1
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Li F, Smoukov SK, Korotkin I, Taiji M, Karabasov S. Interfacial Layer Breaker: A Violation of Stokes' Law in High-Speed Atomic Force Microscope Flows. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:220-226. [PMID: 36537801 PMCID: PMC9835886 DOI: 10.1021/acs.langmuir.2c02418] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Structured water near surfaces is important in nonclassical crystallization, biomineralization, and restructuring of cellular membranes. In addition to equilibrium structures, studied by atomic force microscopy (AFM), high-speed AFM (H-S AFM) can now detect piconewton forces in microseconds. With increasing speeds and decreasing tip diameters, there is a danger that continuum water models will not hold, and molecular dynamic (MD) simulations would be needed for accurate predictions. MD simulations, however, can only evolve over tens of nanoseconds due to memory and computational efficiency/speed limitations, so new methods are needed to bridge the gap. Here, we report a hybrid, multiscale simulation method, which can bridge the size and time scale gaps to existing experiments. Structured water is studied between a moving silica AFM colloidal tip and a cleaved mica surface. The computational domain includes 1,472,766 atoms. To mimic the effect of long-range hydrodynamic forces occurring in water, when moving the AFM tip at speeds from 5 × 10-7 to 30 m/s, a hybrid multiscale method with local atomistic resolution is used, which serves as an effective open-domain boundary condition. The multiscale simulation is thus equivalent to using a macroscopically large computational domain with equilibrium boundary conditions. Quantification of the drag force shows the breaking of continuum behavior. Nonmonotonic dependence on both the tip speed and distance from the surface implies breaking of the hydration layer around the moving tip at time scales smaller than water cluster formation and strong water compressibility effects at the highest speeds.
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Affiliation(s)
- Fan Li
- The
School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1
4NSLondon, United
Kingdom
| | - Stoyan K. Smoukov
- The
School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1
4NSLondon, United
Kingdom
| | - Ivan Korotkin
- The
School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1
4NSLondon, United
Kingdom
- Mathematical
Sciences, University of Southampton, University Road, SO17 1BJSouthampton, United Kingdom
| | - Makoto Taiji
- Laboratory
for Computational Molecular Design, Computational Biology Research
Core, RIKEN Quantitative Biology Center
(QBiC), 1-6-5 Minatojima Minamimachi, Chuo-Ku, Kobe, Hyogo650-0047, Japan
| | - Sergey Karabasov
- The
School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1
4NSLondon, United
Kingdom
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2
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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3
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Affiliation(s)
- Saumyak Mukherjee
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sayantan Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Subhajit Acharya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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4
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Ultrafast dynamics-driven biomolecular recognition where fast activities dictate slow events. J Biosci 2018. [DOI: 10.1007/s12038-018-9776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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5
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6
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Kumari S, Sonu, Sundar G, Saha SK. Effect of organic and a Hofmeister series of inorganic counterions on the solvation dynamics and rotational relaxation in aqueous micelles of hexadecyltrimethylammonium surfactants. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Abstract
Anomalous nonexponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA base pairs exhibits a slow power-law relaxation attributable to weak Hamiltonian chaos, with parameters similar to experimental data. Here, the relationship is studied between this motion and spectroscopic signals measured in DNA with a small molecular photoprobe inserted into the base-pair stack. To this end, the earlier computational approach in combination with an analytical theory is applied to the experimental DNA fragment. It is found that the intensity of breathing dynamics is strongly increased in the internal base pairs that flank the photoprobe, with anomalous relaxation quantitatively close to that in terminal base pairs. A physical mechanism is proposed to explain the coupling between the relaxation of base-pair breathing and the experimental response signal. It is concluded that the algebraic relaxation observed experimentally is very likely a manifestation of weakly chaotic dynamics of hydrogen-bond breathing in the base pairs stacked to the photoprobe and that the weak nanoscale chaos can represent an ubiquitous hidden source of nonexponential relaxation in ultrafast spectroscopy.
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Affiliation(s)
- Alexey K Mazur
- UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris, 75005, France
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8
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Kolář MH, Kubař T. Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer. J Phys Chem B 2017; 121:1520-1532. [PMID: 28121443 DOI: 10.1021/acs.jpcb.6b12109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA proceeds along a single collective coordinate that represents the relative orientation of two consecutive base pairs, namely, a combination of helical parameters shift and tilt. The structure of DNA relaxes on time scales reaching nanoseconds, contributing marginally to the relaxation of energies, which is dominated by the modes of motion of the aqueous solvent. The concept of reaction path averaging (RPA), conveniently exploited in this context, makes it possible to filter out any undesirable noise from the nonequilibrium data, and is applicable to any chemical process in general.
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Affiliation(s)
- Michal H Kolář
- Institute for Advanced Simulations (IAS-5) and Institute of Neuroscience and Medicine (INM-9), Forschungszentrum Jülich , 52428 Jülich, Germany.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , 16610 Praha, Czech Republic
| | - Tomáš Kubař
- Institute of Physical Chemistry & Center for Functional Nanostructures, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany
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9
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González-Jiménez M, Ramakrishnan G, Harwood T, Lapthorn AJ, Kelly SM, Ellis EM, Wynne K. Observation of coherent delocalized phonon-like modes in DNA under physiological conditions. Nat Commun 2016; 7:11799. [PMID: 27248361 PMCID: PMC4895446 DOI: 10.1038/ncomms11799] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/28/2016] [Indexed: 01/10/2023] Open
Abstract
Underdamped terahertz-frequency delocalized phonon-like modes have long been suggested to play a role in the biological function of DNA. Such phonon modes involve the collective motion of many atoms and are prerequisite to understanding the molecular nature of macroscopic conformational changes and related biochemical phenomena. Initial predictions were based on simple theoretical models of DNA. However, such models do not take into account strong interactions with the surrounding water, which is likely to cause phonon modes to be heavily damped and localized. Here we apply state-of-the-art femtosecond optical Kerr effect spectroscopy, which is currently the only technique capable of taking low-frequency (GHz to THz) vibrational spectra in solution. We are able to demonstrate that phonon modes involving the hydrogen bond network between the strands exist in DNA at physiologically relevant conditions. In addition, the dynamics of the solvating water molecules is slowed down by about a factor of 20 compared with the bulk.
