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Biedermannová L, Černý J, Malý M, Nekardová M, Schneider B. Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks. Acta Crystallogr D Struct Biol 2022; 78:1032-1045. [PMID: 35916227 PMCID: PMC9344474 DOI: 10.1107/s2059798322006234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022] Open
Abstract
Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 Å) and correctly reproduced the known features of DNA hydration, for example the `spine of hydration' in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.
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Affiliation(s)
- Lada Biedermannová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Michal Malý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Michaela Nekardová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
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The Seed and the Metabolism Regulation. BIOLOGY 2022; 11:biology11020168. [PMID: 35205035 PMCID: PMC8869448 DOI: 10.3390/biology11020168] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 12/14/2022]
Abstract
Simple Summary Seeds are the reproductive units of higher plants. They have a significant place in agriculture and plant diversity maintenance. Because they are dehydrated, they can remain viable in the environment for centuries. This review explores the dry seed as a metabolically inactive organism, but well organized to protect its components and enter intensive repair to restore metabolic activities upon imbibition for the completion of germination. Metabolism regulation is also critical for the most important seed traits, dormancy, and ageing recovery capacity. Abstract The seed represents a critical stage in the life cycle of flowering plants. It corresponds to a dry structure carrying the plant embryo in dormant or quiescent state. Orthodox seeds possess a very low water content, preventing biochemical reactions, especially respiration. If the desiccation of living organisms leads to a loss of homeostasis, structure, and metabolism, the seeds go through it successfully thanks to their structure, cellular organization, and growth regulation. Seeds set up a certain number of sophisticated molecules to protect valuable macromolecules or organelles from dehydration/rehydration cycles. Moreover, dormancy takes place in a coordinated process with environmental cues in order to ensure embryo development at the most appropriate conditions for the establishment of the new plant. Moreover, repair processes are programmed to be ready to operate to maximize germination success and seed longevity. This review focuses on the physiology of the seed as related to hydration forces, respiration, and biochemical reactions in the transition from thermodynamically undefined dry state to self-sustained living system. Such processes are of importance for basic knowledge of the regulation of metabolism of living organisms, but also for the control of germination in the context of climate change due to global warming.
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Paston SV, Polyanichko AM, Shulenina OV, Osinnikova DN. A Study of the DNA Structure in Films Using FTIR Spectroscopy. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920060159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Rakowska PW, Kogut M, Czub J, Stangret J. Effect of osmolytes of different type on DNA behavior in aqueous solution. Experimental and theoretical studies. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Mohamed HS, Dahy AA, Hassan GS, Eid SSM, Mahfouz RM. Quantum-chemical investigation on 5-fluorouracil anticancer drug. Struct Chem 2017. [DOI: 10.1007/s11224-017-0913-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Samanta S, Raghunathan D, Mukherjee S. Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study. J Mol Graph Model 2016; 66:9-19. [PMID: 27017424 DOI: 10.1016/j.jmgm.2016.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 01/25/2023]
Abstract
DNA within the living cells experiences a diverse range of temperature, ranging from freezing condition to hot spring water. How the structure, the mechanical properties of DNA, and the solvation dynamics around DNA changes with the temperature is important to understand the functionality of DNA under those acute temperature conditions. In that notion, we have carried out molecular dynamics simulations of a DNA oligomer, containing TATA-box sequence for three different temperatures (250K, 300K and 350K). We observed that the structure of the DNA, in terms of backbone torsion angles, sugar pucker, base pair parameters, and base pair step parameters, did not show any unusual properties within the studied range of temperatures, but significant structural alteration was noticed between BI and BII forms at higher temperature. As expected, the flexibility of the DNA, in terms of the torsional rigidity and the bending rigidity is highly temperature dependent, confirming that flexibility increases with increase in temperature. Additionally, the groove widths of the studied DNA showed temperature sensitivity, specifically, the major groove width decreases and the minor groove width increases, respectively, with the increase in temperature. We observed that at higher temperature, water around both the major and the minor groove of the DNA is less structured. However, the water dynamics around the minor groove of the DNA is more restricted as compared to the water around the major groove throughout the studied range of temperatures, without any anomalous behavior.
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Affiliation(s)
- Sudipta Samanta
- BioSystems and Micromechanics IRG (BioSyM), Singapore-MIT Alliance for Research and Technology (SMART), 1 Create Way, 117543, Republic of Singapore; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Devanathan Raghunathan
- Prochem Solutions Pte. Ltd., 89C Science Park Drive, The Rutherford, # 04-13, Singapore Science Park 1, 118261, Singapore
| | - Sanchita Mukherjee
- Indian Institute of Science Education and Research, Kolkata, Mohanpur, West Bengal, 741246, India
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Application of differential scanning calorimetry to measure the differential binding of ions, water and protons in the unfolding of DNA molecules. Biochim Biophys Acta Gen Subj 2015; 1860:990-998. [PMID: 26450631 DOI: 10.1016/j.bbagen.2015.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 09/28/2015] [Accepted: 10/01/2015] [Indexed: 11/24/2022]
Abstract
BACKGROUND The overall stability of DNA molecules globally depends on base-pair stacking, base-pairing, polyelectrolyte effect and hydration contributions. In order to understand how they carry out their biological roles, it is essential to have a complete physical description of how the folding of nucleic acids takes place, including their ion and water binding. SCOPE OF REVIEW To investigate the role of ions, water and protons in the stability and melting behavior of DNA structures, we report here an experimental approach i.e., mainly differential scanning calorimetry (DSC), to determine linking numbers: the differential binding of ions (Δnion), water (ΔnW) and protons (ΔnH(+)) in the helix-coil transition of DNA molecules. GENERAL SIGNIFICANCE We use DSC and temperature-dependent UV spectroscopic techniques to measure the differential binding of ions, water, and protons for the unfolding of a variety of DNA molecules: salmon testes DNA (ST-DNA), one dodecamer, one undecamer and one decamer duplexes, nine hairpin loops, and two triplexes. These methods can be applied to any conformational transition of a biomolecule. MAJOR CONCLUSIONS We determined complete thermodynamic profiles, including all three linking numbers, for the unfolding of each molecule. The favorable folding of a DNA helix results from a favorable enthalpy-unfavorable entropy compensation. DSC thermograms and UV melts as a function of salt, osmolyte and proton concentrations yielded releases of ions and water. Therefore, the favorable folding of each DNA molecule results from the formation of base-pair stacks and uptake of both counterions and water molecules. In addition, the triplex with C(+)GC base triplets yielded an uptake of protons. Furthermore, the folding of a DNA duplex is accompanied by a lower uptake of ions and a similar uptake of four water molecules as the DNA helix gets shorter. In addition, the oligomer duplexes and hairpin thermodynamic data suggest ion and water binding depends on the DNA sequence rather than DNA composition.
