1
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Bubble Relaxation Dynamics in Homopolymer DNA Sequences. Molecules 2023; 28:molecules28031041. [PMID: 36770707 PMCID: PMC9920605 DOI: 10.3390/molecules28031041] [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: 12/21/2022] [Revised: 01/11/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023] Open
Abstract
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule's dynamics, for times between 0.5-500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.
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2
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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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3
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Penkov NV, Penkova N. Key Differences of the Hydrate Shell Structures of ATP and Mg·ATP Revealed by Terahertz Time-Domain Spectroscopy and Dynamic Light Scattering. J Phys Chem B 2021; 125:4375-4382. [PMID: 33882673 DOI: 10.1021/acs.jpcb.1c02276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ATP is one of the main biological molecules. Many of its biological and physicochemical properties, such as energy capacity of the phosphate bonds, significantly depend on hydration. However, the structure of the hydration shell of the ATP molecule is still a matter of discussion. In this work, the hydration shells of ATP in water and MgCl2 solutions were examined by terahertz time-domain spectroscopy and dynamic light scattering. Terahertz spectroscopy reveals the distorted water structure in the ATP water solution displaying tightly bound water molecules, which could be explained by the hydration of phosphate groups. Upon ATP binding to a Mg2+ ion, the situation is principally different: Instead of the distorted water structure, its arranged structure with increased hydrogen bond number is observed. Dynamic light scattering showed that the hydrodynamic diameter of ATP increases by 0.5 nm after Mg2+ binding. Meanwhile, according the characteristics of scattering, the increase of the shell size occurs via formation of a layer with a refraction coefficient similar to water. This layer can be interpreted as hydration shell differing from unaltered water by increased number of hydrogen bonds.
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Affiliation(s)
- Nikita V Penkov
- Institute of Cell Biophysics RAS, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino 142290, Russia
| | - Nadezda Penkova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Russia
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4
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Bravo-Anaya LM, Macías ER, Pérez-López JH, Galliard H, Roux DCD, Landazuri G, Carvajal Ramos F, Rinaudo M, Pignon F, Soltero JFA. Supramolecular Organization in Calf-Thymus DNA Solutions under Flow in Dependence with DNA Concentration. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01174] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- L. Mónica Bravo-Anaya
- LRP, University Grenoble Alpes, F-38000 Grenoble, France
- LRP, CNRS, F-38000 Grenoble, France
- Departamento
de Ingeniería Química, Universidad de Guadalajara, Blvd.
M. García Barragán #1451, C.P. 44430, Guadalajara, Jalisco, México
| | - E. Rebeca Macías
- Departamento
de Ingeniería Química, Universidad de Guadalajara, Blvd.
M. García Barragán #1451, C.P. 44430, Guadalajara, Jalisco, México
| | - J. Humberto Pérez-López
- Departamento
de Ingeniería Química, Universidad de Guadalajara, Blvd.
M. García Barragán #1451, C.P. 44430, Guadalajara, Jalisco, México
| | - Hélène Galliard
- LRP, University Grenoble Alpes, F-38000 Grenoble, France
- LRP, CNRS, F-38000 Grenoble, France
| | - Denis C. D. Roux
- LRP, University Grenoble Alpes, F-38000 Grenoble, France
- LRP, CNRS, F-38000 Grenoble, France
| | - Gabriel Landazuri
- Departamento
de Ingeniería Química, Universidad de Guadalajara, Blvd.
M. García Barragán #1451, C.P. 44430, Guadalajara, Jalisco, México
| | - Francisco Carvajal Ramos
- CUTonalá,
Departamento de Ingenierías, Universidad de Guadalajara, Nuevo
Periférico #555 Ejido San José Tatepozco, C.P. 45425, Tonalá, Jalisco, México
| | | | - Frédéric Pignon
- LRP, University Grenoble Alpes, F-38000 Grenoble, France
- LRP, CNRS, F-38000 Grenoble, France
| | - J. F. Armando Soltero
- Departamento
de Ingeniería Química, Universidad de Guadalajara, Blvd.
M. García Barragán #1451, C.P. 44430, Guadalajara, Jalisco, México
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5
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Deiana M, Mettra B, Matczyszyn K, Piela K, Pitrat D, Olesiak-Banska J, Monnereau C, Andraud C, Samoc M. Interactions of a biocompatible water-soluble anthracenyl polymer derivative with double-stranded DNA. Phys Chem Chem Phys 2016; 17:30318-27. [PMID: 26506886 DOI: 10.1039/c5cp05381a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have studied the interaction of a polymeric water soluble anthracenyl derivative () with salmon testes DNA. The results from UV-Vis, fluorescence, Fourier transform infrared (FT-IR) and circular dichroism spectroscopies indicate that the groove binding process regulates the interaction between and DNA. The binding constants, calculated by absorption spectroscopy at 298, 304 and 310 K, were equal to 3.2 × 10(5) M(-1), 4.7 × 10(5) M(-1), and 6.6 × 10(5) M(-1) respectively, proving a relatively high affinity of for salmon testes DNA. Results of Hoechst 33258 displacement assays strongly support the groove binding mode of to DNA. The association stoichiometry of the :DNA adduct was found to be 1 for every 5 base pairs. FT-IR spectra, recorded at different /DNA molar ratios, indicate the involvement of the phosphate groups and adenine and thymine DNA bases in the association process. Thermodynamic results suggest that hydrophobic forces regulate the binding of with DNA without excluding some extent of involvement of van der Waals forces and hydrogen bonding arising due to surface binding between the hydrophilic polymeric arms of the ligand and the functional groups positioned on the edge of the groove. The resulting composite biomaterial could constitute a valuable candidate for future biological and/or photonic applications.