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Affiliation(s)
| | | | - Thomas Harwood
- Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Adrian J. Lapthorn
- School of Chemistry, WestCHEM, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sharon M. Kelly
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Elizabeth M. Ellis
- Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Klaas Wynne
- School of Chemistry, WestCHEM, University of Glasgow, Glasgow G12 8QQ, UK
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10
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Koley S, Ghosh S. A deeper insight into an intriguing acetonitrile–water binary mixture: synergistic effect, dynamic Stokes shift, fluorescence correlation spectroscopy, and NMR studies. Phys Chem Chem Phys 2016; 18:32308-32318. [DOI: 10.1039/c6cp05024g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An insight study reveals the strong synergistic solvation behaviours from reporter dye molecules within the acetonitrile (ACN)–water (WT) binary mixture.
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Affiliation(s)
- Somnath Koley
- School of Chemical Sciences
- National Institute of Science Education and Research
- HBNI
- Bhubaneswar 751005
- India
| | - Subhadip Ghosh
- School of Chemical Sciences
- National Institute of Science Education and Research
- HBNI
- Bhubaneswar 751005
- India
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11
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Sonu S, Kumari S, Saha SK. Solvation dynamics and rotational relaxation of coumarin 153 in mixed micelles of Triton X-100 and cationic gemini surfactants: effect of composition and spacer chain length of gemini surfactants. Phys Chem Chem Phys 2016; 18:1551-63. [DOI: 10.1039/c5cp03835a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To demonstrate simultaneously how the solvation dynamics and rotational relaxation in nonionic micelles change with the composition of a gemini surfactant and how this change depends on spacer chain length of gemini surfactants.
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Affiliation(s)
- Sonu Sonu
- Department of Chemistry
- Birla Institute of Technology & Science (BITS)
- Pilani
- India
| | - Sunita Kumari
- Department of Chemistry
- Birla Institute of Technology & Science (BITS)
- Pilani
- India
| | - Subit K. Saha
- Department of Chemistry
- Birla Institute of Technology & Science (BITS)
- Pilani
- India
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12
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Mazur AK. Modeling DNA Dynamics under Steady Deforming Forces and Torques. J Chem Theory Comput 2015; 5:2149-57. [PMID: 26613154 DOI: 10.1021/ct900124n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An algorithm is developed for modeling atom-level dynamics of DNA subjected to steady external torques. For completeness, simulations with steady stretching loads are also considered. The algorithms were tested in Brownian dynamics simulations of discrete wormlike chain models with calibrated elastic properties to confirm that the elastic responses induced are of desired type and magnitude and that no side effects appear. The same methods were next used in a series of 100-ns all-atom MD simulations of tetradecamer DNA fragments with explicit water and counterions. The results demonstrate the possibility of probing regular elastic responses in DNA under low, nearly physiological amplitudes of forces and torques.
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Affiliation(s)
- Alexey K Mazur
- CNRS UPR9080, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris 75005, France
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13
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Mazur AK, Shepelyansky DL. Algebraic Statistics of Poincaré Recurrences in a DNA Molecule. PHYSICAL REVIEW LETTERS 2015; 115:188104. [PMID: 26565502 DOI: 10.1103/physrevlett.115.188104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Indexed: 06/05/2023]
Abstract
The statistics of Poincaré recurrences is studied for the base-pair breathing dynamics of an all-atom DNA molecule in a realistic aqueous environment with thousands of degrees of freedom. It is found that at least over five decades in time the decay of recurrences is described by an algebraic law with the Poincaré exponent close to β=1.2. This value is directly related to the correlation decay exponent ν=β-1, which is close to ν≈0.15 observed in the time resolved Stokes shift experiments. By applying the virial theorem we analyze the chaotic dynamics in polynomial potentials and demonstrate analytically that an exponent β=1.2 is obtained assuming the dominance of dipole-dipole interactions in the relevant DNA dynamics. Molecular dynamics simulations also reveal the presence of strong low frequency noise with the exponent η=1.6. We trace parallels with the chaotic dynamics of symplectic maps with a few degrees of freedom characterized by the Poincaré exponent β~1.5.
