1
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Penkov NV. Terahertz spectroscopy as a method for investigation of hydration shells of biomolecules. Biophys Rev 2023; 15:833-849. [PMID: 37974994 PMCID: PMC10643733 DOI: 10.1007/s12551-023-01131-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The hydration of biomolecules is one of the fundamental processes underlying the construction of living matter. The formation of the native conformation of most biomolecules is possible only in an aqueous environment. At the same time, not only water affects the structure of biomolecules, but also biomolecules affect the structure of water, forming hydration shells. However, the study of the structure of biomolecules is given much more attention than their hydration shells. A real breakthrough in the study of hydration occurred with the development of the THz spectroscopy method, which showed that the hydration shell of biomolecules is not limited to 1-2 layers of strongly bound water, but also includes more distant areas of hydration with altered molecular dynamics. This review examines the fundamental features of the THz frequency range as a source of information about the structural and dynamic characteristics of water that change during hydration. The applied approaches to the study of hydration shells of biomolecules based on THz spectroscopy are described. The data on the hydration of biomolecules of all main types obtained from the beginning of the application of THz spectroscopy to the present are summarized. The emphasis is placed on the possible participation of extended hydration shells in the realization of the biological functions of biomolecules and at the same time on the insufficient knowledge of their structural and dynamic characteristics.
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Affiliation(s)
- Nikita V. Penkov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics RAS, 142290 Pushchino, Russia
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2
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Bubon T, Zdorevskyi O, Perepelytsya S. Molecular dynamics study of collective water vibrations in a DNA hydration shell. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:69-79. [PMID: 36920489 DOI: 10.1007/s00249-023-01638-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 03/16/2023]
Abstract
The structure of DNA double helix is stabilized by water molecules and metal counterions that form the ion-hydration shell around the macromolecule. Understanding the role of the ion-hydration shell in the physical mechanisms of the biological functioning of DNA requires detailed studies of its structure and dynamics at the atomistic level. In the present work, the study of collective vibrations of water molecules around the DNA double helix was performed within the framework of classical all-atom molecular dynamics methods. Calculating the vibrational density of states, the vibrations of water molecules in the low-frequency spectra ranged from [Formula: see text]30 to [Formula: see text]300 [Formula: see text] were analyzed for the case of different regions of the DNA double helix (minor groove, major groove, and phosphate groups). The analysis revealed significant differences in the collective vibrations behavior of water molecules in the DNA hydration shell, compared to the vibrations of bulk water. All low-frequency modes of the DNA ion-hydration shell are shifted by about 15-20 [Formula: see text] towards higher frequencies, which is more significant for water molecules in the minor groove region of the double helix. The interactions of water molecules with the atoms of the macromolecule induce intensity decrease of the mode of hydrogen-bond symmetrical stretching near 150 [Formula: see text], leading to the disappearance of this mode in the DNA spectra. The obtained results can provide an interpretation of the experimental data for DNA low-frequency spectra and may be important for the understanding of the processes of indirect protein-nucleic recognition.
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Affiliation(s)
- Tetiana Bubon
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14b, Metrolohichna Str., Kyiv, 03143, Ukraine.
- Condensed Matter and Statistical Physics, Abdus Salam International Centre for Theoretical Physics, Strada Costiera, 11, Trieste, 34151, Italy.
| | - Oleksii Zdorevskyi
- Department of Physics, University of Helsinki, Gustaf Hällströmin katu 2, Helsinki, 00014, Finland
| | - Sergiy Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14b, Metrolohichna Str., Kyiv, 03143, Ukraine
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3
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Singh AK, Wen C, Cheng S, Vinh NQ. Long-range DNA-water interactions. Biophys J 2021; 120:4966-4979. [PMID: 34687717 DOI: 10.1016/j.bpj.2021.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/14/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
DNA functions only in aqueous environments and adopts different conformations depending on the hydration level. The dynamics of hydration water and hydrated DNA leads to rotating and oscillating dipoles that, in turn, give rise to a strong megahertz to terahertz absorption. Investigating the impact of hydration on DNA dynamics and the spectral features of water molecules influenced by DNA, however, is extremely challenging because of the strong absorption of water in the megahertz to terahertz frequency range. In response, we have employed a high-precision megahertz to terahertz dielectric spectrometer, assisted by molecular dynamics simulations, to investigate the dynamics of water molecules within the hydration shells of DNA as well as the collective vibrational motions of hydrated DNA, which are vital to DNA conformation and functionality. Our results reveal that the dynamics of water molecules in a DNA solution is heterogeneous, exhibiting a hierarchy of four distinct relaxation times ranging from ∼8 ps to 1 ns, and the hydration structure of a DNA chain can extend to as far as ∼18 Å from its surface. The low-frequency collective vibrational modes of hydrated DNA have been identified and found to be sensitive to environmental conditions including temperature and hydration level. The results reveal critical information on hydrated DNA dynamics and DNA-water interfaces, which impact the biochemical functions and reactivity of DNA.
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Affiliation(s)
- Abhishek K Singh
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia
| | - Chengyuan Wen
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia
| | - Shengfeng Cheng
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia; Macromolecules Innovation Institute, Blacksburg, Virginia; Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia
| | - Nguyen Q Vinh
- Department of Physics and Center for Soft Matter and Biological Physics, Blacksburg, Virginia; Macromolecules Innovation Institute, Blacksburg, Virginia; Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia.