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Paciaroni A, Orecchini A, Goracci G, Cornicchi E, Petrillo C, Sacchetti F. Glassy Character of DNA Hydration Water. J Phys Chem B 2013; 117:2026-31. [DOI: 10.1021/jp3105437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alessandro Paciaroni
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
- Istituto Officina dei Materiali,
Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
| | - Andrea Orecchini
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
- Istituto Officina dei Materiali,
Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
- Institut Laue Langevin, 6 rue J. Horowitz F-38042 Grenoble, France
| | - Guido Goracci
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
| | - Elena Cornicchi
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
- Istituto Officina dei Materiali,
Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
- Istituto Officina dei Materiali,
Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
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10
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Melting behavior and ligand binding of DNA intramolecular secondary structures. Biophys Chem 2011; 159:162-71. [DOI: 10.1016/j.bpc.2011.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/08/2011] [Accepted: 06/10/2011] [Indexed: 11/23/2022]
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11
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Buckin VA. Hydration of nucleic bases in dilute aqueous solutions. Apparent molar adiabatic and isothermal compressibilities, apparent molar volumes and their temperature slopes at 25 degrees C. Biophys Chem 2008; 29:283-92. [PMID: 17010915 DOI: 10.1016/0301-4622(88)85050-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/1987] [Revised: 11/10/1987] [Accepted: 11/16/1987] [Indexed: 10/18/2022]
Abstract
The concentration increment of the ultrasound velocity has been measured with an accuracy of +/- 0.03 cm/s in dilute aqueous solutions of a variety of nucleic bases and their derivatives in the concentration range 0.5-1.5 mg/g H2O at temperatures of 15-35 degrees C. A new method for the precise measurement of ultrasound velocity in small volumes of liquids has been used. The values of the apparent molar adiabatic compressibilities plus the corresponding temperature slopes, apparent molar volumes with their temperature slopes, and apparent molar isothermal compressibilities at infinite dilution have been obtained. The regularities describing the signs of these values and their dependence on the chemical structure of the solute have been revealed. It is shown that these regularities can be described as a consequence of partial 'normalization' of some of the properties of water around the bases, namely, weaker structural contribution to compressibility, less negative temperature slope of compressibility and less negative structural contribution to the coefficient of thermal expansion of water.
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Affiliation(s)
- V A Buckin
- Institute of Biological Physics, U.S.S.R Academy of Sciences, Pushchino 142292, U.S.S.R
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12
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Brovchenko I, Krukau A, Oleinikova A, Mazur AK. Ion dynamics and water percolation effects in DNA polymorphism. J Am Chem Soc 2007; 130:121-31. [PMID: 18052374 DOI: 10.1021/ja0732882] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The dynamics of ions and water at the surface of DNA are studied by computer simulations in a wide range of hydrations involving the zone of low-hydration polymorphism in DNA. The long-range mobility of ions exhibits a stepwise increase at three distinct hydration levels. The first of them is close to the midpoint of the water percolation transition as well as the midpoint of the transition between A- and B-DNA forms. It coincides with the onset of the dissociation of ion pairs on the DNA surface probably caused by the increase in the water dielectric permittivity due to the appearance of the spanning hydrogen-bonding network. The other two steps are attributed to the formation of percolating water layers on the surface of DNA accompanied by the progressive escape of ions from the DNA surface. The results agree with earlier experimental data and further corroborate the suggested universal mechanism of the low hydration polymorphism in DNA including intraduplex electrostatic condensation close to the water percolation threshold.
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Affiliation(s)
- Ivan Brovchenko
- Physical Chemistry, Technical University of Dortmund, Otto-Hahn-Str. 6, Dortmund, D-44227, Germany
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Brovchenko I, Krukau A, Oleinikova A, Mazur AK. Water Clustering and Percolation in Low Hydration DNA Shells. J Phys Chem B 2007; 111:3258-66. [PMID: 17388475 DOI: 10.1021/jp068776v] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The hydrogen-bonded networks of water at the surface of a model DNA molecule are analyzed. At low hydrations, only small water clusters are attached to the DNA surface, whereas, at high hydrations, it is homogeneously covered by a spanning water network. The spanning water network is formed via a percolation transition at an intermediate hydration number of about 15 water molecules per nucleotide, which is very close to the midpoint of polymorphic transitions between A- and B-forms of the double helix. The percolation transition can occur in both A- and B-DNA hydration shells with nearly identical percolation thresholds. However, the mechanism of the percolation transition in A- and B-DNA is qualitatively different in regard to the roles played by the two opposite grooves of the double helix. Free ions can shift the percolation threshold by preventing some water molecules from hydrogen bond networking. The results corroborate the suggested relationship between water percolation and the low hydration polymorphism in DNA.
