- London Centre for Nanotechnology, University College London, London, UK.
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
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36
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Dzhimak S, Svidlov A, Elkina A, Gerasimenko E, Baryshev M, Drobotenko M. Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque. Int J Mol Sci 2022; 23:ijms23084428. [PMID: 35457247 PMCID: PMC9025193 DOI: 10.3390/ijms23084428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/31/2022] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
The formation and dynamics of the open states in a double-stranded DNA molecule are largely determined by its mechanical parameters. The main one is the torque. However, the experimental study of DNA dynamics and the occurrence of open states is limited by the spatial resolution of available biophysical instruments. Therefore, in this work, on the basis of a mechanical mathematical model of DNA, calculations of the torque effect on the process of occurrence and dynamics of open states were carried out for the interferon alpha 17 gene. It was shown that torsion action leads to the occurrence of rotational movements of nitrogenous bases. This influence is nonlinear, and an increase in the amplitude of the torsion action does not lead to an automatic increase in the amplitude of rotational movements and an increase in the zones’ open states. Calculations with a constant torsion moment demonstrate that open states zones are more often formed at the boundaries of the gen and in regions with a predominance of A–T pairs. It is shown, that for the occurrence of open states in the part of the gene that contains a small number of A–T pairs, a large amount of torque is required. When the torque is applied to a certain region of the gene, the probability of the formation of the open state depends on the content of A–T pairs in this region, the size of this region, and on the exposure time. For this mathematical model, open states zones can be closed when the torsion action stops. The simulation results showed that the values of the torsion moment required for the appearance of open states zones, in some cases, are close to experimentally measured (13–15 pN·nm).
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Affiliation(s)
- Stepan Dzhimak
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (A.E.); (M.B.); (M.D.)
- 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
- Correspondence: ; Tel.: +7-905-408-36-12
| | - Alexandr Svidlov
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (A.E.); (M.B.); (M.D.)
- 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
| | - Anna Elkina
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (A.E.); (M.B.); (M.D.)
- 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
| | - Eugeny Gerasimenko
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices, Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Mikhail Baryshev
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (A.E.); (M.B.); (M.D.)
- 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;
| | - Mikhail Drobotenko
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (A.E.); (M.B.); (M.D.)
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37
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Lutter L, Al-Hilaly YK, Serpell CJ, Tuite MF, Wischik CM, Serpell LC, Xue WF. Structural Identification of Individual Helical Amyloid Filaments by Integration of Cryo-Electron Microscopy-Derived Maps in Comparative Morphometric Atomic Force Microscopy Image Analysis. J Mol Biol 2022; 434:167466. [PMID: 35077765 PMCID: PMC9005780 DOI: 10.1016/j.jmb.2022.167466] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/18/2022] [Indexed: 11/27/2022]
Abstract
The presence of amyloid fibrils is a hallmark of more than 50 human disorders, including neurodegenerative diseases and systemic amyloidoses. A key unresolved challenge in understanding the involvement of amyloid in disease is to explain the relationship between individual structural polymorphs of amyloid fibrils, in potentially mixed populations, and the specific pathologies with which they are associated. Although cryo-electron microscopy (cryo-EM) and solid-state nuclear magnetic resonance (ssNMR) spectroscopy methods have been successfully employed in recent years to determine the structures of amyloid fibrils with high resolution detail, they rely on ensemble averaging of fibril structures in the entire sample or significant subpopulations. Here, we report a method for structural identification of individual fibril structures imaged by atomic force microscopy (AFM) by integration of high-resolution maps of amyloid fibrils determined by cryo-EM in comparative AFM image analysis. This approach was demonstrated using the hitherto structurally unresolved amyloid fibrils formed in vitro from a fragment of tau (297-391), termed 'dGAE'. Our approach established unequivocally that dGAE amyloid fibrils bear no structural relationship to heparin-induced tau fibrils formed in vitro. Furthermore, our comparative analysis resulted in the prediction that dGAE fibrils are structurally closely related to the paired helical filaments (PHFs) isolated from Alzheimer's disease (AD) brain tissue characterised by cryo-EM. These results show the utility of individual particle structural analysis using AFM, provide a workflow of how cryo-EM data can be incorporated into AFM image analysis and facilitate an integrated structural analysis of amyloid polymorphism.