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Affiliation(s)
- Alexey K Mazur
- UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris, 75005, France
| | - D L Shepelyansky
- Laboratoire de Physique Théorique du CNRS (IRSAMC), Université de Toulouse, UPS, F-31062 Toulouse, France
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14
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Sebastiani F, Longo M, Orecchini A, Comez L, De Francesco A, Muthmann M, Teixeira SCM, Petrillo C, Sacchetti F, Paciaroni A. Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: A neutron scattering study. J Chem Phys 2015; 143:015102. [DOI: 10.1063/1.4923213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- F. Sebastiani
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - M. Longo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Elettra—Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - A. Orecchini
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. De Francesco
- CNR-IOM OGG c/o Institut Laue-Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - M. Muthmann
- Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - S. C. M. Teixeira
- EPSAM, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue–Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - C. Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - F. Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
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15
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Choudhury S, Mondal PK, Sharma VK, Mitra S, Sakai VG, Mukhopadhyay R, Pal SK. Direct Observation of Coupling between Structural Fluctuation and Ultrafast Hydration Dynamics of Fluorescent Probes in Anionic Micelles. J Phys Chem B 2015; 119:10849-57. [PMID: 25874585 DOI: 10.1021/jp511899q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The coupling of structural fluctuation and the dynamics of associated water molecules of biological macromolecules is vital for various biological activities. Although a number of molecular dynamics (MD) studies on proteins/DNA predicted the importance of such coupling, experimental evidence of variation of hydration dynamics with controlled structural fluctuation even in model macromolecule is sparse and raised controversies in the contemporary literature. Here, we have investigated dynamics of hydration at the surfaces of two similar anionic micelles sodium dodecyl sulfate (SDS) and sodium dodecylbenzenesulfonate (SDBS) as model macromolecules using coumarin 500 (C500) as spectroscopic probe with femtosecond to picosecond time resolution up to 20 ns time window. The constituting surfactants SDS and SDBS are structurally similar except one benzene moiety in the SDBS may offer additional rigidity to the SDBS micelles through π-stacking and added bulkiness. The structural integrity of the micelles in the aqueous medium is confirmed in dynamic light scattering (DLS) studies. A variety of studies including polarization gated fluorescence spectroscopy and quasielastic neutron scattering (QENS) have been used to confirm differential structural fluctuation of SDS and SDBS micelles. We have also employed femtosecond-resolved Förster resonance energy transfer (FRET) in order to study binding of a cationic organic ligand ethidium bromide (EtBr) salt at the micellar surfaces. The distance distribution of the donor (C500)-acceptor (EtBr) in the micellar media reveals the manifestation of the structural flexibility of the micelles. Our studies on dynamical coupling of the structural flexibility with surface hydration in the nanoscopic micellar media may find the relevance in the "master-slave" type water dynamics in biologically relevant macromolecules.
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Affiliation(s)
- Susobhan Choudhury
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Prasanna Kumar Mondal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - S Mitra
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - V Garcia Sakai
- Science and Technology Facilities Council, Rutherford Appleton Laboratory , Didcot, OX11 0QX, U.K
| | - R Mukhopadhyay
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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16
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Roy S, Yashonath S, Bagchi B. Mode coupling theory analysis of electrolyte solutions: Time dependent diffusion, intermediate scattering function, and ion solvation dynamics. J Chem Phys 2015; 142:124502. [DOI: 10.1063/1.4915274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Susmita Roy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Subramanian Yashonath
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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17
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Izanloo C. Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.
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Affiliation(s)
- C. Izanloo
- Department of Chemistry, Bojnord Branch, Islamic Azad University, Bojnord, Iran
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18
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Galindo-Murillo R, Roe DR, Cheatham TE. On the absence of intrahelical DNA dynamics on the μs to ms timescale. Nat Commun 2014; 5:5152. [PMID: 25351257 PMCID: PMC4215645 DOI: 10.1038/ncomms6152] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 09/05/2014] [Indexed: 01/08/2023] Open
Abstract
DNA helices display a rich tapestry of motion on both short (<100 ns) and long (>1 ms) timescales. However, with the exception of mismatched or damaged DNA, experimental measures indicate that motions in the 1 μs to 1 ms range are effectively absent, which is often attributed to difficulties in measuring motions in this time range. We hypothesized that these motions have not been measured because there is effectively no motion on this timescale, as this provides a means to distinguish faithful Watson-Crick base-paired DNA from damaged DNA. The absence of motion on this timescale would present a 'static' DNA sequence-specific structure that matches the encounter timescales of proteins, thereby facilitating recognition. Here we report long-timescale (~10-44 μs) molecular dynamics simulations of a B-DNA duplex structure that addresses this hypothesis using both an 'Anton' machine and large ensembles of AMBER GPU simulations.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, 2000 East 30 South Skaggs 307, Salt Lake City, Utah 84112, USA
| | - Daniel R Roe
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, 2000 East 30 South Skaggs 307, Salt Lake City, Utah 84112, USA
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, 2000 East 30 South Skaggs 307, Salt Lake City, Utah 84112, USA
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19
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Galindo-Murillo R, Roe DR, Cheatham TE. Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochim Biophys Acta Gen Subj 2014; 1850:1041-1058. [PMID: 25219455 DOI: 10.1016/j.bbagen.2014.09.007] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/01/2014] [Accepted: 09/03/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND The structure and dynamics of DNA are critically related to its function. Molecular dynamics simulations augment experiment by providing detailed information about the atomic motions. However, to date the simulations have not been long enough for convergence of the dynamics and structural properties of DNA. METHODS Molecular dynamics simulations performed with AMBER using the ff99SB force field with the parmbsc0 modifications, including ensembles of independent simulations, were compared to long timescale molecular dynamics performed with the specialized Anton MD engine on the B-DNA structure d(GCACGAACGAACGAACGC). To assess convergence, the decay of the average RMSD values over longer and longer time intervals was evaluated in addition to assessing convergence of the dynamics via the Kullback-Leibler divergence of principal component projection histograms. RESULTS These molecular dynamics simulations-including one of the longest simulations of DNA published to date at ~44μs-surprisingly suggest that the structure and dynamics of the DNA helix, neglecting the terminal base pairs, are essentially fully converged on the ~1-5μs timescale. CONCLUSIONS We can now reproducibly converge the structure and dynamics of B-DNA helices, omitting the terminal base pairs, on the μs time scale with both the AMBER and CHARMM C36 nucleic acid force fields. Results from independent ensembles of simulations starting from different initial conditions, when aggregated, match the results from long timescale simulations on the specialized Anton MD engine. GENERAL SIGNIFICANCE With access to large-scale GPU resources or the specialized MD engine "Anton" it is possible for a variety of molecular systems to reproducibly and reliably converge the conformational ensemble of sampled structures. This article is part of a Special Issue entitled: Recent developments of molecular dynamics.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Daniel R Roe
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, L.S. Skaggs Pharmacy Institute, University of Utah, Salt Lake City, UT 84112, USA.