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Affiliation(s)
- Ivan Brovchenko
- Physical Chemistry, Dortmund University, Otto-Hahn-Str. 6, Dortmund D-44227, Germany.
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15
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Howell PL, Goodfellow JM. Effect of Initial Positions on the Simulation of Water Networks in Crystal Hydrates. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927028808080955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- P. Lynne Howell
- a Department of Crystallography , Birkbeck College, University of London , Malet Street, London , WC1E 7HX , UK
- b Chemistry Department , MIT , Cambridge , MA , 02139 , USA
| | - Julia M. Goodfellow
- a Department of Crystallography , Birkbeck College, University of London , Malet Street, London , WC1E 7HX , UK
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17
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Brovchenko I, Krukau A, Oleinikova A, Mazur AK. Water percolation governs polymorphic transitions and conductivity of DNA. PHYSICAL REVIEW LETTERS 2006; 97:137801. [PMID: 17026075 DOI: 10.1103/physrevlett.97.137801] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Indexed: 05/12/2023]
Abstract
We report on the first computer simulation studies of the percolation transition of water at the surface of the DNA double helix. With increased hydration, the ensemble of small clusters merges into a spanning water network via a quasi-two-dimensional percolation transition. This transition occurs strikingly close to the hydration level where the B form of DNA becomes stable in experiment. Formation of spanning water networks results in sigmoidlike acceleration of long-range ion transport in good agreement with experiment.
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Affiliation(s)
- Ivan Brovchenko
- Physical Chemistry, Dortmund University, Otto-Hahn-Strasse 6, Dortmund, D-44227, Germany.
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18
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Kaur H, Arora A, Wengel J, Maiti S. Thermodynamic, counterion, and hydration effects for the incorporation of locked nucleic acid nucleotides into DNA duplexes. Biochemistry 2006; 45:7347-55. [PMID: 16752924 DOI: 10.1021/bi060307w] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A locked nucleic acid (LNA) monomer is a conformationally restricted nucleotide analogue with an extra 2'-O, 4'-C-methylene bridge added to the ribose ring. LNA-modified oligonucleotides are known to exhibit enhanced hybridization affinity toward complementary DNA and RNA. In this work, we have evaluated the hybridization thermodynamics of a series of LNA-substituted DNA octamers, modified to various extents by one to three LNA substitutions, introduced at either adenine (5'-AGCACCAG) or thymine (5'-TGCTCCTG) nucleotides. To understand the energetics, counterion effects, and the hydration contribution of the incorporation of LNA modification, a combination of spectroscopic and calorimetric techniques was used. The CD spectra of the corresponding duplexes showed that the modified duplexes adopt an A-type conformation. UV and DSC melting studies revealed that each type of duplex unfolds in a two-state transition. A complete thermodynamic profile at 5 degrees C indicated that the net effect of modification on thermodynamic parameters might be positional and that the neighboring bases flanking the modification might influence the favorable formation of the modified duplexes. Furthermore, relative to the formation of the unmodified reference duplexes, the formation of modified duplexes is accompanied by a higher uptake of counterions and a lower uptake of water molecules.
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Affiliation(s)
- Harleen Kaur
- Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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Cooper RL, Lee SA. Differential Scanning Calorimetric Study of the Binding of the Water of Hydration to Deoxyadenosine. J Biomol Struct Dyn 2004; 22:375-80. [PMID: 15473711 DOI: 10.1080/07391102.2004.10507009] [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
Differential scanning calorimetry was used to study the water of hydration in powder samples of deoxyadenosine (dA), a naturally occurring nucleoside. Though water of crystallization is present in samples which have not undergone heat treatment previously, dA was found to rehydrate at room temperature only at relative humidities (RHs) of 88% and higher. Rehydrated samples exhibited a single endothermic peak. At 95% RH, its activation energy was 1.61 +/- 0.06 eV and had an enthalpy change of 190 +/- 30 J/g. Experiments between 88 and 95% RH revealed that the energies are independent of RH, to within experimental error. This range of humidity corresponds to secondary hydration in DNA.
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Affiliation(s)
- R L Cooper
- Department of Physics and Astronomy, University of Toledo, 2801 W. Bancroft Street, Toledo, OH 43606, USA
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Lee SL, Debenedetti PG, Errington JR, Pethica BA, Moore DJ. A Calorimetric and Spectroscopic Study of DNA at Low Hydration. J Phys Chem B 2004. [DOI: 10.1021/jp0311409] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sau Lawrence Lee
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Pablo G. Debenedetti
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Jeffrey R. Errington
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - Brian A. Pethica
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
| | - David J. Moore
- Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, Department of Chemical Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260, Unilever Research US, 45 River Road, Edgewater, New Jersey 07020
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21
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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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Cavanaugh D, Lee SA. Differential scanning calorimetric study of the binding of the primary water of hydration to nucleosides. J Biomol Struct Dyn 2002; 19:709-14. [PMID: 11843632 DOI: 10.1080/07391102.2002.10506777] [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: 10/28/2022]
Abstract
Differential scanning calorimetry was used to study the water of hydration of all of the nucleosides at 59% relative humidity. Hydration was observed in pristine samples of guanosine, (rG), deoxyguanosine, (dG), and deoxyadenosine, (dA). Two inequivalent water sites were observed in dG and one site in rG. Re-hydration was observed in rG and dG, but not in dA. The activation energies for rG were 0.697 +/- 0.051 eV and 0.683 plus minus 0.090 eV for pristine and cycled samples respectively. dG had activation energies of 0.726 +/- 0.026 eV and 0.997 +/- 0.034 eV for the first and second peaks in the pristine samples while the activation energy for cycled dG was 0.671 +/- 0.133 eV.