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Affiliation(s)
- Liisa Lutter
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK. https://twitter.com/LiisaLutter
| | - Youssra K Al-Hilaly
- Sussex Neuroscience, School of Life Sciences, University of Sussex, BN1 9QG Falmer, Brighton, UK; Chemistry Department, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Christopher J Serpell
- School of Physical Sciences, Division of Natural Sciences, University of Kent, CT2 7NH Canterbury, UK. https://twitter.com/@SerpellLab
| | - Mick F Tuite
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK
| | - Claude M Wischik
- Institute of Medical Sciences, University of Aberdeen, UK; TauRx Therapeutics Ltd., Aberdeen, UK
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, BN1 9QG Falmer, Brighton, UK. https://twitter.com/@Serpell1
| | - Wei-Feng Xue
- School of Biosciences, Division of Natural Sciences, University of Kent, CT2 7NJ Canterbury, UK.
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38
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Noer JB, Hørsdal OK, Xiang X, Luo Y, Regenberg B. Extrachromosomal circular DNA in cancer: history, current knowledge, and methods. Trends Genet 2022; 38:766-781. [PMID: 35277298 DOI: 10.1016/j.tig.2022.02.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022]
Abstract
Extrachromosomal circular DNA (eccDNA) is a closed-circle, nuclear, nonplasmid DNA molecule found in all tested eukaryotes. eccDNA plays important roles in cancer pathogenesis, evolution of tumor heterogeneity, and therapeutic resistance. It is known under many names, including very large cancer-specific circular extrachromosomal DNA (ecDNA), which carries oncogenes and is often amplified in cancer cells. Our understanding of eccDNA has historically been limited and fragmented. To provide better a context of new and previous research on eccDNA, in this review we give an overview of the various names given to eccDNA at different times. We describe the different mechanisms for formation of eccDNA and the methods used to study eccDNA thus far. Finally, we explore the potential clinical value of eccDNA.
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Affiliation(s)
- Julie B Noer
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Oskar K Hørsdal
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Xi Xiang
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China; Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
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39
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Zhan S, Jiang J, Zeng Z, Wang Y, Cui H. DNA-templated coinage metal nanostructures and their applications in bioanalysis and biomedicine. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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40
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Abstract
The compaction of linear DNA into micrometer-sized nuclear boundaries involves the establishment of specific three-dimensional (3D) DNA structures complexed with histone proteins that form chromatin. The resulting structures modulate essential nuclear processes such as transcription, replication, and repair to facilitate or impede their multi-step progression and these contribute to dynamic modification of the 3D-genome organization. It is generally accepted that protein–protein and protein–DNA interactions form the basis of 3D-genome organization. However, the constant generation of mechanical forces, torques, and other stresses produced by various proteins translocating along DNA could be playing a larger role in genome organization than currently appreciated. Clearly, a thorough understanding of the mechanical determinants imposed by DNA transactions on the 3D organization of the genome is required. We provide here an overview of our current knowledge and highlight the importance of DNA and chromatin mechanics in gene expression.
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Affiliation(s)
- Rajiv Kumar Jha
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - David Levens
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
| | - Fedor Kouzine
- Gene Regulation Section, Laboratory of Pathology, Nci/nih, Bethesda, MD USA
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41
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Lim W, Randisi F, Doye JPK, Louis AA. The interplay of supercoiling and thymine dimers in DNA. Nucleic Acids Res 2022; 50:2480-2492. [PMID: 35188542 PMCID: PMC8934635 DOI: 10.1093/nar/gkac082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Thymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here, we introduce a model of thymine dimers in the oxDNA forcefield, parametrized by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.