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20
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Bagchi B. Anomalous power law decay in solvation dynamics of DNA: a mode coupling theory analysis of ion contribution. Mol Phys 2014. [DOI: 10.1080/00268976.2014.904943] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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21
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Lomholt MA, Lizana L, Metzler R, Ambjörnsson T. Microscopic origin of the logarithmic time evolution of aging processes in complex systems. PHYSICAL REVIEW LETTERS 2013; 110:208301. [PMID: 25167457 DOI: 10.1103/physrevlett.110.208301] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Indexed: 06/03/2023]
Abstract
There exists compelling experimental evidence in numerous systems for logarithmically slow time evolution, yet its full theoretical understanding remains elusive. We here introduce and study a generic transition process in complex systems, based on nonrenewal, aging waiting times. Each state n of the system follows a local clock initiated at t = 0. The random time τ between clock ticks follows the waiting time density ψ(τ). Transitions between states occur only at local clock ticks and are hence triggered by the local forward waiting time, rather than by ψ(τ). For power-law forms ψ(τ) ≃ τ(-1-α) (0 < α < 1) we obtain a logarithmic time evolution of the state number ⟨n(t)⟩ ≃ log(t/t(0)), while for α > 2 the process becomes normal in the sense that ⟨n(t)⟩ ≃ t. In the intermediate range 1 < α < 2 we find the power-law growth ⟨n(t)⟩ ≃ t(α-1). Our model provides a universal description for transition dynamics between aging and nonaging states.
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Affiliation(s)
- Michael A Lomholt
- MEMPHYS, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Ludvig Lizana
- Department of Physics and Center for Soft Matter Research, New York University, 4 Washington Place, New York, New York 10003, USA and Department of Physics, Integrated Science Lab, Umeå University, SE-901 87 Umeå, Sweden
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany and Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, SE-22362 Lund, Sweden
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22
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Berndt F, Ioffe I, Granovsky AA, Mahrwald R, Tannert S, Kovalenko SA, Ernsting NP. 7-Amino-dibenzofuran-3-carboxylate: A new probe for femtosecond dynamic microsolvation studies of biomolecules. J Photochem Photobiol A Chem 2012. [DOI: 10.1016/j.jphotochem.2012.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Crenshaw CM, Wade JE, Arthanari H, Frueh D, Lane BF, Núñez ME. Hidden in plain sight: subtle effects of the 8-oxoguanine lesion on the structure, dynamics, and thermodynamics of a 15-base pair oligodeoxynucleotide duplex. Biochemistry 2011; 50:8463-77. [PMID: 21902242 PMCID: PMC3188433 DOI: 10.1021/bi201007t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The base lesion 8-oxoguanine is formed readily by oxidation of DNA, potentially leading to G → T transversion mutations. Despite the apparent similarity of 8-oxoguanine-cytosine base pairs to normal guanine-cytosine base pairs, cellular base excision repair systems effectively recognize the lesion base. Here we apply several techniques to examine a single 8-oxoguanine lesion at the center of a nonpalindromic 15-mer duplex oligonucleotide in an effort to determine what, if anything, distinguishes an 8-oxoguanine-cytosine (8oxoG-C) base pair from a normal base pair. The lesion duplex is globally almost indistinguishable from the unmodified parent duplex using circular dichroism spectroscopy and ultraviolet melting thermodynamics. The DNA mismatch-detecting photocleavage agent Rh(bpy)(2)chrysi(3+) cleaves only weakly and nonspecifically, revealing that the 8oxoG-C pair is locally stable at the level of the individual base pairs. Nuclear magnetic resonance spectra are also consistent with a well-conserved B-form duplex structure. In the two-dimensional nuclear Overhauser effect spectra, base-sugar and imino-imino cross-peaks are strikingly similar between parent and lesion duplexes. Changes in chemical shift due to the 8oxoG lesion are localized to its complementary cytosine and to the 2-3 bp immediately flanking the lesion on the lesion strand. Residues further removed from the lesion are shown to be unperturbed by its presence. Notably, imino exchange experiments indicate that the 8-oxoguanine-cytosine pair is strong and stable, with an apparent equilibrium constant for opening equal to that of other internal guanine-cytosine base pairs, on the order of 10(-6). This collection of experiments shows that the 8-oxoguanine-cytosine base pair is incredibly stable and similar to the native pair.