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Affiliation(s)
- D Cavanaugh
- Department of Physics and Astronomy, University of Toledo, Toledo, OH 43606, USA
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Mentré P, Hui Bon Hoa G. Effects of high hydrostatic pressures on living cells: a consequence of the properties of macromolecules and macromolecule-associated water. INTERNATIONAL REVIEW OF CYTOLOGY 2001; 201:1-84. [PMID: 11057830 DOI: 10.1016/s0074-7696(01)01001-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sixty percent of the Earth's biomass is found in the sea, at depths greater than 1000 m, i.e., at hydrostatic pressures higher than 100 atm. Still more surprising is the fact that living cells can reversibly withstand pressure shifts of 1000 atm. One explanation lies in the properties of cellular water. Water forms a very thin film around macromolecules, with a heterogeneous structure that is an image of the heterogeneity of the macromolecular surface. The density of water in contact with macromolecules reflects the physical properties of their different domains. Therefore, any macromolecular shape variations involving the reorganization of water and concomitant density changes are sensitive to pressure (Le Chatelier's principle). Most of the pressure-induced changes to macromolecules are reversible up to 2000 atm. Both the effects of pressure shifts on living cells and the characteristics of pressure-adapted species are opening new perspectives on fundamental problems such as regulation and adaptation.
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Affiliation(s)
- P Mentré
- Station INRA 806, Institut de Biologie Physico-Chimique, Paris, France
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Debije MG, Strickler MD, Bernhard WA. On the efficiency of hole and electron transfer from the hydration layer to DNA: An EPR study of crystalline DNA X-irradiated at 4 K. Radiat Res 2000; 154:163-70. [PMID: 10931688 PMCID: PMC2614480 DOI: 10.1667/0033-7587(2000)154[0163:oteoha]2.0.co;2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The aim of this project was to gain an improved understanding of how the efficiency of hole and electron transfer from the solvation layer to DNA decreases as a function of distance from DNA. The packing of DNA in crystals of known structure makes it possible to calculate the degree of DNA hydration with a precision that is significantly greater than that achievable for amorphous samples. Previous work on oligodeoxynucleotide crystals has demonstrated that the efficiency of free radical trapping by DNA exposed to ionizing radiation at 4 K is relatively insensitive to base sequence, conformation, counterion, or base stacking continuity. Having eliminated these confounding variables, it is now possible to ascertain the degree of radical transfer that occurs from ionized water as a function of DNA hydration (Gamma, in mol water/mol nucleotide). EPR is used to measure the hydroxyl radical concentration in crystals irradiated at 4 K. From a lack of hydroxyl radicals trapped in the inner hydration mantle, we determine that hole transfer to DNA is complete for water molecules located within 8 A. This corresponds to Gamma = 9-11 and indicates that hole transfer is 100% (as efficient as direct ionization of DNA) for water molecules adjacent to DNA. Beyond approximately 8 A (Gamma > 10), hydroxyl radicals are observed; thus deprotonation of the water radical cation is seen to compete with hole transfer to DNA as soon as one water intervenes between the ionized water and DNA. The boundary for 0% hole transfer is projected to occur somewhere between 15 and 20 waters per nucleotide. Electron transfer, on the other hand, is 100% efficient across the entire range studied, 4.2 </= Gamma </= 15.6.
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Affiliation(s)
- M G Debije
- Department of Biochemistry/Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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25
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Kankia BI, Marky LA. DNA, RNA, and DNA/RNA Oligomer Duplexes: A Comparative Study of Their Stability, Heat, Hydration, and Mg2+ Binding Properties. J Phys Chem B 1999. [DOI: 10.1021/jp991614x] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Besik I. Kankia
- Departments of Pharmaceutical Sciences, Biochemistry & Molecular Biology, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Luis A. Marky
- Departments of Pharmaceutical Sciences, Biochemistry & Molecular Biology, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025
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26
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Feig M, Pettitt BM. Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation. J Mol Biol 1999; 286:1075-95. [PMID: 10047483 DOI: 10.1006/jmbi.1998.2486] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hydration around the DNA fragment d(C5T5).(A5G5) is presented from two molecular dynamics simulations of 10 and 12 ns total simulation time. The DNA has been simulated as a flexible molecule with both the CHARMM and AMBER force fields in explicit solvent including counterions and 0.8 M additional NaCl salt. From the previous analysis of the DNA structure B-DNA conformations were found with the AMBER force-field and A-DNA conformations with CHARMM parameters. High-resolution hydration patterns are compared between the two conformations and between C.G and T.A base-pairs from the homopolymeric parts of the simulated sequence. Crystallographic results from a statistical analysis of hydration sites around DNA crystal structures compare very well with the simulation results. Differences between the crystal sites and our data are explained by variations in conformation, sequence, and limitations in the resolution of water sites by crystal diffraction. Hydration layers are defined from radial distribution functions and compared with experimental results. Excellent agreement is found when the measured experimental quantities are compared with the equivalent distribution of water molecules in the first hydration shell. The number of water molecules bound to DNA was found smaller around T.A base-pairs and around A-DNA as compared to B-DNA. This is partially offset by a larger number of water molecules in hydrophobic contact with DNA around T.A base-pairs and around A-DNA. The numbers of water molecules in minor and major grooves have been correlated with helical roll, twist, and inclination angles. The data more fully explain the observed B-->A transition at low humidity.