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Affiliation(s)
- Marco Deiana
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Bastien Mettra
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Katarzyna Matczyszyn
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Katarzyna Piela
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Delphine Pitrat
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Joanna Olesiak-Banska
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
| | - Cyrille Monnereau
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Chantal Andraud
- Laboratoire de Chimie, CNRS UMR 5182, Ecole Normale Supérieure de Lyon, Université, Lyon 1, Lyon, France
| | - Marek Samoc
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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6
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He Y, Shang Y, Liu Y, Zhao S, Liu H. Melting dynamics of short dsDNA chains in saline solutions. SPRINGERPLUS 2015; 4:777. [PMID: 26697287 PMCID: PMC4679706 DOI: 10.1186/s40064-015-1581-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022]
Abstract
DNA melting has attracted much attention due to its importance in understanding the life-reproduction and metabolism and in the applications of modern DNA-based technologies. While numerous works have been contributed to the determination of melting profiles in diverse environments, the understanding of DNA melting dynamics is still limited. By employing three-site-per-nucleotide (3SPN) double-stranded DNA (dsDNA) model, we here demonstrate the melting dynamics of an isolated short dsDNA under different conditions (different temperatures, ionic concentrations and DNA chain lengths) can be accessed by coarse-grained simulation studies. We particularly show that at dilute ionic concentration the dsDNA, regardless being symmetric or asymmetric, opens at both ends with roughly equal probabilities, while at high ionic concentration the asymmetric dsDNA chain opens at the A-T-rich end. The comparisons of our simulation results to available data are discussed, and overall good agreements have been found.
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Affiliation(s)
- Yichen He
- State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China
| | - Yazhuo Shang
- State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China
| | - Yu Liu
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Shuangliang Zhao
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Honglai Liu
- State Key Laboratory of Chemical Engineering and Department of Chemistry, East China University of Science and Technology, Shanghai, 200237 China
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7
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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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8
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Monserud JH, Schwartz DK. Mechanisms of surface-mediated DNA hybridization. ACS NANO 2014; 8:4488-4499. [PMID: 24708278 PMCID: PMC4046783 DOI: 10.1021/nn4064874] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/07/2014] [Indexed: 06/03/2023]
Abstract
Single-molecule total internal reflection fluorescence microscopy was employed in conjunction with resonance energy transfer (RET) to observe the dynamic behavior of donor-labeled ssDNA at the interface between aqueous solution and a solid surface decorated with complementary acceptor-labeled ssDNA. At least 100,000 molecular trajectories were determined for both complementary strands and negative control ssDNA. RET was used to identify trajectory segments corresponding to the hybridized state. The vast majority of molecules from solution adsorbed nonspecifically to the surface, where a brief two-dimensional search was performed with a 7% chance of hybridization. Successful hybridization events occurred with a characteristic search time of ∼0.1 s, and unsuccessful searches resulted in desorption from the surface, ultimately repeating the adsorption and search process. Hybridization was reversible, and two distinct modes of melting (i.e., dehybridization) were observed, corresponding to long-lived (∼15 s) and short-lived (∼1.4 s) hybridized time intervals. A strand that melted back onto the surface could rehybridize after a brief search or desorb from the interface. These mechanistic observations provide guidance for technologies that involve DNA interactions in the near-surface region, suggesting a need to design surfaces that both enhance the complex multidimensional search process and stabilize the hybridized state.
