1
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Barbero-Aparicio JA, Cuesta-Lopez S, García-Osorio CI, Pérez-Rodríguez J, García-Pedrajas N. Nonlinear physics opens a new paradigm for accurate transcription start site prediction. BMC Bioinformatics 2022; 23:565. [PMID: 36585618 PMCID: PMC9801560 DOI: 10.1186/s12859-022-05129-4] [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: 09/29/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
There is evidence that DNA breathing (spontaneous opening of the DNA strands) plays a relevant role in the interactions of DNA with other molecules, and in particular in the transcription process. Therefore, having physical models that can predict these openings is of interest. However, this source of information has not been used before either in transcription start sites (TSSs) or promoter prediction. In this article, one such model is used as an additional information source that, when used by a machine learning (ML) model, improves the results of current methods for the prediction of TSSs. In addition, we provide evidence on the validity of the physical model, as it is able by itself to predict TSSs with high accuracy. This opens an exciting avenue of research at the intersection of statistical mechanics and ML, where ML models in bioinformatics can be improved using physical models of DNA as feature extractors.
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Affiliation(s)
- José Antonio Barbero-Aparicio
- grid.23520.360000 0000 8569 1592Departamento de Informática, Universidad de Burgos, Avda. de Cantabria s/n, 09006 Burgos, Spain
| | - Santiago Cuesta-Lopez
- grid.23520.360000 0000 8569 1592Universidad de Burgos, Hospital del Rey, s/n, 09001 Burgos, Spain ,ICAMCyL Foundation, Internacional Center for Advanced Materials and Raw Materials of Castilla y León, León Technology Park, main building, first floor, offices 106-108, C/Julia Morros s/n, Armunia, 24009 León, Spain
| | - César Ignacio García-Osorio
- grid.23520.360000 0000 8569 1592Departamento de Informática, Universidad de Burgos, Avda. de Cantabria s/n, 09006 Burgos, Spain
| | - Javier Pérez-Rodríguez
- grid.449008.10000 0004 1795 4150Departamento de Métodos Cuantitativos, Universidad de Loyola Andalucía, Escritor Castilla Aguayo, 4, 14004 Córdoba, Spain
| | - Nicolás García-Pedrajas
- grid.411901.c0000 0001 2183 9102Department of Computing and Numerical Analysis, University of Córdoba, Edificio Albert Einstein, Campus de Rabanales, 14071 Córdoba, Spain
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2
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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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3
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Calabrò E, Goswami HK, Magazù S. Chromosome aberration in typical biological systems under exposure to low- and high-intensity magnetic fields. Electromagn Biol Med 2020; 39:97-108. [PMID: 32138556 DOI: 10.1080/15368378.2020.1737812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The aim of this study was to investigate the response of chromosomes in typical human and plant cells under applied low-frequency magnetic fields at low and high intensities. Neuronal-like cells and roots of Allium sativum and Vicia faba were used to investigate chromosome's response to a static and 50 Hz magnetic fields at intensities ranging from 1 mT to 0.8 T, generated by two Helmholtz coils driven by direct current or alternate current voltage. Vertex spectrometer and Olympus microscope with camera were used. A significant decrease in intensity of the phosphate bands in the DNA infrared region was observed by FTIR spectroscopy analysis after exposure of neuronal-like cells to static and 50 Hz magnetic field at low intensity of 1 mT, which can be explained assuming that uncoiling and unpackaging of chromatin constituents occurred after exposure. This effect was directly observed by microscope in roots of Allium sativum and Vicia faba under exposure to a static magnetic field at high intensity of 0.8 T. These findings can be explained assuming that exposure to both low- and high-intensity magnetic fields of chromosomes in typical human and plant cells induces uncoiling and unpackaging of chromatin constituents, followed by chromosome alignment towards the direction of applied magnetic field, providing further demonstration that magnetic fields can induce the orientation of organic macromolecules even at low-intensity values.