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4
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Penkova NA, Sharapov MG, Penkov NV. Hydration Shells of DNA from the Point of View of Terahertz Time-Domain Spectroscopy. Int J Mol Sci 2021; 22:ijms222011089. [PMID: 34681747 PMCID: PMC8538832 DOI: 10.3390/ijms222011089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/09/2021] [Accepted: 10/10/2021] [Indexed: 11/16/2022] Open
Abstract
Hydration plays a fundamental role in DNA structure and functioning. However, the hydration shell has been studied only up to the scale of 10-20 water molecules per nucleotide. In the current work, hydration shells of DNA were studied in a solution by terahertz time-domain spectroscopy. The THz spectra of three DNA solutions (in water, 40 mm MgCl2 and 150 mM KCl) were transformed using an effective medium model to obtain dielectric permittivities of the water phase of solutions. Then, the parameters of two relaxation bands related to bound and free water molecules, as well as to intermolecular oscillations, were calculated. The hydration shells of DNA differ from undisturbed water by the presence of strongly bound water molecules, a higher number of free molecules and an increased number of hydrogen bonds. The presence of 40 mM MgCl2 in the solution almost does not alter the hydration shell parameters. At the same time, 150 mM KCl significantly attenuates all the found effects of hydration. Different effects of salts on hydration cannot be explained by the difference in ionic strength of solutions, they should be attributed to the specific action of Mg2+ and K+ ions. The obtained results significantly expand the existing knowledge about DNA hydration and demonstrate a high potential for using the THz time-domain spectroscopy method.
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Affiliation(s)
- Nadezda A. Penkova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Mars G. Sharapov
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;
| | - Nikita V. Penkov
- Institute of Cell Biophysics RAS, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia;
- Correspondence:
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5
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Bubon TL, Perepelytsya SM. Low-frequency vibrations of water molecules in DNA minor groove. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:84. [PMID: 34165657 DOI: 10.1140/epje/s10189-021-00080-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Water molecules around the DNA form the hydration shell having different structural and dynamical features in different regions of the double helix. In the DNA minor groove, water molecules are highly ordered and in the case of AT nucleotide sequence, the formation of a hydration spine is observed. In the present research, the vibrations of the hydration spine have been studied to establish the mode of translational vibrations of water molecules in the DNA low-frequency spectra (water-spine vibrations). Using the developed phenomenological model with the parameters determined for different nucleotides of the DNA fragment CGCGAATTCGCG, the frequencies of vibrations of the hydration spine have been obtained within 185 ± 20 cm[Formula: see text] depending on type of nucleotide. The obtained frequencies are in the same region as the translational vibrations of water molecules in the bulk. To select the mode of water-spine vibrations from those modes that are present in the bulk water, the dynamics of DNA with different nucleotide contents has been analyzed, and the possible influence of heavy water has been estimated. The determined features of the mode of water vibrations in the hydration spine of DNA minor groove indicate that this mode may be observed in the experimental spectra.
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Affiliation(s)
- T L Bubon
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14-b, Metrolohichna Str., Kiev, 03143, Ukraine.
| | - S M Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the National Academy of Sciences of Ukraine, 14-b, Metrolohichna Str., Kiev, 03143, Ukraine
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6
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Hydration of counterions interacting with DNA double helix: a molecular dynamics study. J Mol Model 2018; 24:171. [DOI: 10.1007/s00894-018-3704-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/06/2018] [Indexed: 12/12/2022]
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7
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Concentration-dependent effects on fully hydrated DNA at terahertz frequencies. J Biol Phys 2015; 41:247-56. [PMID: 25698575 DOI: 10.1007/s10867-015-9377-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 01/06/2015] [Indexed: 10/24/2022] Open
Abstract
Using terahertz time-domain spectroscopy (THz-TDS), the frequency-dependent dielectric constant of deoxyribonucleic acid (DNA) in solution was measured. The response of the buffer solution is dominated by two Debye modes in this frequency range, and, from an analysis of the concentration dependence, the presence of the DNA increases the main relaxation time and dielectric constant. This reflects the fact that the water in the hydration layer is more tightly bound under the influence of the DNA molecule in comparison to bulk water. This dynamical slowing down with increasing DNA concentration is similar to what is observed with purine nucleotides, but opposite to the behavior of pyrimidine nucleotides. In addition, a suspension model was used with the concentration-dependent data to isolate the dielectric response of the hydrated DNA molecule. The data for the hydrated DNA molecule is still dominated by a Debye response. It is also possible to determine the thickness of the hydration layer, and the DNA molecule influences the surrounding water out to 16 or 17 Å, which corresponds to about six effective hydration layers.