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Affiliation(s)
- Charisse M. Crenshaw
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138
| | - Jacqueline E. Wade
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston MA 02115
| | - Dominique Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore MD 21205
| | | | - Megan E. Núñez
- Department of Chemistry, Mount Holyoke College, South Hadley, Massachusetts 01075
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24
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Sajadi M, Furse KE, Zhang XX, Dehmel L, Kovalenko SA, Corcelli SA, Ernsting NP. Beobachtung einer DNA-Ligand-Schwingung über zeitaufgelöste Fluoreszenzmessung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Sajadi M, Furse KE, Zhang XX, Dehmel L, Kovalenko SA, Corcelli SA, Ernsting NP. Detection of DNA-Ligand Binding Oscillations by Stokes-Shift Measurements. Angew Chem Int Ed Engl 2011; 50:9501-5. [DOI: 10.1002/anie.201102942] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/24/2011] [Indexed: 11/10/2022]
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26
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Furse KE, Corcelli SA. Effects of an unnatural base pair replacement on the structure and dynamics of DNA and neighboring water and ions. J Phys Chem B 2011; 114:9934-45. [PMID: 20614919 DOI: 10.1021/jp105761b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Incorporating small molecule probes into biomolecular systems to report on local structure and dynamics is a powerful strategy that underlies a wide variety of experimental techniques, including fluorescence, electron paramagnetic resonance (EPR), and Forster resonance energy transfer (FRET) measurements. When an unnatural probe is inserted into a protein or DNA, the degree to which the presence of the probe has perturbed the local structure and dynamics it was intended to study is always an important concern. Here, molecular dynamics (MD) simulations are used to systematically study the effect of replacing a DNA base pair with a fluorescent probe, coumarin 102 deoxyriboside, at six unique sites along an A-tract DNA dodecamer. While the overall structure of the DNA oligonucleotide remains intact, replacement of A*T base pairs leads to widespread structural and dynamic perturbations up to four base pairs away from the probe site, including widening of the minor groove and increased DNA flexibility. New DNA conformations, not observed in the native sequence, are sometimes found in the vicinity of the probe and its partner abasic site analog. Strong correlations are demonstrated between DNA surface topology and water mobility.
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Affiliation(s)
- K E Furse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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27
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Cole RL, Barisas BG, Levinger NE. Logarithmic based optical delay for time-resolved data collection. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2010; 81:093101. [PMID: 20886970 DOI: 10.1063/1.3474226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A method has been established that generates values spaced according to a mathematical function, specifically the logarithm function that can be applied to a stepper motor. Here, it is applied to yield logarithmically spaced time delay points for subnanosecond interferometric time-resolved experiments using a stepper motor controlled translation stage. Application of this method is discussed in terms of three input parameters: the optical delay stage time resolution, dt; the time of maximum delay, d(stop); and the desired number of data points, N. The method improves the efficiency of interferometric time-resolved data collection while providing data collection effective to determine decay parameters. In principle, this technique could be generalized to any mathematical function.
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Affiliation(s)
- Richard L Cole
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, USA
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28
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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29
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Carlos LD, Pacheco JM, Ferreira RAS, Videira ALL. Hierarchically constrained dynamics and emergence of complex behavior in nanohybrids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:386-390. [PMID: 20025077 DOI: 10.1002/smll.200900899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- L D Carlos
- Departamento de Física, CICECO Universidade de Aveiro, Aveiro 3810-193, Portugal.
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30
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Furmanchuk A, Isayev O, Shishkin OV, Gorb L, Leszczynski J. Hydration of nucleic acid bases: a Car–Parrinello molecular dynamics approach. Phys Chem Chem Phys 2010; 12:3363-75. [DOI: 10.1039/b923930h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Ponomarev SY, Putkaradze V, Bishop TC. Relaxation dynamics of nucleosomal DNA. Phys Chem Chem Phys 2009; 11:10633-43. [PMID: 20145808 DOI: 10.1039/b910937b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experimental and theoretical evidence demonstrates that proteins and water in the hydration layer can follow complex stretched exponential or power law relaxation dynamics. Here, we report on a 50 ns all atom molecular dynamics (MD) simulation of the yeast nucleosome, where the interactions between DNA, histones, surrounding water and ions are explicitly included. DNA interacts with the histone core in 14 locations, approximately every 10.4 base pairs. We demonstrate that all sites of interaction exhibit anomalously slow power law relaxation, extending up to 10 ns, while fast exponential relaxation dynamics of hundreds of picoseconds applies to DNA regions outside these locations. The appearance of 1/f(alpha) noise or pink noise in DNA dynamics is ubiquitous. For histone-bound nucleotide dynamics alpha --> 1 and is a signature of complexity of the protein-DNA interactions. For control purposes two additional DNA simulations free of protein are conducted. Both utilize the same sequence of DNA, as found the in the nucleosome. In one simulation the initial conformation of the double helix is a straight B-form. In the other, the initial conformation is super helical. Neither of these simulations exhibits the variation of alpha as a function of position, the measure of power law for dynamical behavior, which we observe in the nucleosome simulation. The unique correspondence (high alpha to DNA-histone interaction sites, low alpha to free DNA sites), suggests that alpha may be an important and new quantification of protein-DNA interactions for future experiments.
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Affiliation(s)
- Sergei Y Ponomarev
- Tulane University, Center for Computational Science, Lindy Boggs Center Suite, 500 New Orleans, LA 70118, USA.