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Affiliation(s)
- Emanuele Calabrò
- Department of Mathematical and Informatics Sciences, Physical Sciences and Earth Sciences, University of Messina, Messina, Italy.,CISFA, Interuniversity Consortium of Applied Physical Sciences, Messina, Italy
| | - Hit Kishore Goswami
- Retired Professor of Genetics, Barkatullah University Bhopal (MP), Bhopal, India
| | - Salvatore Magazù
- Department of Mathematical and Informatics Sciences, Physical Sciences and Earth Sciences, University of Messina, Messina, Italy.,CISFA, Interuniversity Consortium of Applied Physical Sciences, Messina, Italy.,Le Studium, Loire Valley Institute for Advanced Studies, Orleans, France.,Centre de Biophysique Moleculaire (CBM), CNRS UPR 4301 du CNRS, Orleans, France.,UMR, Laboratoire Interfaces, Confinement, Mat_eriaux Et Nanostructures (ICMN) 7374 CNRS, Universitè d'Orleans, Orleans, France.,Istituto Nazionale Di Alta Matematica "F. Severi" - INDAM, Gruppo Nazionale per La Fisica Matematica - GNFM, Rome, Italy
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4
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Liangruksa M, Wongwises S. An elastic model of DNA under thermal induced stress. Math Biosci 2018; 300:47-54. [PMID: 29559328 DOI: 10.1016/j.mbs.2018.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 11/24/2017] [Accepted: 02/05/2018] [Indexed: 01/21/2023]
Abstract
DNAs (deoxyribonucleic acids) have the ability to alter its conformation in response to temperature changes to relieve the internal stress. The mistakenly structured DNA can lead to diseases or deformities. The conformation also influences the binding between DNA and other molecular complexes. In the present paper, we investigate the DNA elasticity under the influence of thermal induced stress by employing Kirchhoff's model of a thin elastic rod. The problem is solved by perturbation method to find equilibrium configurations of DNA at different modes. In addition, the model is validated with existing literature in which DNA is stretched or compressed. The behaviors of the helical structure under various temperatures are investigated with the melting temperature of DNA around 80 °C. This elasticity study of DNA could be a groundwork leading to better understandings on the effects of thermal induced stress to DNA's deformation and relevant biological processes in living cells.
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Affiliation(s)
- Monrudee Liangruksa
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand.
| | - Somchai Wongwises
- Fluid Mechanics, Thermal Engineering and Multiphase Flow Research Lab (FUTURE), Department of Mechanical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangmod, Bangkok 10140, Thailand
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5
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González A, Wildes A, Marty-Roda M, Cuesta-López S, Mossou E, Studer A, Demé B, Moiroux G, Garden JL, Theodorakopoulos N, Peyrard M. Melting Transition of Oriented DNA Fibers Submerged in Poly(ethylene glycol) Solutions Studied by Neutron Scattering and Calorimetry. J Phys Chem B 2018; 122:2504-2515. [DOI: 10.1021/acs.jpcb.7b11608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adrián González
- Institut Laue Langevin, 71, avenue des Martyrs - CS20156 - 38042 Grenoble Cedex 9 - France
- ICCRAM, University of Burgos, Plaza Misael Bañuelos, 09001 Burgos, Spain
| | - Andrew Wildes
- Institut Laue Langevin, 71, avenue des Martyrs - CS20156 - 38042 Grenoble Cedex 9 - France
| | - Marta Marty-Roda
- ICCRAM, University of Burgos, Plaza Misael Bañuelos, 09001 Burgos, Spain
| | | | - Estelle Mossou
- Institut Laue Langevin, 71, avenue des Martyrs - CS20156 - 38042 Grenoble Cedex 9 - France
- Faculty of Natural Sciences, Keele University, Staffordshire ST5 5BG, United Kingdom
| | - Andrew Studer
- ANSTO, Locked Bag 2001, Kirrawee DC, NSW 2232, Australia
| | - Bruno Demé
- Institut Laue Langevin, 71, avenue des Martyrs - CS20156 - 38042 Grenoble Cedex 9 - France
| | - Gaël Moiroux
- Institut Néel, University Grenoble Alpes, F-38042 Grenoble, France
- Institut Néel, CNRS, 25 Avenue des Martyrs, F-38042 Grenoble, France
| | - Jean-Luc Garden
- Institut Néel, University Grenoble Alpes, F-38042 Grenoble, France
- Institut Néel, CNRS, 25 Avenue des Martyrs, F-38042 Grenoble, France
| | - Nikos Theodorakopoulos
- Fachbereich Physik, Universität Konstanz, D-78457 Konstanz, Germany
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Vasileos Constantinou 48, 116 35 Athens, Greece
| | - Michel Peyrard
- Université de Lyon, Ecole Normale Supérieure de Lyon, Laboratoire de Physique, CNRS, UMR 5672, 46 allée d’Italie, F-69364 Lyon Cedex 7, France
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6
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Singh AR, Granek R. Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies. J Chem Phys 2017; 145:144101. [PMID: 27782499 DOI: 10.1063/1.4964285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We study DNA denaturation by integrating elasticity - as described by the Gaussian network model - with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds. Despite of its great simplicity, for several known DNA sequences our results are in accord with available theoretical and experimental studies. Moreover, we report free-energy profiles along the denaturation pathway, which allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers. Our approach allows to study very long DNA strands with commonly available computational power, as we demonstrate for a few random sequences in the range 200-800 base-pairs. For the latter, we also elucidate the self-averaging property of the system. Implications for the well known breathing dynamics of DNA are elucidated.