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Affiliation(s)
- M Feig
- Department of Chemistry and Institute for Molecular Design, University of Houston, 4800 Calhoun, Houston, TX, 77204-5641, USA
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27
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Current Trends in Modeling Interactions of DNA Fragments with Polar Solvents. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1380-7323(99)80080-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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28
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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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29
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Rousseau V, Pouliquen D, Darcel F, Jallet P, Le Jeune JJ. Glial tumoral proliferation induces changes in the state and physical properties of water during ENU-induction of brain tumors in rats. J Neurooncol 1998; 37:35-43. [PMID: 9525836 DOI: 10.1023/a:1005844521045] [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: 02/06/2023]
Abstract
Modifications of water state were analyzed during ethylnitrosourea-induction of brain tumor in rats. Four different steps were identified in the cancerization process according to NMR and histological findings. Two analogies were observed in the pattern of bound' water at decreasing temperatures: first the pattern was similar in tumor area and white matter, second the pattern was similar in the same area of normal brain tissue and cortical gray matter. This phenomenon, which corroborates previous reports on liver cancerization, points out that pathological proliferation of glial cells, and their progressive organization into multiple layers, is accompanied by a transformation of water properties at the cellular level.
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Affiliation(s)
- V Rousseau
- Laboratoire de Biophysique, Faculté de Médecine, Angers, France
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30
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Lee I, Bai C, Wang C, Wang X. Computational analysis of triplex formation of oligonucleotides: protonated and 5-methylated py-pu-py motif. ACTA ACUST UNITED AC 1997. [DOI: 10.1007/bf02876401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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31
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Hummer G, García AE, Soumpasis DM. Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes. Biophys J 1995; 68:1639-52. [PMID: 7542034 PMCID: PMC1282065 DOI: 10.1016/s0006-3495(95)80381-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A computationally efficient method to describe the organization of water around solvated biomolecules is presented. It is based on a statistical mechanical expression for the water-density distribution in terms of particle correlation functions. The method is applied to analyze the hydration of small nucleic acid molecules in the crystal environment, for which high-resolution x-ray crystal structures have been reported. Results for RNA [r(ApU).r(ApU)] and DNA [d(CpG).d(CpG) in Z form and with parallel strand orientation] and for DNA-drug complexes [d(CpG).d(CpG) with the drug proflavine intercalated] are described. A detailed comparison of theoretical and experimental data shows positional agreement for the experimentally observed water sites. The presented method can be used for refinement of the water structure in x-ray crystallography, hydration analysis of nuclear magnetic resonance structures, and theoretical modeling of biological macromolecules such as molecular docking studies. The speed of the computations allows hydration analyses of molecules of almost arbitrary size (tRNA, protein-nucleic acid complexes, etc.) in the crystal environment and in aqueous solution.
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Affiliation(s)
- G Hummer
- Los Alamos National Laboratory, New Mexico 87545, USA
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32
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Phole W, Bohl M. Infrared spectroscopic data favor a global mode hydration in determining DNA conformation by water activity. ACTA ACUST UNITED AC 1995. [DOI: 10.1002/bspy.350010203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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33
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Hummer G, Soumpasis DM. Statistical mechanical treatment of the structural hydration of biological macromolecules: Results for B-DNA. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 50:5085-5095. [PMID: 9962594 DOI: 10.1103/physreve.50.5085] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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34
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Sugawara Y, Iimura Y, Iwasaki H, Urabe H, Saito H. Reversible crystal transition of guanosine between the dihydrate and anhydrous states coupled with adsorption-desorption process. J Biomol Struct Dyn 1994; 11:721-9. [PMID: 8204210 DOI: 10.1080/07391102.1994.10508028] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Relative humidity induces the reversible crystal transition of guanosine between the dihydrate and the anhydrous state. The characteristics of the transition was investigated by means of X-ray powder diffraction analysis and high-resolution solid-state 13C NMR spectroscopy. Adsorption-desorption hysteresis was observed. Guanosine dihydrate (the H-state) which is crystallized from an aqueous solution rapidly loses crystal water below 10% relative humidity (rh), and is anhydrous at 0% rh (the A-state). The crystals gradually recover the H-state at approximate 20% rh. In the adsorption process between 10-20% rh, there exists one intermediate state, M, with 1.2-1.3 moles water per mole guanosine. The lattice of the M-state was determined to be orthorhombic with the cell parameters of a = 16.248(1), b = 11.603(1), and c = 13.643(2) A. The base-stacking structure is retained throughout the transition. On the other hand, conformational changes of the riboses and break of the hydrogen-bonding network between the bases would be induced in the A-state in conformity with lack of crystal water.
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Affiliation(s)
- Y Sugawara
- Institute of Physical and Chemical Research (RIKEN), Saitama, Japan
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35
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Rentzeperis D, Kupke DW, Marky LA. Volume changes correlate with entropies and enthalpies in the formation of nucleic acid homoduplexes: differential hydration of A and B conformations. Biopolymers 1993; 33:117-25. [PMID: 8427928 DOI: 10.1002/bip.360330111] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have used a combination of densimetric, calorimetric, and uv absorption techniques to obtain a complete thermodynamic characterization for the formation of nucleic acid homoduplexes of known sequence and conformation. The volume change delta V accompanying the formation of four duplexes was interpreted to reflect changes in hydration based on the electrostriction phenomenon. In 10 mM sodium phosphate buffer at pH 7, the magnitude of the measured delta V's ranged from -2.0 to +7.2 ml/mol base pair and followed the order of poly(rA).poly(dT) approximately poly(dA).poly(dT) < poly(rA).poly(dU) approximately poly(rA).poly(rU). Inclusion of 100 mM NaCl in the same buffer gave the range of -17.4 to -2.3 mL/mol base pair and the following order: poly(dA).poly(dT) < poly(rA).poly(dT) < poly(rA).poly(rU) approximately poly(rA).polyr(dU). Standard thermodynamic profiles of forming these duplexes from their corresponding complementary single strands indicated similar free energies that resulted from the compensation of favorable enthalpies with unfavorable entropies along with a similar counterion uptake at both ionic strengths. The differences in these compensating effects of entropy and enthalpy correlated very well with the volume change measurements in a manner suggesting that the homoduplexes in the B conformation are more hydrated than are those in the A conformation. Moreover, the increased thermal stability of these homoduplexes resulted from an increase in the salt concentration corresponding to larger hydration levels as reflected by the delta V results.