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Affiliation(s)
- Wilber Lim
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Ferdinando Randisi
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- FabricNano Limited, 192 Drummond St, London NW1 3HP, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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42
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Esmaeeli R, Andal B, Perez A. Searching for Low Probability Opening Events in a DNA Sliding Clamp. Life (Basel) 2022; 12:life12020261. [PMID: 35207548 PMCID: PMC8876151 DOI: 10.3390/life12020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/27/2022] Open
Abstract
The β subunit of E. coli DNA polymererase III is a DNA sliding clamp associated with increasing the processivity of DNA synthesis. In its free form, it is a circular homodimer structure that can accomodate double-stranded DNA in a nonspecific manner. An open state of the clamp must be accessible before loading the DNA. The opening mechanism is still a matter of debate, as is the effect of bound DNA on opening/closing kinetics. We use a combination of atomistic, coarse-grained, and enhanced sampling strategies in both explicit and implicit solvents to identify opening events in the sliding clamp. Such simulations of large nucleic acid and their complexes are becoming available and are being driven by improvements in force fields and the creation of faster computers. Different models support alternative opening mechanisms, either through an in-plane or out-of-plane opening event. We further note some of the current limitations, despite advances, in modeling these highly charged systems with implicit solvent.
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43
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Kristoffersen EL, Burman M, Noy A, Holliger P. Rolling circle RNA synthesis catalysed by RNA. eLife 2022; 11:75186. [PMID: 35108196 PMCID: PMC8937235 DOI: 10.7554/elife.75186] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-catalyzed RNA replication is widely considered a key step in the emergence of life’s first genetic system. However, RNA replication can be impeded by the extraordinary stability of duplex RNA products, which must be dissociated for re-initiation of the next replication cycle. Here, we have explored rolling circle synthesis (RCS) as a potential solution to this strand separation problem. We observe sustained RCS by a triplet polymerase ribozyme beyond full-length circle synthesis with strand displacement yielding concatemeric RNA products. Furthermore, we show RCS of a circular Hammerhead ribozyme capable of self-cleavage and re-circularization. Thus, all steps of a viroid-like RNA replication pathway can be catalyzed by RNA alone. Finally, we explore potential RCS mechanisms by molecular dynamics simulations, which indicate a progressive build-up of conformational strain upon RCS with destabilization of nascent strand 5′- and 3′-ends. Our results have implications for the emergence of RNA replication and for understanding the potential of RNA to support complex genetic processes. Many organisms today rely on a trio of molecules for their survival: DNA, to store their genetic information; proteins, to conduct the biological processes required for growth or replication; and RNA, to mainly act as an intermediary between DNA and proteins. Yet, how these inanimate molecules first came together to form a living system remains unclear. Circumstantial evidence suggests that the first lifeforms relied to a much greater exrtent on RNA to conduct all necessary biological processes. There is no trace of this ‘RNA world’ today, but molecular ‘fossils’ may exist in current biology. Viroids, for example, are agents which can infect and replicate inside plant cells. They are formed of nothing but a circular strand of RNA that serves not only as genetic storage but also as ribozymes (RNA-based enzymes). Viroids need proteins from the host plant to replicate, but scientists have been able to engineer ribozymes that can copy complex RNA strands. This suggests that viroid-like replication could be achieved using only RNA. Kristoffersen et al. put this idea to the test and showed that it is possible to use RNA enzymatic activity alone to carry out all the steps of a viroid-like copying mechanism. This process included copying a viroid-like RNA circle with RNA, followed by trimming the copy to the right size and reforming the circle. These two latter steps could be carried out by a ribozyme that could itself be encoded on the RNA circle. A computer simulation indicated that RNA synthesis on the circle caused increasing tension that could ease some of the barriers to replication. These results increase our understanding of how RNA copying by RNA could be possible. This may lead to developing molecular models of a primordial RNA-based replication, which could be used to investigate early genetic systems and may have potential applications in synthetic biology.