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Affiliation(s)
- Amit Raj Singh
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
| | - Rony Granek
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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7
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Husain MA, Ishqi HM, Rehman SU, Sarwar T, Afrin S, Rahman Y, Tabish M. Elucidating the interaction of sulindac with calf thymus DNA: biophysical and in silico molecular modelling approach. NEW J CHEM 2017. [DOI: 10.1039/c7nj03698a] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Sulindac is one of the most effective NSAIDs and belongs to the arylalkanoic acid class.
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Affiliation(s)
| | | | - Sayeed Ur Rehman
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Tarique Sarwar
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Shumaila Afrin
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Yusra Rahman
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Mohammad Tabish
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
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8
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Mi R, Tu B, Bai XT, Chen J, Ouyang Y, Hu YJ. Binding properties of palmatine to DNA: spectroscopic and molecular modeling investigations. LUMINESCENCE 2015; 30:1344-51. [PMID: 25829078 DOI: 10.1002/bio.2904] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 02/21/2015] [Accepted: 02/22/2015] [Indexed: 12/20/2022]
Abstract
Palmatine, an isoquinoline alkaloid, is an important medicinal herbal extract with diverse pharmacological and biological properties. In this work, spectroscopic and molecular modeling approaches were employed to reveal the interaction between palmatine and DNA isolated from herring sperm. The absorption spectra and iodide quenching results indicated that groove binding was the main binding mode of palmatine to DNA. Fluorescence studies indicated that the binding constant (K) of palmatine and DNA was ~ 10(4)L·mol(-1). The associated thermodynamic parameters, ΔG, ΔH, and ΔS, indicated that hydrogen bonds and van der Waals forces played major roles in the interaction. The effects of chemical denaturant, thermal denaturation and pH on the interaction were investigated and provided further support for the groove binding mode. In addition to experimental approaches, molecular modeling was conducted to verify binding pattern of palmatine-DNA.
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Affiliation(s)
- Ran Mi
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Bao Tu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Xiao-Ting Bai
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Jun Chen
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Yu Ouyang
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Yan-Jun Hu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
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9
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Wildes A, Khadeeva L, Trewby W, Valle-Orero J, Studer A, Garden JL, Peyrard M. Melting of Highly Oriented Fiber DNA Subjected to Osmotic Pressure. J Phys Chem B 2015; 119:4441-9. [DOI: 10.1021/acs.jpcb.5b01343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew Wildes
- Institut Laue-Langevin, CS 20156,
71 Avenue des Martyrs, 38042 Grenoble, France
| | - Liya Khadeeva
- Institut Laue-Langevin, CS 20156,
71 Avenue des Martyrs, 38042 Grenoble, France
- Institut de Physique de Rennes, UMR UR1 - CNRS 6251, 35042 Rennes Cedex, France
| | - William Trewby
- Institut Laue-Langevin, CS 20156,
71 Avenue des Martyrs, 38042 Grenoble, France
- Department
of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Jessica Valle-Orero
- Institut Laue-Langevin, CS 20156,
71 Avenue des Martyrs, 38042 Grenoble, France
| | - Andrew Studer
- ANSTO, Locked Bag 2001, Kirrawee
DC, NSW 2232, Australia
| | - Jean-Luc Garden
- CNRS, Institut
NÉEL, F-38042 Grenoble, France
- Université Grenoble Alpes, Inst NEEL, F-3800 Grenoble, France
| | - Michel Peyrard
- Laboratoire
de Physique, Ecole Normale Supérieure de Lyon, 46 Allée
d’Italie, 69364 Lyon Cedex 07, France
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10
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Husain MA, Rehman SU, Ishqi HM, Sarwar T, Tabish M. Spectroscopic and molecular docking evidence of aspirin and diflunisal binding to DNA: a comparative study. RSC Adv 2015. [DOI: 10.1039/c5ra09181k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Deciphering the binding mode between aspirin/diflunisal with Ct-DNA.