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32
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Dallmann A, Pfaffe M, Mügge C, Mahrwald R, Kovalenko SA, Ernsting NP. Local THz Time Domain Spectroscopy of Duplex DNA via Fluorescence of an Embedded Probe. J Phys Chem B 2009; 113:15619-28. [DOI: 10.1021/jp906037g] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- André Dallmann
- Department of Chemistry, Humboldt University of Berlin, Germany
| | - Matthias Pfaffe
- Department of Chemistry, Humboldt University of Berlin, Germany
| | - Clemens Mügge
- Department of Chemistry, Humboldt University of Berlin, Germany
| | - Rainer Mahrwald
- Department of Chemistry, Humboldt University of Berlin, Germany
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33
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Furse KE, Corcelli SA. Effects of Long-Range Electrostatics on Time-Dependent Stokes Shift Calculations. J Chem Theory Comput 2009; 5:1959-67. [DOI: 10.1021/ct9001416] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristina E. Furse
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, Indiana 46556
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34
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Zhong D. Hydration Dynamics and Coupled Water-Protein Fluctuations Probed by Intrinsic Tryptophan. ADVANCES IN CHEMICAL PHYSICS 2009. [DOI: 10.1002/9780470508602.ch3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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35
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Molecular recognition of plant DNA: does it differ from conventional animal DNA? Int J Biol Macromol 2009; 44:133-7. [PMID: 19059281 DOI: 10.1016/j.ijbiomac.2008.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 10/07/2008] [Accepted: 11/05/2008] [Indexed: 11/20/2022]
Abstract
The recognition mechanism of DNA with small drugs/ligands is an important field of research from pharmacological point of view. Such studies are ample with DNAs extracted from animal cells, but are rare for those extracted from plant cells. However, such a study is strongly demanding for the formulation of pesticides and other agrochemicals. In this contribution, for the first time, we report the interaction of two well-known DNA binder ethidium bromide (EB) and Hoechst 33258 (H33258) with two genomic DNAs extracted from the leaves of Ricinus communis L. (castor bean) and Mangifera indica (mango) using steady-state and picosecond-resolved fluorescence spectroscopy. The purity of the extracted DNAs is confirmed from gel electrophoresis and optical absorption studies. As evidenced from the circular dichroism (CD) measurements the DNAs retain physiologically relevant B forms. The well-known DNA intercalator EB has been found to show an additional electrostatic mode of binding with the DNAs, which is not present in the conventional animal DNAs. The binding affinity of EB is found to be even weaker for the DNA extracted from M. indica compared to that in R. communis L. On the other hand, the binding affinity of H33258 with the plant DNAs is found to be comparable to that of animal DNAs. The difference in interaction could be rationalized from the possible differences in the base sequences.
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36
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Sen S, Andreatta D, Ponomarev SY, Beveridge DL, Berg MA. Dynamics of water and ions near DNA: comparison of simulation to time-resolved stokes-shift experiments. J Am Chem Soc 2009; 131:1724-35. [PMID: 19191698 PMCID: PMC2750815 DOI: 10.1021/ja805405a] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-resolved Stokes-shift experiments measure the dynamics of biomolecules and of the perturbed solvent near them on subnanosecond time scales, but molecular dynamics simulations are needed to provide a clear interpretation of the results. Here we show that simulations using standard methods quantitatively reproduce the main features of TRSS experiments in DNA and provide a molecular assignment for the dynamics. The simulations reproduce the magnitude and unusual power-law dynamics of the Stokes shift seen in recent experiments [ Andreatta, D., et al. J. Am. Chem. Soc. 2005, 127, 7270 ]. A polarization model is introduced to eliminate cross-correlations between the different components contributing to the signal. Using this model, well-defined contributions of the DNA, water, and counterion to the experimental signal are extracted. Water is found to have the largest contribution and to be responsible for the power-law dynamics. The counterions have a smaller, but non-negligible, contribution with a time constant of 220 ps. The contribution to the signal of the DNA itself is minor and fits a 30 ps stretched exponential. Both time-averaged and dynamic distributions are calculated. They show a small subset of ions with a different coupling but no other evidence of substates or rate heterogeneity.
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Affiliation(s)
- Sobhan Sen
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067 India
| | - Daniele Andreatta
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
| | | | | | - Mark A. Berg
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208
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37
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Mazur AK. Kinetic and Thermodynamic DNA Elasticity at Micro- and Mesoscopic Scales. J Phys Chem B 2009; 113:2077-89. [DOI: 10.1021/jp8098945] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexey K. Mazur
- CNRS UPR9080, Institut de Biologie Physico-Chimique 13, rue Pierre et Marie Curie, Paris 75005, France
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38
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Lindquist BA, Furse KE, Corcelli SA. Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview. Phys Chem Chem Phys 2009; 11:8119-32. [DOI: 10.1039/b908588b] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Banerjee D, Pal SK. Conformational dynamics at the active site of alpha-chymotrypsin and enzymatic activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:8163-8168. [PMID: 18572890 DOI: 10.1021/la8010184] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The role of dynamical flexibility at the active site of a proteolytic enzyme alpha-chymotrypsin (CHT) has been correlated with its catalytic activity. The temperature-dependent efficiency of catalysis reveals a bell-shaped feature with a peak at 37 degrees C, the typical body temperature of homeothermal animals. The overall structural integrity of the enzyme in our experimental temperature range has been confirmed from dynamic light scattering (DLS) and circular dichroism (CD) studies. We have followed the dynamical evolution at the active site of CHT with temperature using picosecond-resolved fluorescence anisotropy of anthraniloyl probe (covalently attached to the serine-195 residue) and a substrate mimic (inhibitor) proflavin. The conformational dynamics at the active site is found to have a distinct connection with the enzyme functionality. The conformational flexibility of the enzyme is also evidenced from the compressibility studies on the enzyme. The site selective fluorescence detected circular dichroism (FDCD) studies reveal that the conformational flexibility of the enzyme has an effect on the structural perturbation at the active site. We have also proposed the possible implications of the dynamics in the associated energetics.