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Affiliation(s)
- D Rentzeperis
- Department of Chemistry, New York University, New York 10003
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36
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Abstract
We present a systematic analysis of water structure around nucleic acid bases. We have examined 28 crystal structures of oligonucleotides, and have studied the patterns of water around the four bases, guanine, cytosine, adenine, and thymine. The geometries of water positions were calculated up to 4.00 A from base atoms. We have found conformation-dependent differences in both the geometry and extent of hydration of the bases.
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Affiliation(s)
- B Schneider
- Department of Chemistry, Rutgers, State University of New Jersey, New Brunswick 08903
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37
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Eisenhaber F, Mannik JH, Tumanyan VG. Structural principles of B-DNA grooves hydration in fibers as revealed by Monte Carlo simulations and X-ray diffraction. Biopolymers 1990; 29:1453-64. [PMID: 2361155 DOI: 10.1002/bip.360291012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Being interested in possible effects of sequence-dependent hydration of B-DNA with mixed sequence in fibers, we performed a series of Monte Carlo calculations of hydration of polydeoxyribonucleotides in B form, considering all sequences with dinucleotide repeat. The computational results allow the ten base-stacking types to be classified in accordance with their primary hydration in the minor groove. As a rule, the minor groove is occupied by two water molecules per base pair in the depth of the groove, which are located nearly midway between the planes of successive base pairs and symmetrically according to the dyad there. The primary hydration of the major groove depends on the type of the given base pair. The coordinates of 3 water molecules per base pair in the depth of the major groove are determined by the type of this pair together with its position and orientation in the helix, and are practically independent on the adjacent base pairs. A/T-homopolymer tracts do not fit into this hydration pattern; the base pair edges are hydrated autonomously in both grooves. Analysis of the Li-B-DNA x-ray diffraction intensities reveals those two water positions in the minor groove. In the major groove, no electronic density peaks in sufficient distance from the base edges were found, thus confirming the absence of any helical invariance of primary hydration in this region. With the help of the rules proposed in this paper it is possible to position the water molecules of the first hydration shell in the grooves of canonical B-DNA for any given sequence.
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Affiliation(s)
- F Eisenhaber
- Academy of Sciences of the GDR, Central Institute of Molecular Biology, Berlin, GDR
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38
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Subramanian PS, Pitchumani S, Beveridge DL, Berman HM. A Monte Carlo simulation study of the aqueous hydration of r(GpC)2: comparison with crystallographic ordered water sites. Biopolymers 1990; 29:771-83. [PMID: 2383642 DOI: 10.1002/bip.360290411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Monte Carlo computer simulation is described for the dinucleotide duplex rGpC together with 562 water molecules at an environmental density of 1 g/cc in a cubic cell under periodic boundary conditions. Water-water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the nonbonded interactions from the AMBER 3.0 force field. The simulation was subjected to proximity analysis to obtain solute coordinate numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove side, the minor groove side and the sugar-phosphate backbone were examined, and the probabilities of occurrence for one- and two-water bridges in the simulation were enumerated. The results were compared with observations of crystallographic ordered water sites from x-ray diffraction studies on G and C containing small molecules, and in crystal structure determinations of the sodium, calcium, and ammonium salts of rGpC. The calculated results are generally consistent with the observed sites, except for cytosine N4, where a hydration site is predicted yet none observed in rGpC salts, and for guanine N3, which appears in this calculation to compete unfavorably with the adjacent donor site at guanine N2. There is, however, a significant probability of finding a one-water G-N3-W-G-N2 bridge indicated in the simulation. An explanation for the guanine N3 discrepancy in terms of electrostatic potentials is also offered. The calculated one- and two-water bridges in the rGpC hydration complex coincide in a number of cases to those observed in the ordered water structure of the sodium rGpC crystal hydrate.
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Affiliation(s)
- P S Subramanian
- Chemistry Department, Wesleyan University, Middletown, Connecticut 06457
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39
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Marky LA, Kupke DW. Probing the hydration of the minor groove of A.T synthetic DNA polymers by volume and heat changes. Biochemistry 1989; 28:9982-8. [PMID: 2559775 DOI: 10.1021/bi00452a016] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The minor-groove ligand netropsin provides a sensitive probe of the hydration difference between poly(dA).poly(dT) and poly[d(AT)].poly[d(AT)]. We have measured the volume change delta V accompanying binding of netropsin to these polymers, using an improved magnetic suspension densimeter. For poly(dA).poly(dT) we find delta V = +97 mL/mol of bound netropsin at pH 7.0 and 10 mM sodium phosphate buffer. For poly[d(AT)].poly[d(AT)] we find delta V = -16 mL/mol of bound netropsin. This striking differential effect suggests that the poly(dA).poly(dT) duplex compresses more water (or is more extensively hydrated). From our enthalpy and entropy results we estimate the approximately 10 water molecules, immobilized in the minor groove of this system, are displaced by each netropsin bound. The volume increase, however, is substantially larger than can be explained by a simple melting of these immobilized water molecules in the minor groove. A decompression of at least 40 water molecules must attend the complexation to the poly(dA).poly(dT) duplex. This suggests that the conformation change attending the binding of the drug to this polymer duplex causes a further dehydration, whereas no such change in dehydration and configuration for the heteropolymer system is indicated.