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8
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Bansal A, Prasad M, Roy K, Kukreti S. A short GC-rich palindrome of human mannose receptor gene coding region displays a conformational switch. Biopolymers 2012; 97:950-62. [PMID: 22987586 DOI: 10.1002/bip.22111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Conformational switching in DNA is fundamental to biological processes. The structural status of a palindromic GC-rich dodecamer DNA sequence, integral part of human MRC2 coding region, and a related sequence of opposite polarity from human FDX1 gene were characterized and compared. UV-melting, circular dichroism, and gel electrophoresis experiments demonstrated the formation of intermolecular structures. Although stability and molecularity of both the oligomeric structures were found to be almost identical, their secondary structures differed remarkably as A1 MRC2 sequence showed A-like and B-like DNA conformation, whereas the A2 FDX1 sequence exhibited only the A-like signatures. The study is relevant for understanding structural polymorphism at genomic locations depending on DNA sequence and solution environment.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi 110007, India
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10
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Glancy P, Beyermann WP. Dielectric properties of fully hydrated nucleotides in the terahertz frequency range. J Chem Phys 2010; 132:245102. [PMID: 20590216 DOI: 10.1063/1.3457941] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We use terahertz time domain spectroscopy (THz-TDS) to determine the complex frequency-dependent dielectric response of all four nucleotides at different dilute concentrations. In addition, the suspension model's ability to extract the dielectric response of just the nucleotide with the hydration shell epsilon(b) excluding the dielectric information relating to the bulk will be verified. The suspension model enables us to make the determination that the nucleotides have influences on the water molecules out to the fourth hydration shell. We use a two Debye relaxation fit model for water, all concentrations and all epsilon(b) values. We observed how the nucleotides affect the relaxation parameters in relation to that of pure bulk water. With this information, we notice a transition between purines and pyrimidines, where one is a hydrogen-bond network structure building type material with a low concentration increment and the other is a structure breaking type material with a low concentration decrement. Due to conductivity measurements, we determine that kinetic depolarization is a negligible affect compared to that of dielectric saturation, which we find to dominate where a decrement is found.
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Affiliation(s)
- P Glancy
- Department of Physics and Astronomy, University of California, Riverside, Riverside, California 92521, USA.
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11
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Smith MS, Lee SA, Rupprecht A. The Stability of the B Conformation in Wet-spun Films of CaDNA: A Raman Study as a Function of Water Content. J Biomol Struct Dyn 2009; 27:105-10. [DOI: 10.1080/07391102.2009.10507300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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12
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Perepelytsya SM, Volkov SN. Counterion vibrations in the DNA low-frequency spectra. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2007; 24:261-269. [PMID: 18060594 DOI: 10.1140/epje/i2007-10236-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 10/26/2007] [Indexed: 05/25/2023]
Abstract
The vibrations of univalent metal cations with respect to phosphate groups of the DNA backbone are described using the four-mass model approach (S.N. Volkov, S.N. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991)) extended in this paper. The force constant of the counterion-phosphate interaction is determined by considering the DNA with counterions as a lattice of ion crystal. For such ion-phosphate lattice the Madelung constant and the dielectric constant are estimated. The obtained value of the Madelung constant is lower than for the NaCl crystal, and its value is about 1.3. The dielectric constant is within 2.3-2.7 depending on the counterion type and form of the double helix. The calculations of the low-frequency spectra show that for the DNA with metal cations Na(+) , K(+) , Rb(+) and Cs(+) the frequency of ion-phosphate vibrations decreases from 174 to 96 cm(-1) as the counterion mass increases. The obtained frequencies agree well with the vibrational spectra of polynucleotides in a dry state which prove our suggestion about the existence of the ion-phosphate lattice around the DNA double helix. The amplitudes of conformational vibrations for DNA in B -form are calculated as well. The results demonstrate that light counterions ( Na(+) do not disturb the internal dynamics of the DNA. However, heavy counterions ( Cs(+) have effect on the internal vibrations of the DNA structural elements.
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Affiliation(s)
- S M Perepelytsya
- Department of Physics, Taras Shevchenko National University, 64 Volodymyrska St., 01033, Kiev, Ukraine.
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13
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Rudd L, Lee DJ, Kornyshev AA. The role of electrostatics in the B to A transition of DNA: from solution to assembly. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2007; 19:416103. [PMID: 28192335 DOI: 10.1088/0953-8984/19/41/416103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
On the basis of a wealth of published experimental data and computer simulations, we build a simple physical model that allows us to rationalize the A to B transition of DNA in solution and in aggregates. In both cases we find that the electrostatic interactions are strong enough, alone, to induce the transition independently of other energetic contributions, e.g. those related to hydration. On the basis of this analysis we conclude that in ethanol/water mixtures, the effect responsible for the transition is the reduction of dielectric constant in the mixture. This is manifested in electrostatic self-energy terms that include the interaction of phosphate charges with condensed counterions. But in dense aggregates, electrostatics plays a dual role, giving rise to two competing effects. In the absence of groove localized counterions the electrostatic self-energy favours the B form, and the electrostatic interaction energy between neighbouring DNA favours the A form. However, the addition of enough counterions localized in the narrow groove reverses this. In dry aggregates of DNA both terms, in most cases, conspire to keep DNA in the A form. The analysis gives a broad picture of the B to A transition and sets a number of new research goals, particularly concerning simulations that may test our simple model for aggregates.