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Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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40
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Weightman P, Bowler M, Clarke JA, Farrell T, Flavell W, Harrison P, Martin DS, Papiz MZ, Poole MA, Quinn F, Seddon EA, Smith CI, Smith S, Surman M. Reflection anisotropy spectroscopy of biological molecules with the 4GLS source. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/pssc.200779109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Singh PK, Nath S, Kumbhakar M, Bhasikuttan AC, Pal H. Quantitative Distinction between Competing Intramolecular Bond Twisting and Solvent Relaxation Dynamics: An Ultrafast Study. J Phys Chem A 2008; 112:5598-603. [DOI: 10.1021/jp801862j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Prabhat K. Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Manoj Kumbhakar
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | | | - Haridas Pal
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
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42
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Banerjee D, Pal SK. Dynamics in the DNA recognition by DAPI: exploration of the various binding modes. J Phys Chem B 2008; 112:1016-21. [PMID: 18171050 DOI: 10.1021/jp077090f] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two distinct modes of interaction of the fluorescent probe 4',6-diamidino-2-phenylindole (DAPI), depending on the sequence of DNA, have been reported in the literature. In the present study, the dynamics of solvation has been utilized to explore the binding interaction of DAPI to DNA oligomers of different sequences. Picosecond-resolved fluorescence and polarization-gated anisotropy have been used to characterize the binding of DAPI to the different oligomers. In the double-stranded dodecamer of sequence CGCGAATTCGCG (oligo1), the solvation relaxation dynamics of the probe reveals time constants of 0.130 ns (75%) and 2.35 ns (25%). Independent exploration of the minor-groove environment of oligo1 using another well-known minor-groove binder Hoechst 33258 (H258) shows similar timescales, further confirming minor-groove binding of DAPI to oligo1. In the double-stranded dodecamer (oligo2) having the sequence GCGCGCGCGCGC, where intercalation has been reported in the literature, no solvation is observed in our experimental window. DAPI bound to oligo2 shows quenching of fluorescence compared to that of DAPI in a buffer. The quenching of fluorescence of DAPI intercalated in DNA is also borne out by the appearance of a fast component of 30 ps in the fluorescence lifetime, revealing electron transfer to DAPI from GC base pairs, between which it intercalates. In addition to this, the excited-state lifetime of the probe in the DAPI-DNA complex also shows a time constant similar to that of the dye in a buffer, indicating that the excited-state photoprocesses associated with the free dye is also operative in this binding mode, consistent with the binding geometry of the DAPI in the DNA. The dynamics of DAPI in calf thymus DNA having a random sequence of base pairs is similar to that associated with the DNA minor groove. Our studies clearly explore the structure-dynamics correlation of the DAPI-DNA complex in the two distinct modes of interaction of DAPI with DNA.
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Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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43
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Berg MA, Coleman RS, Murphy CJ. Nanoscale structure and dynamics of DNA. Phys Chem Chem Phys 2008; 10:1229-42. [DOI: 10.1039/b715272h] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Sarkar R, Pal SK. Interaction of Hoechst 33258 and Ethidium with Histone1−DNA Condensates. Biomacromolecules 2007; 8:3332-9. [PMID: 17902690 DOI: 10.1021/bm700690p] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report structural and dynamical aspects of DNAs from various sources including synthetic oligonucleotides in bulk buffer and as a complex with histone1 (H1). High-resolution transmission electron microscopic (HRTEM) studies reveal the structural change of the DNAs upon complexation with H1 leading to formation of compact-globular and hollow-toroidal particles. In order to explore the functionality of ligand binding of the DNAs and their complexes with H1, we have used two biologically common fluorescent probes Hoechst 33258 (H33258) and Ethidium (EB) as model ligands. Picosecond resolved fluorescence and polarization gated anisotropy studies examined that the minor groove binding of H33258 to the genomic DNA-H1 complex remains almost unaltered. However, the intercalative interaction of EB with the DNA in the complex is severely perturbed compared to that with the DNA in bulk buffer. Time-dependent solvochromic effect of the probe H33258 further elucidates the dynamical solvation, which is reflective of the overall environmental relaxation of the DNAs upon condensation by H1. We have also performed circular dichroism (CD) studies on the DNAs and their complexes with H1, which reveal the change in conformation of the DNAs in the complexes. Our studies in the ligand-binding mechanisms of the DNA-H1 complex are important to understand the mechanism of drug binding to linker DNA in condensed chromatin.
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Affiliation(s)
- Rupa Sarkar
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata, India
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45
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Kwok WM, Ma C, Phillips DL. Femtosecond time- and wavelength-resolved fluorescence and absorption spectroscopic study of the excited states of adenosine and an adenine oligomer. J Am Chem Soc 2007; 128:11894-905. [PMID: 16953630 DOI: 10.1021/ja0622002] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By employing broadband femtosecond Kerr-gated time-resolved fluorescence (KTRF) and transient absorption (TA) techniques, we report the first (to our knowledge) femtosecond combined time- and wavelength-resolved study on an ultraviolet-excited nucleoside and a single-stranded oligonucleotide (namely adenosine (Ado) and single-stranded adenine oligomer (dA)(20)) in aqueous solution. With the advantages of the ultrafast time resolution, the broad spectral and temporal probe window, and a high sensitivity, our KTRF and TA results enable the real time monitoring and spectral characterization of the excited-state relaxation processes of the Ado nucleoside and (dA)(20) oligonucleotide investigated. The temporal evolution of the 267 nm excited Ado KTRF spectra indicates there are two emitting components with lifetimes of approximately 0.13 ps and approximately 0.45 ps associated with the L(a) and L(b) pipi* excited states, respectively. These Ado results reveal no obvious evidence for the involvement of the npi* state along the irradiative internal conversion pathway. A distinct mechanism involving only the two pipi* states has been proposed for the ultrafast Ado deactivation dynamics in aqueous solution. The time dependence of the 267 nm excited (dA)(20) KTRF and TA spectra reveals temporal evolution from an ultrafast "A-like" state (with a approximately 0.39 ps decay time) to a relatively long-lived E(1) "excimer" (approximately 4.3 ps decay time) and an E(2) "excimer-like" (approximately 182 ps decay time) state. The "A-like" state has a spectral character closely resembling the excited state of Ado. Comparison of the spectral evolution between the results for Ado and (dA)(20) provides unequivocal evidence for the local excitation character of the initially photoexcited (dA)(20). The rapid transformation of the locally excited (dA)(20) component into the delocalized E(1) "excimer" state which then further evolves into the E(2) "excimer-like" state indicates that base stacking has a high ability to modify the excited-state deactivation pathway. This modification appears to occur by suppressing the internal conversion pathway of an individually excited base component where the stacking interaction mediates efficient interbase energy transfer and promotes formation of the collective excited states. This feature of the local excitation that is subsequently followed by rapid energy delocalization into nearby bases may occur in many base multimer systems. Our results provide an important new contribution to better understanding DNA photophysics.
