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Barion G, Canal C, Panozzo A, Moore SS, Piotto S, Vamerali T. The contrasting photosynthesis and growth response of young test species irrigated with electro-chemical modified water. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108780. [PMID: 38850726 DOI: 10.1016/j.plaphy.2024.108780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
The study evaluated the effects of treating irrigation water with a coaxial flow variator (CFV) on the morpho-physiology of pot-cultivated test species, including cucumber (Cucumis sativus, CU), lettuce (Lactuca sativa, LE), and sorghum (Sorghum vulgare, SO), in early stages of growth. CFV caused a lower oxidation reduction potential (ORP), increased pH and flow resistance and inductance. It induced changes in the absorbance characteristics of water in specific spectral regions, likely associated with greater stretching and reduced bending vibrations compared to untreated water. While assimilation rate and photosynthetic efficiency were not significantly affected at 60 days after sowing, treated water increased the stomatal conductance to water vapour gsw (+79%) and the electron transport rate ETR (+10%) in CU, as well as the non-photochemical quenching NPQ (+33%) in SO. Treated water also reduced leaf temperature in all species (-0.86 °C on average). This translated into improved plant biomass (leaves: +34%; roots: +140%) and reduced leaf-to-root biomass ratio (-42%) in SO, allowing both faster aerial growth and soil colonization, which can be exploited to improve plant tolerance against abiotic stresses. In the C3 species CU and LE, plant biomass was instead reduced, although significantly in LE only, while the leaf-to-root biomass ratio was generally enhanced, a result likely profitable in the cultivation of leafy vegetables. This is a preliminary trial on the effects of functionalized water and much remains to be investigated in other physiological processes, plant species, and growth stages for the full exploitation of this water treatment in agronomy.
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Affiliation(s)
- Giuseppe Barion
- Department of Agronomy Food Natural Resources Animals and the Environment, Padua University, Viale dell'università 16, 35020, Legnaro, Padua, Italy
| | - Camilla Canal
- Department of Agronomy Food Natural Resources Animals and the Environment, Padua University, Viale dell'università 16, 35020, Legnaro, Padua, Italy
| | - Anna Panozzo
- Department of Agronomy Food Natural Resources Animals and the Environment, Padua University, Viale dell'università 16, 35020, Legnaro, Padua, Italy.
| | - Selina Sterup Moore
- Department of Agroecology, Aarhus University, Blichers Allè 20, 8830, Tjele, Denmark
| | - Simone Piotto
- Department of Agronomy Food Natural Resources Animals and the Environment, Padua University, Viale dell'università 16, 35020, Legnaro, Padua, Italy
| | - Teofilo Vamerali
- Department of Agronomy Food Natural Resources Animals and the Environment, Padua University, Viale dell'università 16, 35020, Legnaro, Padua, Italy
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2
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Morozov VN, Klimovich MA, Shibaeva AV, Klimovich ON, Koshevaya ED, Kolyvanova MA, Kuzmin VA. Optical Polymorphism of Liquid-Crystalline Dispersions of DNA at High Concentrations of Crowding Polymer. Int J Mol Sci 2023; 24:11365. [PMID: 37511123 PMCID: PMC10379083 DOI: 10.3390/ijms241411365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Optically active liquid-crystalline dispersions (LCD) of nucleic acids, obtained by polymer- and salt-induced (psi-) condensation, e.g., by mixing of aqueous saline solutions of low molecular weight DNA (≤106 Da) and polyethylene glycol (PEG), possess an outstanding circular dichroism (CD) signal (so-called psi-CD) and are of interest for sensor applications. Typically, such CD signals are observed in PEG content from ≈12.5% to ≈22%. However, in the literature, there are very conflicting data on the existence of psi-CD in DNA LCDs at a higher content of crowding polymer up to 30-40%. In the present work, we demonstrate that, in the range of PEG content in the system above ≈24%, optically polymorphic LCDs can be formed, characterized by both negative and positive psi-CD signals, as well as by ones rather slightly differing from the spectrum of isotropic DNA solution. Such a change in the CD signal is determined by the concentration of the stock solution of PEG used for the preparation of LCDs. We assume that various saturation of polymer chains with water molecules may affect the amount of active water, which in turn leads to a change in the hydration of DNA molecules and their transition from B-form to Z-form.