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9
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Batabyal S, Mondol T, Choudhury S, Mazumder A, Pal SK. Ultrafast interfacial solvation dynamics in specific protein DNA recognition. Biochimie 2013; 95:2168-76. [DOI: 10.1016/j.biochi.2013.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/06/2013] [Indexed: 12/14/2022]
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10
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Polley D, Patra A, Mitra RK. Dielectric relaxation of the extended hydration sheathe of DNA in the THz frequency region. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.09.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Lin J, Liu Y, Liu L, Song L. Studies on the toxic interaction mechanism between 2-naphthylamine and herring sperm DNA. J Biochem Mol Toxicol 2013; 27:279-85. [PMID: 23625636 DOI: 10.1002/jbt.21488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/11/2013] [Accepted: 03/25/2013] [Indexed: 12/30/2022]
Abstract
The toxic interaction between 2-naphthylamine (2-NA) and herring sperm deoxyribonucleic acid (hs-DNA) has been thoroughly investigated by UV absorption, fluorescence, and circular dichroism (CD) spectroscopic methods. UV absorption result indicates that 2-NA may intercalate into the stack base pairs of DNA during the toxic interaction of 2-NA with DNA. A fluorescence quenching study shows that DNA quenches the intrinsic fluorescence of 2-NA via a static pathway. The studies on effects of ionic strength and anionic quenching rule out electrostatic and groove bindings as the dominant binding modes. Further studies on denatured DNA fluorescence quenching and thermal melting studies confirm that the dominant binding mode of 2-NA-DNA is intercalative binding. A CD spectral study shows that the binding interaction of 2-NA with DNA leads to the disorganization of the neat double-helical structure of hs-DNA.
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Affiliation(s)
- Jingjing Lin
- The State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, People's Republic of China
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12
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Banerjee S, Sarkar S, Lakshman K, Dutta J, Pal SK. UVA Radiation Induced Ultrafast Electron Transfer from a Food Carcinogen Benzo[a]pyrene to Organic Molecules, Biological Macromolecules, and Inorganic Nano Structures. J Phys Chem B 2013; 117:3726-37. [DOI: 10.1021/jp312536x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Soma Banerjee
- UNANST, Department of Chemical,
Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector
III, Salt Lake, Kolkata 700 098, India
| | - Soumik Sarkar
- UNANST, Department of Chemical,
Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector
III, Salt Lake, Kolkata 700 098, India
| | - Karthik Lakshman
- Water Research Center, Sultan Qaboos University, P.O. Box 17, 123 Al-Khoudh,
Sultanate of Oman
| | - Joydeep Dutta
- Water Research Center, Sultan Qaboos University, P.O. Box 17, 123 Al-Khoudh,
Sultanate of Oman
| | - Samir Kumar Pal
- UNANST, 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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13
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Markarian MZ, Schlenoff JB. Effect of molecular crowding and ionic strength on the isothermal hybridization of oligonucleotides. J Phys Chem B 2010; 114:10620-7. [PMID: 20701389 DOI: 10.1021/jp103213w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The isothermal hybridization of complementary oligonucleotides, 15-mer, 25-mer, 35-mer, and a molecular beacon, was investigated under varying conditions of molecular crowding and ionic strength, using hypochromicity to follow strand pairing and polyethylene glycol as a crowding agent. Thermodynamic analysis of the results revealed the addition of counterions to the oligonucleotide backbones, DeltaPsi, to be dependent on the strand GC content and the molecular crowding. A decrease in DeltaPsi was observed, with both increasing GC% and solution PEG content. In contrast, the number of bound water molecules depended on the activity of Na(+), where two regimes were observed. At a(Na(+)) < 0.05 and increasing molecular crowding, water molecules were released into the DNA solutions, and oligonucleotide pairing was favored with both increasing hydrophobic forces, whereas at a(Na(+)) >or= 0.05, water molecules were bound to the strands, and the extent of double strand formation decreased with increasing PEG wt %.
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Affiliation(s)
- Marie Z Markarian
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, USA
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14
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Banerjee D, Makhal A, Pal SK. Sequence dependent femtosecond-resolved hydration dynamics in the minor groove of DNA and histone-DNA complexes. J Fluoresc 2009; 19:1111-8. [PMID: 19565329 DOI: 10.1007/s10895-009-0512-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 06/22/2009] [Indexed: 10/20/2022]
Abstract
Understanding the sequence dependent molecular recognition of DNA is crucial for the rational design of many drugs. Femtosecond resolved studies on the hydration dynamics of the dodecamer duplexes having sequences (CGCGAATTCGCG)2 and (CGCAAATTTGCG)2, and their complexes with the nucleic protein histone 1 (H1) reveal significant correlation of the molecular recognition of the DNA and DNA-protein complexes with the dynamics of hydration. The different molecular recognition of DNA and DNA-protein complexes is also borne out by circular dichroism (CD) and fluorescence detected CD measurements.
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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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15
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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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16
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Starikov E, Quintilla A, Nganou C, Lee K, Cuniberti G, Wenzel W. Single-molecule DNA conductance in water solutions: Role of DNA low-frequency dynamics. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2008.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Banerjee D, Pal SK. Excited-State Solvation and Proton Transfer Dynamics of DAPI in Biomimetics and Genomic DNA. J Phys Chem A 2008; 112:7314-20. [DOI: 10.1021/jp801778e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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
| | - Samir Kumar Pal
- 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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18
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Banerjee D, Pal SK. Solvation dynamics of LDS 750 in micelles, reverse micelles and proteins. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2007.12.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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