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Affiliation(s)
- Wai-Ming Kwok
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S. A. R., P. R. China
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Banerjee D, Pal SK. Direct Observation of Essential DNA Dynamics: Melting and Reformation of the DNA Minor Groove. J Phys Chem B 2007; 111:10833-8. [PMID: 17676797 DOI: 10.1021/jp074697n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dynamics of bound water and ions present in the minor groove of a dodecamer DNA has been decoupled from that of the long-range twisting/bending of the DNA backbone, using the minor groove binder Hoechst 33258 as a fluorescence reporter in the picosecond-resolved time window. The bound water and ions are essential structural components of the minor groove and are destroyed with the destruction of the minor groove when the dodecamer melts at high temperatures and reforms on subsequent cooling of the melted DNA. The melting and rehybridization of the DNA has been monitored by the changes in secondary structure using circular dichroism (CD) spectroscopy. The change in the relaxation dynamics of the DNA has been studied with picosecond resolution at different temperatures, following the temperature-dependent melting and rehybridization profile of the dodecamer, using time-resolved emission spectra (TRES). At room temperature, the relaxation dynamics of DNA is governed by a 40 ps (30%) and a 12.3 ns (70%) component. The dynamics of bound water and ions present in the minor groove is characterized by the 40 ps component in the relaxation dynamics of the probe bound in the minor groove of the dodecamer DNA. Analyses of the TRES taken at different temperatures show that the contribution of this component decreases and ultimately vanishes with the destruction of the minor groove and reappears again with the reformation of the groove. The dynamical behavior of bound water molecules and ions of a genomic DNA (from salmon testes) at different temperatures is also found to be consistent with that of the dodecamer. The longer component of approximately 10 ns in the DNA dynamics is found to be associated with the long-range bending/twisting of the DNA backbone and the associated counterions. The transition from bound water to free water at the DNA surface, indicative of the change in the hydration number associated with each base pair, has also been ascertained in the case of the genomic DNA at different temperatures by employing densimetric and acoustic techniques.
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Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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Trifonov A, Raytchev M, Buchvarov I, Rist M, Barbaric J, Wagenknecht HA, Fiebig T. Ultrafast energy transfer and structural dynamics in DNA. J Phys Chem B 2007; 109:19490-5. [PMID: 16853518 DOI: 10.1021/jp052108c] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrafast structural dynamics concomitant to excitation energy transfer in DNA has been studied using a pair of pyrene-labeled DNA bases. The temporal evolution of the femtosecond pump-probe spectra reveals the existence of two electronic coupling pathways, through-base stack and through-space, which lead to excitation energy transfer and excimer formation even when the labeled DNA bases are separated by one AT base pair. The electronic coupling which mediates through-base stack energy transfer is so strong that a new absorption band arises in the excited-state absorption spectrum within 300 fs. From the analysis of time-dependent spectral shifts due to through-space excimer formation, the local structural dynamics and flexibility of DNA are characterized on the picosecond and nanosecond time scale.
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Affiliation(s)
- A Trifonov
- Eugene F. Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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Greco NJ, Tor Y. Furan Decorated Nucleoside Analogues as Fluorescent Probes: synthesis, photophysical evaluation and site-specific incorporation. Tetrahedron 2007; 63:3515-3527. [PMID: 18431439 DOI: 10.1016/j.tet.2007.01.073] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The synthesis and photophysical evaluation of modified nucleoside analogues in which a five-membered heterocycle (furan, thiophene, oxazole and thiazole) is attached to the 5 position of 2'-deoxyuridine are reported. The furan containing derivative is identified as the most promising responsive nucleoside of this family due to its emission quantum efficiency and degree of sensitivity to its microenvironment. The furan moiety was then attached to the 5 position of 2'-deoxycytidine as well as the 8 position of adenosine and guanosine. Photophysical evaluation of these four furan containing nucleoside analogues reveal distinct differences in the absorption, emission and quantum efficiency depending upon the class of nucleoside (pyrimidine or purine). Comparing the photophysical properties of all furan containing nucleosides, identifies the furan thymidine analogue, 5-(fur-2-yl)-2'-deoxyuridine, as the best candidate for use as a responsive fluorescent probe in nucleic acids. 5-(fur-2-yl)-2'-deoxyuridine was then converted to the corresponding phosphoramidite and site specifically incorporated into DNA oligonucleotides with greater than 88% coupling efficiency. Such furan-modified oligonucleotides form stable duplexes upon hybridization to their complementary DNA strands and display favorable fluorescent features.
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Affiliation(s)
- Nicholas J Greco
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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Coleman RS, Berg MA, Murphy CJ. Coumarin base-pair replacement as a fluorescent probe of ultrafast DNA dynamics. Tetrahedron 2007. [DOI: 10.1016/j.tet.2006.12.096] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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