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Affiliation(s)
| | - Matthew Burman
- Department of Physics, University of York, York, United Kingdom
| | - Agnes Noy
- Department of Physics, University of York, York, United Kingdom
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44
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Yeou S, Lee NK. Single-Molecule Methods for Investigating the Double-Stranded DNA Bendability. Mol Cells 2022; 45:33-40. [PMID: 34470919 PMCID: PMC8819492 DOI: 10.14348/molcells.2021.0182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/27/2022] Open
Abstract
The various DNA-protein interactions associated with the expression of genetic information involve double-stranded DNA (dsDNA) bending. Due to the importance of the formation of the dsDNA bending structure, dsDNA bending properties have long been investigated in the biophysics field. Conventionally, DNA bendability is characterized by innate averaging data from bulk experiments. The advent of single-molecule methods, such as atomic force microscopy, optical and magnetic tweezers, tethered particle motion, and single-molecule fluorescence resonance energy transfer measurement, has provided valuable tools to investigate not only the static structures but also the dynamic properties of bent dsDNA. Here, we reviewed the single-molecule methods that have been used for investigating dsDNA bendability and new findings related to dsDNA bending. Single-molecule approaches are promising tools for revealing the unknown properties of dsDNA related to its bending, particularly in cells.
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Affiliation(s)
- Sanghun Yeou
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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45
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Watson G, Velasco-Berrelleza V, Noy A. Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments. Methods Mol Biol 2022; 2476:95-109. [PMID: 35635699 DOI: 10.1007/978-1-0716-2221-6_8] [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] [Indexed: 06/15/2023]
Abstract
Atomic-level computer simulations are a very useful tool for describing the structure and dynamics of complex biomolecules such as DNA and for providing detail at a resolution where experimental techniques cannot arrive. Molecular dynamics (MD) simulations of mechanically distorted DNA caused by agents like supercoiling and protein binding are computationally challenging due to the large size of the associated systems and timescales. However, nowadays they are achievable thanks to the efficient usage of GPU and to the improvements of continuum solvation models. This together with the concurrent improvements in the resolution of single-molecule experiments, such as atomic force microscopy (AFM), makes possible the convergence between the two. Here we present detailed protocols for doing so: for performing molecular dynamics (MD) simulations of DNA adopting complex three-dimensional arrangements and for comparing the outcome of the calculations with single-molecule experimental data with a lower resolution than atomic.
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Affiliation(s)
- George Watson
- Department of Physics, University of York, Heslington, York, UK
| | | | - Agnes Noy
- Department of Physics, University of York, Heslington, York, UK.
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46
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Watson GD, Chan EW, Leake MC, Noy A. Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF. Comput Struct Biotechnol J 2022; 20:5264-5274. [PMID: 36212531 PMCID: PMC9519438 DOI: 10.1016/j.csbj.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/03/2022] Open
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47
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Shepherd JW, Leake MC. The End Restraint Method for Mechanically Perturbing Nucleic Acids In Silico. Methods Mol Biol 2022; 2476:249-262. [PMID: 35635708 DOI: 10.1007/978-1-0716-2221-6_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Far from being a passive information store, the genome is a mechanically dynamic and diverse system in which torsion and tension fluctuate and combine to determine structure and help regulate gene expression. Much of this mechanical perturbation is due to molecular machines such as topoisomerases which must stretch and twist DNA as part of various functions including DNA repair and replication. While the broad-scale mechanical response of nucleic acids to tension and torsion is well characterized, detail at the single base pair level is beyond the limits of even super-resolution imaging. Here, we present a straightforward, flexible, and extensible umbrella-sampling protocol to twist and stretch nucleic acids in silico using the popular biomolecular simulation package Amber-though the principles we describe are applicable also to other packages such as GROMACS. We discuss how to set up the simulation system, decide force fields and solvation models, and equilibrate. We then introduce the torsionally constrained stretching protocol, and finally we present some analysis techniques we have used to characterize structural motif formation. Rather than defining forces or fictional pseudoatoms, we instead define a fixed translation of specified atoms between each umbrella-sampling step, which allows comparison with experiment without needing to estimate applied forces by simply using the fractional end-to-end displacement as a comparison metric. We hope that this easy-to-implement solution will be valuable for interrogating optical and magnetic tweezers data on nucleic acids at base pair resolution.