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Affiliation(s)
- Laura Rudd
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, SW7 2AZ London, UK
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14
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Sharma VK, Klibanov AM. Moisture-induced aggregation of lyophilized DNA and its prevention. Pharm Res 2006; 24:168-75. [PMID: 17041790 DOI: 10.1007/s11095-006-9138-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2006] [Accepted: 07/27/2006] [Indexed: 11/28/2022]
Abstract
PURPOSE To investigate the moisture-induced aggregation (i.e., a loss of solubility in water) of DNA in a solid state and to develop rational strategies for its prevention. METHODS Lyophilized calf thymus DNA was exposed to relative humidity (RH) levels from 11% to 96% at 55 degrees C. Following a 24-h incubation under these stressed conditions, the solubility of DNA in different aqueous solutions and the water uptake of DNA were determined. The effects of solution pH and NaCl concentration and the presence of excipients (dextran and sucrose) on the subsequent moisture-induced aggregation of DNA were examined. The extent of this aggregation was compared with that of a supercoiled plasmid DNA. RESULTS Upon a 24-h incubation at 55 degrees C, calf thymus DNA underwent a major moisture-induced aggregation reaching a maximum at a 60% RH; in contrast, the single-stranded DNA exhibited the maximal aggregation at a 96% RH. Moisture uptake and aqueous solubility studies revealed that the aggregation was primarily due to formation of inter-strand hydrogen bonds. Aggregation of DNA also proceeded at 37 degrees C, albeit at a slower rate. Solution pH and NaCl concentration affected DNA aggregation only at higher RH levels. This aggregation was markedly reduced by co-lyophilization with dextran or sucrose (but not with PEG). The aggregation pattern of a supercoiled plasmid DNA was similar to that of its linear calf thymus counterpart. CONCLUSIONS The moisture-induced aggregation of lyophilized DNA is caused mainly by non-covalent cross-links between disordered, single-stranded regions of DNA. At high RH levels, renaturation and aggregation of DNA compete with each other. The aggregation is minimized at low RH levels, at optimal solution pH and salt concentration prior to lyophilization, and by co-lyophilizing with excipients capable of forming multiple hydrogen bonds, e.g., dextran and sucrose.
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Affiliation(s)
- Vikas K Sharma
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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15
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Affiliation(s)
- E.B. Starikov
- a Institute of Radiophysics & Electronics, Ukrainian Academy of Sciences , 310085 , Kharkov , Ukraine (C.I.S.)
- b Institute fuer Kristallographie, Freie Universitaet Berlin , Takustr., 6, 1000 , Berlin 33 , Germany
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16
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Affiliation(s)
- X. Fang
- a Department of Polymer Science , The University of Akron , Akron, Ohio, 44325-3909
| | - D. H. Reneker
- a Department of Polymer Science , The University of Akron , Akron, Ohio, 44325-3909
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17
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Leal C, Wadsö L, Olofsson G, Miguel M, Wennerström H. The Hydration of a DNA−Amphiphile Complex. J Phys Chem B 2004. [DOI: 10.1021/jp030850b] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cecilia Leal
- Physical Chemistry 1, Lund University, POB 124, 221 00 Lund, Sweden, Building Materials, Lund University, POB 118, 221 00 Lund, Sweden, and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Lars Wadsö
- Physical Chemistry 1, Lund University, POB 124, 221 00 Lund, Sweden, Building Materials, Lund University, POB 118, 221 00 Lund, Sweden, and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Gerd Olofsson
- Physical Chemistry 1, Lund University, POB 124, 221 00 Lund, Sweden, Building Materials, Lund University, POB 118, 221 00 Lund, Sweden, and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Maria Miguel
- Physical Chemistry 1, Lund University, POB 124, 221 00 Lund, Sweden, Building Materials, Lund University, POB 118, 221 00 Lund, Sweden, and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Håkan Wennerström
- Physical Chemistry 1, Lund University, POB 124, 221 00 Lund, Sweden, Building Materials, Lund University, POB 118, 221 00 Lund, Sweden, and Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
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18
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Rupprecht A, Piškur J, Schultz J, Nordenskiöld L, Song Z, Lahajnar G. Mechanochemical study of conformational transitions and melting of Li-, Na-, K-, and CsDNA fibers in ethanol-water solutions. Biopolymers 2004. [DOI: 10.1002/bip.360340709] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Marlowe RL, Szabó A, Lee SA, Rupprecht A. Experimental studies on the nature of bonding of DNA*bipyridyl-(ethylenediamine)platinum(II) and DNA*netropsin complexes in solution and oriented wet-spun films. J Biomol Struct Dyn 2002; 19:681-90. [PMID: 11843629 DOI: 10.1080/07391102.2002.10506774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The stability of complexes of NaDNA with bipyridyl- (ethylenediamine)platinum(II) (abbreviated [(bipy)Pt(en)](2+)) and with netropsin has been studied using two techniques: (i) ultraviolet (UV) melting experiments were done on NaDNA* [(bipy)Pt(en)](2+), showing that the [(bipy)Pt(en)](2+) ligand stabilizes the DNA double helix structure; and (ii) swelling measurements (via optical microscopy) as a function of relative humidity were done on wet-spun oriented films of NaDNA*[(bipy)Pt(en)](2+) and of NaDNA*netropsin. The swelling data shows that an irreversible transition of the films occurs at high relative humidity, first for the NaDNA*netropsin, then for pure NaDNA, and lastly for the NaDNA*[(bipy)Pt(en)](2+). These results are indicative that the [(bipy)Pt(en)](2+) complex stabilizes the intermolecular bonds which mediate the film swelling characteristics. A model is suggested for the binding of [(bipy)Pt(en)](2+) to DNA to explain why the swelling experiments show this ligand as increasing the intermolecular bond strength between the DNA double helices, while netropsin decreases this degree of stabilization.