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Affiliation(s)
| | - Sayeed Ur Rehman
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | | | - Tarique Sarwar
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Mohammad Tabish
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
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11
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Capovilla G, Schmid M, Posé D. Control of flowering by ambient temperature. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:59-69. [PMID: 25326628 DOI: 10.1093/jxb/eru416] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The timing of flowering is a crucial decision in the life cycle of plants since favourable conditions are needed to maximize reproductive success and, hence, the survival of the species. It is therefore not surprising that plants constantly monitor endogenous and environmental signals, such as day length (photoperiod) and temperature, to adjust the timing of the floral transition. Temperature in particular has been shown to have a tremendous effect on the timing of flowering: the effect of prolonged periods of cold, called the vernalization response, has been extensively studied and the underlying epigenetic mechanisms are reasonably well understood in Arabidopsis thaliana. In contrast, the effect of moderate changes in ambient growth temperature on the progression of flowering, the thermosensory pathway, is only starting to be understood on the molecular level. Several genes and molecular mechanisms underlying the thermosensory pathway have already been identified and characterized in detail. At a time when global temperature is rising due to climate change, this knowledge will be pivotal to ensure crop production in the future.
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Affiliation(s)
- Giovanna Capovilla
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstr. 35, D-72076 Tübingen, Germany
| | - Markus Schmid
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstr. 35, D-72076 Tübingen, Germany
| | - David Posé
- Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
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12
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Sebastiani F, Pietrini A, Longo M, Comez L, Petrillo C, Sacchetti F, Paciaroni A. Melting of DNA Nonoriented Fibers: A Wide-Angle X-ray Diffraction Study. J Phys Chem B 2014; 118:3785-92. [DOI: 10.1021/jp411096d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Federico Sebastiani
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Alberto Pietrini
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Marialucia Longo
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Elettra − Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Lucia Comez
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- CNR,
Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento
di Fisica, Università degli Studi di Perugia, I-06123 Perugia, Italy
| | - Alessandro Paciaroni
- Dipartimento
di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
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13
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14
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Li XL, Hu YJ, Mi R, Li XY, Li PQ, Ouyang Y. Spectroscopic exploring the affinities, characteristics, and mode of binding interaction of curcumin with DNA. Mol Biol Rep 2013; 40:4405-13. [DOI: 10.1007/s11033-013-2530-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 04/29/2013] [Indexed: 12/13/2022]
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15
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Chien CC, Velizhanin KA, Dubi Y, Zwolak M. Tunable thermal switching via DNA-based nano-devices. NANOTECHNOLOGY 2013; 24:095704. [PMID: 23396127 DOI: 10.1088/0957-4484/24/9/095704] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
DNA has a well-defined structural transition--the denaturation of its double-stranded form into two single strands--that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA denaturation, one can engineer DNA 'heattronic' devices that have a rapidly increasing thermal conductance over a narrow temperature range across the denaturation transition (∼350 K). The origin of this rapid increase of conductance, or 'switching', is the softening of the lattice and suppression of nonlinear effects as the temperature crosses the transition temperature and DNA denatures. Most importantly, we demonstrate that DNA nano-junctions have a broad range of thermal tunability by varying the sequence and length, and exploiting the underlying nonlinear behavior. We discuss the role of disorder in the base sequence, as well as the relation to genomic DNA. These results set the basis for developing thermal devices out of materials with nonlinear structural dynamics, as well as understanding the underlying mechanisms of DNA denaturation.
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Affiliation(s)
- Chih-Chun Chien
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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16
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Gonzalez O, Petkevičiūtė D, Maddocks JH. A sequence-dependent rigid-base model of DNA. J Chem Phys 2013; 138:055102. [DOI: 10.1063/1.4789411] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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17
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Valle-Orero J, Wildes A, Garden JL, Peyrard M. Purification of A-Form DNA Fiber Samples by the Removal of B-Form DNA Residues. J Phys Chem B 2013; 117:1849-56. [DOI: 10.1021/jp311199f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jessica Valle-Orero
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Andrew Wildes
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Jean-Luc Garden
- Institut Néel, CNRS - Université Joseph Fourier, 25 rue des Martyrs, BP
166, 38042 Grenoble cedex 9, France
| | - Michel Peyrard
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée
d’Italie, 69364 Lyon Cedex 07, France
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18
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Tempestini A, Cassina V, Brogioli D, Ziano R, Erba S, Giovannoni R, Cerrito MG, Salerno D, Mantegazza F. Magnetic tweezers measurements of the nanomechanical stability of DNA against denaturation at various conditions of pH and ionic strength. Nucleic Acids Res 2012; 41:2009-19. [PMID: 23248010 PMCID: PMC3561983 DOI: 10.1093/nar/gks1206] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The opening of DNA double strands is extremely relevant to several biological functions, such as replication and transcription or binding of specific proteins. Such opening phenomenon is particularly sensitive to the aqueous solvent conditions in which the DNA molecule is dispersed, as it can be observed by considering the classical dependence of DNA melting temperature on pH and salt concentration. In the present work, we report a single-molecule study of the stability of DNA against denaturation when subjected to changes in solvent. We investigated the appearance of DNA instability under specific external applied force and imposed twist values, which was revealed by an increase in the temporal fluctuations in the DNA extension. These fluctuations occur in the presence of a continuous interval of equilibrium states, ranging from a plectonemic state to a state characterized by denaturation bubbles. In particular, we observe the fluctuations only around a characteristic force value. Moreover, this characteristic force is demonstrated to be notably sensitive to variations in the pH and ionic strength. Finally, an extension of a theoretical model of plectoneme formation is used to estimate the average denaturation energy, which is found to be linearly correlated to the melting temperature of the DNA double strands.