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Affiliation(s)
| | - Mark C Leake
- Departments of Physics and Biology, University of York, York, UK
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48
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Homologous basic helix–loop–helix transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism. QRB DISCOVERY 2022. [PMID: 37529292 PMCID: PMC10392670 DOI: 10.1017/qrd.2022.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Abstract
Changing torsional restraints on DNA is essential for the regulation of transcription. Torsional stress, introduced by RNA polymerase, can propagate along chromatin facilitating topological transitions and modulating the specific binding of transcription factors (TFs) to DNA. Despite the importance, the mechanistic details on how torsional stress impacts the TFs-DNA complexation remain scarce. Herein, we address the impact of torsional stress on DNA complexation with homologous human basic helix–loop–helix (BHLH) hetero- and homodimers: MycMax, MadMax and MaxMax. The three TF dimers exhibit specificity towards the same DNA consensus sequence, the E-box response element, while regulating different transcriptional pathways. Using microseconds-long atomistic molecular dynamics simulations together with the torsional restraint that controls DNA total helical twist, we gradually over- and underwind naked and complexed DNA to a maximum of ± 5°/bp step. We observe that the binding of the BHLH dimers results in a similar increase in DNA torsional rigidity. However, under torsional stress the BHLH dimers induce distinct DNA deformations, characterised by changes in DNA grooves geometry and a significant asymmetric DNA bending. Supported by bioinformatics analyses, our data suggest that torsional stress may contribute to the execution of differential transcriptional programs of the homologous TFs by modulating their collaborative interactions.
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Three-dimensional genome organization via triplex-forming RNAs. Nat Struct Mol Biol 2021; 28:945-954. [PMID: 34759378 DOI: 10.1038/s41594-021-00678-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 09/30/2021] [Indexed: 11/08/2022]
Abstract
An increasing number of long noncoding RNAs (lncRNAs) have been proposed to act as nuclear organization factors during interphase. Direct RNA-DNA interactions can be achieved by the formation of triplex helix structures where a single-stranded RNA molecule hybridizes by complementarity into the major groove of double-stranded DNA. However, whether and how these direct RNA-DNA associations influence genome structure in interphase chromosomes remain poorly understood. Here we theorize that RNA organizes the genome in space via a triplex-forming mechanism. To test this theory, we apply a computational modeling approach of chromosomes that combines restraint-based modeling with polymer physics. Our models suggest that colocalization of triplex hotspots targeted by lncRNAs could contribute to large-scale chromosome compartmentalization cooperating, rather than competing, with architectural transcription factors such as CTCF.
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Svidlov A, Drobotenko M, Basov A, Gerasimenko E, Elkina A, Baryshev M, Nechipurenko Y, Dzhimak S. Influence of Environmental Parameters on the Stability of the DNA Molecule. ENTROPY (BASEL, SWITZERLAND) 2021; 23:1446. [PMID: 34828144 PMCID: PMC8622188 DOI: 10.3390/e23111446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022]
Abstract
Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation-dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases' vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.
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Affiliation(s)
- Alexander Svidlov
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- 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, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
| | - Alexander Basov
- Department of Radiophysics and Nanothechnology, 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;
| | - Anna Elkina
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- 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;
| | - Mikhail Baryshev
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- 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;
| | - Yury Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Stepan Dzhimak
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- 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;
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