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Affiliation(s)
- R L Marlowe
- Department of Physics, Geology, and Astronomy, The University of Tennessee, Chattanooga, TN 37403, USA
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20
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Albiser G, Lamiri A, Premilat S. The A--B transition: temperature and base composition effects on hydration of DNA. Int J Biol Macromol 2001; 28:199-203. [PMID: 11251226 DOI: 10.1016/s0141-8130(00)00160-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Natural DNAs and some polynucleotides organised in fiber present the A--B form transition at a relative humidity (r.h.) which depends on the temperature. A shift of the midpoint of that helix--helix transition to higher r.h. values is observed when the temperature is risen. It is shown that the average number of water molecules associated to a nucleotide pair is the relevant parameter for the A-B transition and that this parameter can be given a precise value by a combination of different r.h. and temperature values. The minimum number of water molecules necessary to get the B form depends on the base composition of the DNA. It is observed that AT base pairs have a higher affinity toward water molecules than GC base pairs. In the B form there are 27 water molecules per GC nucleotide pair and 44 per AT pair. Moreover, we noted that the fraction of nucleotides in the B form as a function of the average number of water molecules associated per base pair does not depend on the temperature. The A helical form is obtained with about 11 water molecules per nucleotide pair and this number is not very sensitive to the base composition of DNA.
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Affiliation(s)
- G Albiser
- Laboratoire de Biophysique Moleculaire, UMR 7565 Universite H. Poincare, Faculte des Sciences, BP 239, 54506, Vandoeuvre les Nancy, France
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21
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Marlowe RL, Hoppe A, Rupprecht A, Lee SA. Mediation of a phase transition in hyaluronate films by the counterions Li, Cs, Mg and Ca as observed by infrared spectroscopy, optical microscopy and optical birefringence. J Biomol Struct Dyn 1999; 17:607-16. [PMID: 10636094 DOI: 10.1080/07391102.1999.10508390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Infrared (IR) spectroscopy and optical microscopy have been performed as a function of relative humidity (rh) on wet-spun oriented films of hyaluronate (HA) prepared with various counterions. Complete swelling measurements have been obtained through optical microscopy for films of Cs-, Mg-, and CaHA. IR spectroscopy of Cs-, Mg-, Ca-, and LiHA films was performed for skeletal vibrations (800-1000 cm(-1)) and for vibrational modes (1150-1300 cm(-1)) attributed to C-C and C-O stretching modes and C-C-H and C-O-H bending modes. These techniques reveal evidence of a counterion-dependent phase transition occuring at high relative humidities. Optical birefringence measurements on the polycrystalline samples showed order before and disorder after the transition from lower to higher humidity.
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Affiliation(s)
- R L Marlowe
- Dept. of Physics, Geology and Astronomy, The University of Tennessee at Chattanooga, 37403, USA
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van Dam L, Lyubartsev AP, Laaksonen A, Nordenskiöld L. Self-Diffusion and Association of Li+, Cs+, and H2O in Oriented DNA Fibers. An NMR and MD Simulation Study. J Phys Chem B 1998. [DOI: 10.1021/jp983225t] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Lorens van Dam
- Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
| | | | - Aatto Laaksonen
- Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
| | - Lars Nordenskiöld
- Physical Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden
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23
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Kornyshev AA, Leikin S. Electrostatic interaction between helical macromolecules in dense aggregates: an impetus for DNA poly- and meso-morphism. Proc Natl Acad Sci U S A 1998; 95:13579-84. [PMID: 9811842 PMCID: PMC24861 DOI: 10.1073/pnas.95.23.13579] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA exhibits a surprising multiplicity of structures when it is packed into dense aggregates. It undergoes various polymorphous transitions (e.g., from the B to A form) and mesomorphous transformations (from hexagonal to orthorhombic or monoclinic packing, changes in the mutual alignment of nearest neighbors, etc). In this report we show that such phenomena may have their origin in the specific helical symmetry of the charge distribution on DNA surface. Electrostatic interaction between neighboring DNA molecules exhibits strong dependence on the patterns of molecular surface groups and adsorbed counter-ions. As a result, it is affected by such structural parameters as the helical pitch, groove width, the number of base pairs per helical turn, etc. We derive expressions which relate the energy of electrostatic interaction with these parameters and with the packing variables characterizing the axial and azimuthal alignment between neighboring macromolecules. We show, in particular, that the structural changes upon the B-to-A transition reduce the electrostatic energy by approximately kcal/mol per base pair, at a random adsorption of counter ions. Ion binding into the narrow groove weakens or inverts this effect, stabilizing B-DNA, as it is presumably the case in Li+-DNA assemblies. The packing symmetry and molecular alignment in DNA aggregates are shown to be affected by the patterns of ion binding.