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Affiliation(s)
- Vladimir N Morozov
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
| | - Mikhail A Klimovich
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
- Burnazyan Federal Medical Biophysical Center, Federal Medical Biological Agency of the Russian Federation, 23 Marshala Novikova, 123182 Moscow, Russia
| | - Anna V Shibaeva
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
| | - Olga N Klimovich
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
| | - Ekaterina D Koshevaya
- Burnazyan Federal Medical Biophysical Center, Federal Medical Biological Agency of the Russian Federation, 23 Marshala Novikova, 123182 Moscow, Russia
| | - Maria A Kolyvanova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
- Burnazyan Federal Medical Biophysical Center, Federal Medical Biological Agency of the Russian Federation, 23 Marshala Novikova, 123182 Moscow, Russia
| | - Vladimir A Kuzmin
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, 119334 Moscow, Russia
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3
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Krall JB, Nichols PJ, Henen MA, Vicens Q, Vögeli B. Structure and Formation of Z-DNA and Z-RNA. Molecules 2023; 28:843. [PMID: 36677900 PMCID: PMC9867160 DOI: 10.3390/molecules28020843] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 01/17/2023] Open
Abstract
Despite structural differences between the right-handed conformations of A-RNA and B-DNA, both nucleic acids adopt very similar, left-handed Z-conformations. In contrast to their structural similarities and sequence preferences, RNA and DNA exhibit differences in their ability to adopt the Z-conformation regarding their hydration shells, the chemical modifications that promote the Z-conformation, and the structure of junctions connecting them to right-handed segments. In this review, we highlight the structural and chemical properties of both Z-DNA and Z-RNA and delve into the potential factors that contribute to both their similarities and differences. While Z-DNA has been extensively studied, there is a gap of knowledge when it comes to Z-RNA. Where such information is lacking, we try and extend the principles of Z-DNA stability and formation to Z-RNA, considering the inherent differences of the nucleic acids.
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Affiliation(s)
- Jeffrey B. Krall
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Parker J. Nichols
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Morkos A. Henen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Beat Vögeli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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4
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Behavior of B- and Z-DNA Crystals under High Hydrostatic Pressure. CRYSTALS 2022. [DOI: 10.3390/cryst12060871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Single crystals of B-DNA and Z-DNA oligomers were analyzed under high hydrostatic pressure and their behavior was compared to the A-DNA crystals already known. The amplitude of the base compression, when compared to the A-form of DNA (0.13 Å/GPa), was higher for the Z-DNA (0.32 Å/GPa) and was the highest for the B-DNA (0.42 Å/GPa). The B-DNA crystal degraded rapidly around 400–500 MPa, while the Z-structure was more resistant, up to 1.2 GPa.
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5
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Maurel MC, Leclerc F, Hervé G. Ribozyme Chemistry: To Be or Not To Be under High Pressure. Chem Rev 2019; 120:4898-4918. [DOI: 10.1021/acs.chemrev.9b00457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Sorbonne Université, Muséum National d’Histoire Naturelle, EPHE, F-75005 Paris, France
| | - Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, F-91198 Gif-sur-Yvette, France
| | - Guy Hervé
- Laboratoire BIOSIPE, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Campus Pierre et Marie Curie, F-75005 Paris, France
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6
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7
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Arns L, Knop JM, Patra S, Anders C, Winter R. Single-molecule insights into the temperature and pressure dependent conformational dynamics of nucleic acids in the presence of crowders and osmolytes. Biophys Chem 2019; 251:106190. [PMID: 31146215 DOI: 10.1016/j.bpc.2019.106190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/19/2022]
Abstract
In this review we discuss results from temperature and pressure dependent single-molecule Förster resonance energy transfer (smFRET) studies on nucleic acids in the presence of macromolecular crowders and organic osmolytes. As representative examples, we have chosen fragments of both DNAs and RNAs, i.e., a synthetic DNA hairpin, a human telomeric G-quadruplex and the microROSE RNA hairpin. To mimic the effects of intracellular components, our studies include the macromolecular crowding agent Ficoll, a copolymer of sucrose and epichlorohydrin, and the organic osmolytes trimethylamine N-oxide, urea and glycine as well as natural occurring osmolyte mixtures from deep sea organisms. Furthermore, the impact of mutations in an RNA sequence on the conformational dynamics is examined. Different from proteins, the effects of the osmolytes and crowding agents seem to strongly dependent on the structure and chemical make-up of the nucleic acid.