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Affiliation(s)
- Alessia Tempestini
- Dipartimento di Scienze della Salute, Università di Milano-Bicocca, via Cadore 48, Monza (MB) 20900, Italy
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19
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Zoli M. Anharmonic stacking in supercoiled DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:195103. [PMID: 22495298 DOI: 10.1088/0953-8984/24/19/195103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking anharmonicity stabilizes the double helix against thermal disruption of the hydrogen bonds. Twisting is essential in the model to capture the importance of nonlinear effects on the thermodynamical properties. In a ladder model with zero twist, anharmonic stacking scarcely affects the thermodynamics. Moderately untwisted helices, with respect to the equilibrium conformation, show an energetic advantage against the overtwisted ones. Accordingly moderately untwisted helices better sustain local fluctuational openings and make more unlikely the thermally driven complete strand separation.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology-CNISM, University of Camerino, Camerino, Italy.
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20
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Valle-Orero J, Garden JL, Richard J, Wildes A, Peyrard M. Glassy Behavior of Denatured DNA Films Studied by Differential Scanning Calorimetry. J Phys Chem B 2012; 116:4394-402. [DOI: 10.1021/jp301128j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jessica Valle-Orero
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Jean-Luc Garden
- Institut Néel, CNRS - Université Joseph Fourier, 25 rue des Martyrs, BP 166, 38042 Grenoble Cedex 9, France
| | - Jacques Richard
- Institut Néel, CNRS - Université Joseph Fourier, 25 rue des Martyrs, BP 166, 38042 Grenoble Cedex 9, France
| | - Andrew Wildes
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Michel Peyrard
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
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21
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Li XL, Hu YJ, Wang H, Yu BQ, Yue HL. Molecular spectroscopy evidence of berberine binding to DNA: comparative binding and thermodynamic profile of intercalation. Biomacromolecules 2012; 13:873-80. [PMID: 22316074 DOI: 10.1021/bm2017959] [Citation(s) in RCA: 199] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Berberine (BH) is an important traditional medicinal herb endowed with diverse pharmacological and biological activities. In this work, the binding characteristics and molecular mechanism of the interaction between the BH and herring sperm DNA were explored by UV-vis absorbance and fluorescence spectroscopy. In the mechanism discussion, fluorescence quenching, absorption spectra, competition experiment, and iodide quenching experiment studies hinted at an intercalative mode of binding for BH to DNA. Fluorescence studies revealed the binding constant (K) of BH-DNA was ∼10(4) L·mol(-1). The effects of temperature, chemical denaturants, thermal denaturation, and pH were studied to show the factors of the interaction and provided further support for the intercalative binding mode. The results of thermodynamic parameters ΔG, ΔH, and ΔS at different temperatures indicated that the hydrogen bonds and van der Waals interactions played major roles in the reaction, and the effect of ionic strength indicated that electrostatic attraction between the BH and DNA was also a component of the interaction.
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Affiliation(s)
- Xiao-Ling Li
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi 435002, PR China
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22
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Theodorakopoulos N, Peyrard M. Base pair openings and temperature dependence of DNA flexibility. PHYSICAL REVIEW LETTERS 2012; 108:078104. [PMID: 22401261 DOI: 10.1103/physrevlett.108.078104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Indexed: 05/31/2023]
Abstract
The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot model with soft and hard joints, corresponding to open and closed base pairs, and sequence-dependent statistical information about the state of each pair provided by a Peyrard-Bishop-Dauxois (PBD) model calculation with no freely adjustable parameters.