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24
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Abstract
Water distributions around phosphate groups in 59 B-, A-, and Z-DNA crystal structures were analyzed. It is shown that the waters are concentrated in six hydration sites per phosphate and that the positions and occupancies of these sites are dependent on the conformation and type of nucleotide. The patterns of hydration that are characteristic of the backbone of the three DNA helical types can be attributed in part to the interactions of these hydration sites.
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Affiliation(s)
- B Schneider
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic
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25
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Kim JS, Lee SA, Carter BJ, Rupprecht A. Stabilization of the B conformation in unoriented films of calf thymus DNA by NaCl: a Raman and IR study. Biopolymers 1997; 41:233-8. [PMID: 9004554 DOI: 10.1002/(sici)1097-0282(199702)41:2<233::aid-bip9>3.0.co;2-u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Unoriented films of calf thymus NaDNA with either 3.0 or 5.0 NaCl per base pair were prepared by dehydrating unstressed gels. These films were studied by Raman and ir spectroscopy. The 5.0 samples showed very strong vibrational modes characteristic of the B conformation at relative humidities (RH) as low as 30%, indicating that those samples were entirely in the B conformation. The 3.0 samples showed weaker features: some of the DNA in these samples were in the B conformation at 80% RH while the DNA is essentially in a disordered phase at 30% RH.
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Affiliation(s)
- J S Kim
- Department of Physics and Astronomy, University of Toledo, OH 43606, USA
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26
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Marlowe RL, Lukan AM, Lee SA, Anthony L, Chandrasekaran R, Rupprecht A. Differential scanning calorimetric and X-ray study of the binding of the water of primary hydration to calf-thymus DNA. J Biomol Struct Dyn 1996; 14:373-9. [PMID: 9016414 DOI: 10.1080/07391102.1996.10508132] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Differential scanning calorimetry has been used to study the thermal properties of hydrated films of calf-thymus Na-, K- and CsDNA between 20 and 320 degrees C. A broad endothermic transition near 75 degrees C and a sharp exothermic transition near 240 degrees C are observed. The broad transition is due to the dehydration of the DNA, while the exothermic transition is due to pyrolysis of the sample. the peak temperatures of both transitions increase as the scan rate is increased. Based on a Kissinger analysis, the net activation energy for the desorption of the primary water of hydration is about 0.6 eV while that for the pyrolysis is about 1.9 eV. X-ray diffraction patterns suggest that heating the DNA films to 180 degrees C once does not, but thrice does, destroy their structural ordering.
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Affiliation(s)
- R L Marlowe
- Department of Physics & Astronomy, University of Tennessee at Chattanooga 37403, USA
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27
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Szabó A, Shi B, Lee SA, Rupprecht A. A Raman study of the time variability for the A-to-B transition in wet-spun films of calf-thymus DNA. J Biomol Struct Dyn 1996; 13:1029-33. [PMID: 8832385 DOI: 10.1080/07391102.1996.10508917] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The time evolution of the A-to-B transition has been monitored by Raman spectroscopy and found to vary significantly for different samples. Though all samples were prepared in the identical fashion, some samples completed the transition on the time scale of several hours while other samples took days. The shortest time required for the A conformation to disappear was about 2 hours, as determined by the disappearance of the A-form Raman band at 807 cm-1. For these fastest transforming samples, the B-form Raman band at 835 cm-1 was clearly evident after about 5 hours. These data are consistent with the hypothesis that the A conformation of DNA is stabilized by intermolecular interactions.
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Affiliation(s)
- A Szabó
- Department of Physics & Astronomy, University of Toledo, OH 43606, USA
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28
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Lee SA, Vansteenberg ML, Lavalle N, Rupprecht A, Song Z. Electronic and optical properties of wet-spun films of Li- and Na-hyaluronate. Biopolymers 1994. [DOI: 10.1002/bip.360341112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Adams PJ, VanSteenberg ML, Lee SA, Rupprecht A. Optical properties of CsDNA films as a function of hydration. J Biomol Struct Dyn 1994; 11:1277-86. [PMID: 7946074 DOI: 10.1080/07391102.1994.10508068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The refractive indices of wet-spun films of CsDNA have been measured for light polarized parallel and perpendicular to the helical axis as a function of relative humidity (RH). These data have been combined with previously published data (Biopolymers 30 (1990) 877-887) for the volume per base pair and water content as a function of RH in order to extract the optical polarizabilities. This work was motivated by the study of Weidlich et al. (Biopolymers 26 (1987) 439-453) who reported a approximately 35% increase at the A-to-B transition in the parallel and perpendicular polarizabilities of NaDNA. In contrast, a much smaller increase in the polarizabilities of CsDNA is found near the A-to-B transition: approximately 12% for the perpendicular direction and < or = 4% for the parallel direction.