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Affiliation(s)
- L A Marky
- Department of Chemistry, New York University, New York 10003
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40
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Buckin VA, Kankiya BI, Kazaryan RL. Hydration of nucleosides in dilute aqueous solutions. Ultrasonic velocity and density measurements. Biophys Chem 1989; 34:211-23. [PMID: 2482087 DOI: 10.1016/0301-4622(89)80060-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The values of the concentration increments of the ultrasound velocity and their temperature slopes, apparent molar volumes, apparent molar expansibilities, apparent molar adiabatic compressibilities and their temperature gradients for 12 nucleosides and their analogs, as well as for ribose and deoxyribose, have been obtained using precision measurements of ultrasound velocity and density. The following hydration parameters for the atomic groups of the nucleosides, reflecting the state of water in the hydration shells of these groups, have been analyzed: (1) the contribution of ribose to the values of the concentration increment of ultrasound velocity A, the apparent molar volumes phi v and apparent molar adiabatic compressibilities phi ks of nucleosides; (2) contributions of the CH3, NH2 and O = ... -H groups of nucleic bases to the A, phi v and phi ks values of nucleosides and free nucleic bases; (3) contributions of the 2'-OH group of ribose to the values of A, phi v and phi ks nucleosides; (4) changes in the A values of nucleosides and free nucleic bases upon their protonation and deprotonation. Data have been obtained on the mutual influence of the atomic groups of nucleosides on their hydration. It is shown that the GC pairs of free deoxynucleosides undergo hydration more vigorously than the AT pairs, which contrasts with the relation of the degree of hydration of the GC and AT pairs of the double helix.
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Affiliation(s)
- V A Buckin
- Institute of Biological Physics, Academy of Sciences of the U.S.S.R., Moscow Region
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41
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Brandes R, Rupprecht A, Kearns DR. Interaction of water with oriented DNA in the A- and B-form conformations. Biophys J 1989; 56:683-91. [PMID: 2554988 PMCID: PMC1280524 DOI: 10.1016/s0006-3495(89)82715-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
High resolution 2H nuclear magnetic resonance (NMR) was used to investigate the interaction of D2O with solid samples of uniaxially oriented Li-DNA (B-form DNA) and Na-DNA (A- and B-form DNA). At low levels of hydration, 0 approximately 4 D2O/nucleotide, the 2H spectra shows a very weak (due to short T2) broad single resonance, suggestive of unrestricted rotational diffusion of the water. At approximately 5 or more D2O/nucleotide, the Li-DNA (B-form) spectra suddenly exhibit a large doublet splitting, characteristic of partially ordered water. With increasing hydration, the general trend is a decrease of this splitting. From our analysis we show that the DNA water structure reorganizes as the DNA is progressively hydrated. The D2O interaction with Na-DNA is rather different than with Li-DNA. Below 10 D2O/nucleotide Na-DNA is normally expected to be in the A-form, and a small, or negligible splitting is observed. In the range 9-19 D2O/nucleotide, the splitting increases with increasing hydration. Above approximately 20 D2O/nucleotide Na-DNA converts entirely to the B-form and the D2O splittings are then similar to those found in Li-DNA. We show that the complex Na-DNA results obtained in the range 0-20 D2O/nucleotide are caused by a mixture of A- and B-DNA in those samples.
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Affiliation(s)
- R Brandes
- Department of Chemistry, University of California, San Diego, La Jolla 92093-0342
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42
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Buckin VA, Kankiya BI, Sarvazyan AP, Uedaira H. Acoustical investigation of poly(dA).poly(dT), poly[d(A-T)], poly(A).poly(U) and DNA hydration in dilute aqueous solutions. Nucleic Acids Res 1989; 17:4189-203. [PMID: 2740215 PMCID: PMC317928 DOI: 10.1093/nar/17.11.4189] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Apparent molar adiabatic compressibilities and apparent molar volumes of poly[d(A-T)].poly[d(A-T)], poly(dA).poly(dT), DNA and poly(A).poly(U) in aqueous solutions were determined at 1 degree C. The change of concentration increment of the ultrasonic velocity upon replacing counter ion Cs+ by the Mg2+ ion was also determined for these polymers. The following conclusions have been made: (1) the hydration of the double helix of poly(dA).poly(dT) is remarkably larger than that of other polynucleotides; (2) the hydration of the AT pair in the B-form DNA is larger than that of the GC pair; (3) the substitution of Cs+ for Mg2+ ions as counter ions results in a decrease of hydration of the system polynucleotide plus Mg2+, and (4) the magnitude of this dehydration depends on the nucleotide sequence; the following rule is true: the lesser is a polynucleotide hydration, the larger dehydration upon changing Cs+ for Mg2+ ions in the ionic atmosphere of polynucleotide.