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Affiliation(s)
- Nikos Theodorakopoulos
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Athens, Greece
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23
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Lee OC, Sung W. Enhanced bubble formation in looped short double-stranded DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:021902. [PMID: 22463239 DOI: 10.1103/physreve.85.021902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 12/13/2011] [Indexed: 05/31/2023]
Abstract
Recent experiments have shown the double-stranded (ds) DNAs readily bend and loop over the scale much shorter than their persistence length (50 nm). In an effort to unveil this seemingly surprising phenomenon, we study the emergence of bubbles in short ds DNA loops by simulating the breathing DNA model. We analyze the bubble size distributions and the melting curves for varying contour lengths, which are critically compared with those of linear DNA of the same lengths. We analytically evaluate the free energies associated with double-strand bending and single-strand bubble formation to explain the simulation data. It is found that in shorter looped DNA the bubbles are more easily initiated and formed to release the large bending energy, giving rise to melting at a lower temperature and a lower contour length.
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Affiliation(s)
- O-chul Lee
- Department of Physics and PCTP, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea. ochul
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24
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25
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Behnia S, Akhshani A, Panahi M, Mobaraki A, Ghaderian M. Multifractal analysis of thermal denaturation based on the Peyrard-Bishop-Dauxois model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:031918. [PMID: 22060414 DOI: 10.1103/physreve.84.031918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 08/15/2011] [Indexed: 05/31/2023]
Abstract
The theory of DNA dynamics is exceedingly complex and not easily explained. In the past two decades, by adapting methods of statistical physics, the dynamics of DNA in contact with a thermal bath is widely studied. In this paper, the thermal denaturation of DNA in the framework of the Peyrard-Bishop-Dauxois (PBD) model through the Rényi dimension is investigated. As a result, the Rényi dimension spectrum of the melting transition process reveals the multifractal nature of the dynamics of the Peyrard-Bishop-Dauxois model. Also, it can be concluded that the Rényi dimension (D(q)) at negative values of q is the characteristic signature of pre-melting and thermal denaturation of DNA. Furthermore, this approach is in excellent agreement with previous experimental studies.
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Affiliation(s)
- S Behnia
- Department of Physics, Urmia University of Technology, Orumieh, Iran.
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26
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van Eijck L, Merzel F, Rols S, Ollivier J, Forsyth VT, Johnson MR. Direct determination of the base-pair force constant of DNA from the acoustic phonon dispersion of the double helix. PHYSICAL REVIEW LETTERS 2011; 107:088102. [PMID: 21929208 DOI: 10.1103/physrevlett.107.088102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Indexed: 05/31/2023]
Abstract
Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3 N/m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83 N/m. Structural and dynamic order persists unchanged to within 15 K of the melting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants.
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Affiliation(s)
- L van Eijck
- Reactor Institute Delft, Delft University of Technology, Mekelweg 15, 2629JB, Delft, The Netherlands.
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27
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Zoli M. Stacking interactions in denaturation of DNA fragments. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:68. [PMID: 21751094 DOI: 10.1140/epje/i2011-11068-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 06/07/2011] [Accepted: 07/14/2011] [Indexed: 05/31/2023]
Abstract
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time-dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the adenine-thymine-rich portions of the fragment. The harmonic stacking coupling shifts, along the T -axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble, we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.
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Affiliation(s)
- M Zoli
- School of Science and Technology - CNISM, Università di Camerino, I-62032 Camerino, Italy.
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28
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Wildes A, Theodorakopoulos N, Valle-Orero J, Cuesta-López S, Garden JL, Peyrard M. Structural correlations and melting of B-DNA fibers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:061923. [PMID: 21797419 DOI: 10.1103/physreve.83.061923] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Indexed: 05/31/2023]
Abstract
Despite numerous attempts, understanding the thermal denaturation of DNA is still a challenge due to the lack of structural data on the transition since standard experimental approaches to DNA melting are made in solution and do not provide spatial information. We report a measurement using neutron scattering from oriented DNA fibers to determine the size of the regions that stay in the double-helix conformation as the melting temperature is approached from below. A Bragg peak from the B form of DNA is observed as a function of temperature and its width and integrated intensity are measured. These results, complemented by a differential calorimetry study of the melting of B-DNA fibers as well as electrophoresis and optical observation data, are analyzed in terms of a one-dimensional mesoscopic model of DNA.
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