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Affiliation(s)
- P J Adams
- Department of Physics and Astronomy, University of Toledo, OH 43606
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30
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Schultz J, Rupprecht A, Song Z, Piskur J, Nordenskiöld L, Lahajnar G. A mechanochemical study of MgDNA fibers in ethanol-water solutions. Biophys J 1994; 66:810-9. [PMID: 8011913 PMCID: PMC1275779 DOI: 10.1016/s0006-3495(94)80857-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Highly oriented calf-thymus MgDNA fibers, prepared by a wet spinning method, were studied with a simple mechanochemical set-up. The relative fiber length, L/Lo, was measured with the fibers submerged in ethanol-water solutions. In one type of experiment L/Lo was measured as a function of ethanol concentration at room temperature. No substantial decrease in L/Lo with increasing ethanol concentration was observed, indicating that MgDNA fibers stay in the B form even when the water activity is very low. For low ethanol concentrations the fiber structure is stable and does not dissolve even at very high water activities. In a second type of experiment, the heat-induced helix-coil transition was manifested by a marked contraction of the fibers. The transition temperature decreases linearly with increasing ethanol concentration between 52 and 68% ethanol. At higher ethanol concentrations the helix-coil transition temperature increases due to strong aggregation within the DNA fibers, and above 77% ethanol the fibers do not contract at all, not even at the upper temperature limit of the experiments, approximately 80 degrees C. This behavior is discussed with reference to dried DNA and the P form of DNA. The helix-coil transition temperature of the MgDNA fibers in 70% ethanol does not show any dependence on the MgCl2 concentration. It is shown that the Poisson-Boltzmann cylindrical cell model can account qualitatively for this lack of salt dependence.
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Affiliation(s)
- J Schultz
- Division of Physical Chemistry, Arrhenius Laboratory, University of Stockholm, Sweden
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31
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Szabó A, Wang Y, Lee SA, Simon HJ, Rupprecht A. Optical third harmonic generation study of the hydration of DNA films. Biophys J 1993; 65:2656-60. [PMID: 8312499 PMCID: PMC1226005 DOI: 10.1016/s0006-3495(93)81307-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Optical third harmonic generation (THG) has been observed for the first time from DNA films. The THG signal is observed from NaDNA films exposed to relative humidities (RHs) between 0% and 98%. A strong enhancement (approximately 5x) of the THG signal from NaDNA is observed at 84% RH; no enhancement is observed for RbDNA. The most likely mechanism for such an enhancement is an increased coherence length. A model calculation using estimates of the refractive indices at both the fundamental and third harmonic frequencies supports this interpretation. The observed THG signal has the same polarization as the incident (fundamental) light. For the A conformation, the THG signal polarized perpendicular to the helical axis is approximately twice as strong as the signal polarized parallel to the helical axis. No such anisotropy is observed for either the disordered conformation (below about 50% RH) or the B conformation (above 92% RH).
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Affiliation(s)
- A Szabó
- Department of Physics & Astronomy, University of Toledo, Ohio 43606-3390
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32
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Schneider B, Cohen DM, Schleifer L, Srinivasan AR, Olson WK, Berman HM. A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. Biophys J 1993; 65:2291-303. [PMID: 8312469 PMCID: PMC1225971 DOI: 10.1016/s0006-3495(93)81306-7] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A new method to analyze the distribution of water molecules around the bases in DNA is presented. This method relies on the notion of a "hydrated building block," which represents the joint observed hydration around all bases of a particular type, in structures of a particular conformation type. The hydrated building blocks were constructed using atomic coordinates from 40 structures contained in the Nucleic Acid Database. Pseudoelectron densities were calculated for water molecules in each hydrated building block using standard crystallographic procedures. The electron densities were fitted to obtain "average building blocks," which represent bases with waters only at average or probable positions. Both types of building blocks were used to construct models of hydrated DNA oligomers. The essential features of the solvent structure around d(CGCGAATTCGCG)2 in the B form and d(CGCGCG)2 in the Z form were reproduced.
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Affiliation(s)
- B Schneider
- Department of Chemistry, Rutgers University, New Brunswick, New Jersey 08903
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33
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K. Mukherjea-(Nayak) K, Bhattacharyya R. Binding mode and conformational status of DNA via interaction with [Cu3 (ATP) 2· 6H2O]2−: Spectroscopic and thermal denaturation studies. J Inorg Biochem 1993. [DOI: 10.1016/0162-0134(93)85620-n] [Citation(s) in RCA: 2] [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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34
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Lee SA, Sclavi B, Powell JW, Williamson W, Rupprecht A. Vibrational dynamics of wet-spun films of the NaDNA-netropsin complex: A Raman and infrared study. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 48:2240-2245. [PMID: 9960843 DOI: 10.1103/physreve.48.2240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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35
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Lee SA, Flowers MR, Oliver WF, Rupprecht A, Lindsay SM. Brillouin-scattering study of hyaluronic acid: Dynamic coupling with the water of hydration and phase transitions. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1993; 47:677-683. [PMID: 9960043 DOI: 10.1103/physreve.47.677] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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36
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Schultz J, Nordenskiöld L, Rupprecht A. A study of the quadrupolar NMR splittings of 7Li+, 23Na+, and 133Cs+ counterions in macroscopically oriented DNA fibers. Biopolymers 1992; 32:1631-42. [PMID: 1472648 DOI: 10.1002/bip.360321206] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The hydration and temperature dependencies of the 23Na+, 133Cs+, and 7Li+ quadrupolar splitting have been determined in hydrated, macroscopically oriented DNA fibers. At low water contents the quadrupolar splitting is found to decrease as the water content increases, regardless of counterion, while at high water contents the hydration dependence is reversed. The 23Na+ and 133Cs+ quadrupolar splittings decrease as the temperature increases, while the 7Li+ splitting shows the opposite behavior. At high water contents the 23Na+ and 133Cs+ splittings decrease, and then, after passing zero splitting, increase as the temperature increases. The interpretation of the temperature dependence is discussed in terms of a two-site model (free and bound ions) and a three-site model (free ions and specifically or nonspecifically bound ions). It is suggested that a three-site model is more consistent with the data for the present system. At high water contents, the temperature dependence of the 7Li+ splitting vanishes, indicating counterion condensation. The behavior of the 7Li+ splitting is confirmed by measurements on DNA fibers in equilibrium with a C2H5OD-D2O-LiCl solution. The salt dependence in this system is weak. The counterion quadrupolar splitting is seen to be very sensitive to structural transitions in double-helical DNA.