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Affiliation(s)
- V A Buckin
- Institute of Biological Physics, USSR Academy of Sciences, Moscow
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43
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Subramanian PS, Beveridge DL. A theoretical study of the aqueous hydration of canonical B d(CGCGAATTCGCG): Monte Carlo simulation and comparison with crystallographic ordered water sites. J Biomol Struct Dyn 1989; 6:1093-122. [PMID: 2684218 DOI: 10.1080/07391102.1989.10506539] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Monte Carlo computer simulation is described for the dodecamer d(CGCGAATTCGCG) together with 1777 water molecules at an environmental density of 1 gm/cc in a cubic cell under periodic boundary conditions. Water-water interactions were treated using the TIP4P potential and the solute water interactions by TIP4P spliced with the non-bonded interactions from the AMBER 3.0 force field. The stimulation was subjected to proximity analysis to obtain solute coordination numbers and pair interaction energies for each solute atom. Hydration density distributions partitioned into contributions from the major groove side, the minor groove side and the sugar-phosphate backbone were examined, and the probabilities of occurence for one- and two-water bridges in the simulation were enumerated. The results were compared with observations of crystallographic ordered water sites from x-ray diffraction studies on the native dodecamer by Dickerson and coworkers.
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Affiliation(s)
- P S Subramanian
- Chemistry Department, Hall-Atwater Laboratories, Wesleyan University, Middletown, CT 06457
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44
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Abstract
Nucleotide hydration is important for the understanding of the stability of and the transitions between the different helical conformations of DNA. We have used energy minimization and geometric criteria in order to look for possible sites for solvent which can bridge more than one polar or charged atomic group on a nucleotide. Such bridging sites between phosphate groups have been seen experimentally and used to explain the A to B transition. We show that these phosphate bridging sites occur at energy minima around A-DNA but do not occur around B-DNA. We also find that there are further low energy bridging sites which depend on sequence and which enable the more economical hydration of the A form.
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Affiliation(s)
- F Vovelle
- Centre de Biophysique Moleculaire, Orleans, France
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45
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Gekko K, Sakaki T, Shindo H. Preferential Hydration and B–A Transition of Deoxyribonucleic Acid in Ethanol–Water Mixtures. Polym J 1988. [DOI: 10.1295/polymj.20.751] [Citation(s) in RCA: 3] [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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46
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Abstract
Four crystal structures of transfer RNA molecules were refined at 3 A resolution with the inclusion of the solvent molecules found in the difference maps: yeast tRNA-phe in the orthorhombic form, yeast tRNA-phe in the monoclinic form and yeast tRNA-asp in the A and B forms. Over 100 solvent molecules were located in each tRNA crystal. Several hydration schemes are found repeatedly in the 4 crystals. The tertiary interactions in the corner of the L-shaped molecule attract numerous solvent molecules which bridge the ribose hydroxyl O(2') atoms, base exocyclic atoms and phosphate anionic oxygen atoms. Conservation of bases leads to conservative localized hydration patterns. Several solvent molecules are found stabilizing unusual base pairs like the G-U pairs and those involving the pseudouridine base. Water bridges between the O(2') and the exocyclic atom O2 of pyrimidines or the N3 atom of purines are common. Water bridges occur frequently between successive anionic oxygen atoms of each strand as well as between N7 or other exocyclic atoms of successive bases in the major groove. Magnesium ions or spermine molecules are found to bind in the major groove of tRNA helices without specific interactions.
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Affiliation(s)
- E Westhof
- Laboratoire de Cristallographie Biologique, Centre National de la Recherche Scientifique, Strasbourg, France
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47
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Abstract
Fourier-transform infrared (F.t.-i.r.) spectra of some synthetic mono-, oligo-, and poly-nucleotides and a natural DNA extracted from crab gonad have been recorded. Assignments of the observed frequencies are proposed by reference to our previous interpretation of laser-Raman and F.t.-i.r. spectra of constituents of nucleic acids. The spectra reflected structural differences between poly[d(A-T).d(A-T)] and crab gonad DNA (which is extremely rich in d(A-T) base-pairing). Such differences are mainly due to the effect of hydration on the conformational properties of natural DNA. Although the degree of complexity of the molecules investigated is higher than that of mononucleotides, most of the characteristic i.r. bands remain recognizable and assignable by comparison with the spectra of nucleic acid constituents previously studied.
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Affiliation(s)
- A M Seuvre
- Laboratoire de Chimie des Oligomères, Faculté des Sciences et Techniques de Rouen, Mont Saint Aignan, France
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48
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Swamy KN, Clementi E. Hydration structure and dynamics of B- and Z-DNA in the presence of counterions via molecular dynamics simulations. Biopolymers 1987; 26:1901-27. [PMID: 3689876 DOI: 10.1002/bip.360261106] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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49
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Elliott RJ, Goodfellow JM. Monte Carlo simulations of nucleotide crystal hydrates and their counter-ions. J Theor Biol 1987; 127:403-12. [PMID: 2832659 DOI: 10.1016/s0022-5193(87)80138-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A knowledge of structural and energetic aspects of water- and ion-nucleic acid interactions is essential for the understanding of the role of solvent and counterions in stabilising the various helical forms of nucleic acids. In this study, Monte Carlo computer simulation techniques have been used to predict structural properties of solvent networks in small nucleic acid crystal hydrates containing the ions sodium, ammonium and calcium. Appropriate parameters to describe the interaction potentials of the ions are added to those previously developed for water and nucleic acid atoms. A comparison is made between the predicted and experimental results and it is concluded that the potential functions used lead to simulated solvent structure in reasonable agreement with experimental data, at least in the cases of sodium and calcium. It is now feasible to use these functions in studies of hydration of larger helical fragments of nucleic acids of more direct biological interest.
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Affiliation(s)
- R J Elliott
- Department of Crystallography, Birkbeck College, London, U.K
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50
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Bonincontro A, Di Biasio A, Pedone F. Temperature dependence of dielectric constant at 10 GHz of Na-DNA gels. Biopolymers 1986; 25:241-7. [PMID: 3955190 DOI: 10.1002/bip.360250206] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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