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Affiliation(s)
- J Schultz
- Division of Physical Chemistry, Arrhenius Laboratory, University of Stockholm, Sweden
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37
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Tajmir-Riahi HA, Messaoudi S. The effects of monovalent cations Li+, Na+, K+, NH4+, Rb+ and Cs+ on the solid and solution structures of the nucleic acid components. Metal ion binding and sugar conformation. J Biomol Struct Dyn 1992; 10:345-65. [PMID: 1334674 DOI: 10.1080/07391102.1992.10508652] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The interactions of the monovalent ions Li+, Na+, K+, NH4+, Rb+ and Cs+ with adenosine-5'-monophosphoric acid (H2-AMP), guanosine-5'-monophosphoric acid (H2-GMP) and deoxyguanosine-5'-monophosphoric acid (H2-dGMP) were investigated in aqueous solution at physiological pH. The crystalline salts M2-nucleotide.nH2O, where M = Li+, Na+, K+ NH4+, Rb+ and Cs+, nucleotide = AMP, GMP and dGMP anions and n = 2-4 were isolated and characterized by Fourier Transform infrared (FTIR) and 1H-NMR spectroscopy. Spectroscopic evidence showed that these ions are in the form of M(H2O)n+ with no direct metal-nucleotide interaction, in aqueous solution. In the solid state, Li+ ions bind to the base N-7 site and the phosphate group (inner-sphere), while the NH4+ cations are in the vicinity of the N-7 position and the phosphate group, through hydrogen bonding systems. The Na-nucleotides and K-nucleotides are structurally similar. The Na+ ions bind to the phosphate group of the AMP through metal hydration shell (outer-sphere), whereas in the Na2-GMP, the hydrated metal ions bind to the base N-7 or the ribose hydroxyl groups (inner-sphere). The Na2-dGMP contains hydrated metal-carbonyl and metal-phosphate bindings (inner-sphere). The Rb+ and Cs+ ions are directly bonded to the phosphate groups and indirectly to the base moieties (via H2O). The ribose moiety shows C2'-endo/anti conformation for the free AMP acid and its alkali metal ion salts. In the free GMP acid, the ribose ring exhibits C3'-endo/anti conformer, while a C2'-endo/anti sugar pucker was found in the Na2-GMP and K2-GMP salts and a C3'-endo/anti conformation for the Li+, NH4+, Rb+ and Cs+ salts. The deoxyribose has C3'-endo/anti conformation in the free dGMP acid and O4'-endo/anti in the Na2-dGMP, K2-dGMP and a C3'-endo/anti for the Li+, NH4+, Rb+ and Cs+ salts. An equilibrium mixture of the C2'-endo/anti and C3'-endo/anti sugar puckers was found for these metal-nucleotide salts in aqueous solution.
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Affiliation(s)
- H A Tajmir-Riahi
- Centre de Recherche en Photobiophysique, Université du Québec à Trois-Riviéres, Canada
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38
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Flowers MR, Marlow RL, Lee SA, Lavalle N, Rupprecht A. Optical and physical properties of wet-spun films of Na-hyaluronate. Evidence of a phase transition. Biophys J 1992; 63:323-6. [PMID: 1420880 PMCID: PMC1262155 DOI: 10.1016/s0006-3495(92)81604-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The refractive indices, water content, and volume of wet-spun films of Na-hyaluronate have been measured as a function of relative humidity (rh). These data are used with the Lorentz-Lorenz formula to determine the optical polarizabilities of Na-hyaluronate parallel and perpendicular to the helical axis. The analysis reveals a drop in the optical polarizabilities of approximately 20% between 80 and 88% rh, indicating a phase transition.
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Affiliation(s)
- M R Flowers
- Department of Physics and Astronomy, University of Toledo, Ohio 43606
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39
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Saxena VK. Effect of counterions on the spectrum of dissolved DNA polymers. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1992; 45:7610-7620. [PMID: 9906833 DOI: 10.1103/physreva.45.7610] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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40
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Lee SA, Oliver WF, Rupprecht A, Song Z, Lindsay SM. Observation of a phase transition in wet-spun films of Na-hyaluronate. Biopolymers 1992; 32:303-6. [PMID: 1581549 DOI: 10.1002/bip.360320310] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- S A Lee
- Department of Physics and Astronomy, University of Toledo, Ohio 43606
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41
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42
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Lavalle N, Lee SA, Flox LS. Lattice-dynamical model of crystalline DNA: Intermolecular bonds and the A to B transition. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1991; 43:3126-3130. [PMID: 9905381 DOI: 10.1103/physreva.43.3126] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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