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Affiliation(s)
- Loana Arns
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Jim-Marcel Knop
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Satyajit Patra
- Aix Marseille Université, CNRS, Centralle Marseille, Institut Fresnel, F-13013 Marseille, France
| | - Christian Anders
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| | - Roland Winter
- TU Dortmund University, Faculty of Chemistry and Chemical Biology, Physical Chemistry, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany.
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8
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Migliorati V, Filipponi A, Di Cicco A, De Panfilis S, D’Angelo P. Structure of Water in Zn2+ Aqueous Solutions from Ambient Conditions up to the Gigapascal Pressure Range: A XANES and Molecular Dynamics Study. Inorg Chem 2017; 56:14013-14022. [DOI: 10.1021/acs.inorgchem.7b02151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valentina Migliorati
- Dipartimento di
Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
| | - Adriano Filipponi
- Dipartimento di Scienze
Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio, 67100 L’Aquila, Italy
| | - Andrea Di Cicco
- Sezione di Fisica,
Scuola di Scienze e Tecnologie, Università di Camerino, 62032 Camerino (MC), Italy
| | - Simone De Panfilis
- Centre
for Life Nano Science - IIT@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161 Rome, Italy
| | - Paola D’Angelo
- Dipartimento di
Chimica, Università di Roma “La Sapienza”, P.le
A. Moro 5, 00185 Roma, Italy
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9
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Saran R, Kleinke K, Zhou W, Yu T, Liu J. A Silver-Specific DNAzyme with a New Silver Aptamer and Salt-Promoted Activity. Biochemistry 2017; 56:1955-1962. [PMID: 28345892 DOI: 10.1021/acs.biochem.6b01131] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Most RNA-cleaving DNAzymes require a metal ion to interact with the scissile phosphate for activity. Therefore, few unmodified DNAzymes work with thiophilic metals because of their low affinity for phosphate. Recently, an Ag+-specific Ag10c DNAzyme was reported via in vitro selection. Herein, Ag10c is characterized to rationalize the role of the strongly thiophilic Ag+. Systematic mutation studies indicate that Ag10c is a highly conserved DNAzyme and its Ag+ binding is unrelated to C-Ag+-C interaction. Its activity is enhanced by increasing Na+ concentrations in buffer. At the same metal concentration, activity decreases in the following order: Li+ > Na+ > K+. Ag10c binds one Na+ ion and two Ag+ ions for catalysis. The pH-rate profile has a slope of ∼1, indicating a single deprotonation step. Phosphorothioate substitution at the scissile phosphate suggests that Na+ interacts with the pro-Rp oxygen of the phosphate, and dimethyl sulfate footprinting indicates that the DNAzyme loop is a silver aptamer binding two Ag+ ions. Therefore, Ag+ exerts its function allosterically, while the scissile phosphate interacts with Na+, Li+, Na+, or Mg2+. This work suggests the possibility of isolating thiophilic metal aptamers based on DNAzyme selection, and it also demonstrates a new Ag+ aptamer.
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Affiliation(s)
- Runjhun Saran
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Kimberly Kleinke
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Wenhu Zhou
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Tianmeng Yu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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10
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Rayan G, Macgregor RB. A look at the effect of sequence complexity on pressure destabilisation of DNA polymers. Biophys Chem 2015; 199:34-8. [DOI: 10.1016/j.bpc.2015.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/11/2015] [Accepted: 02/13/2015] [Indexed: 11/16/2022]
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11
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Kumar PS, Mukherjee A, Hazra A. Theoretical Study of Structural Changes in DNA under High External Hydrostatic Pressure. J Phys Chem B 2015; 119:3348-55. [DOI: 10.1021/jp5107185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- P. Sudheer Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, Maharashtra 411
008, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, Maharashtra 411
008, India
| | - Anirban Hazra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, Maharashtra 411
008, India
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12
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Nagata Y, Takeda R, Suginome M. Pressure-dependent helix inversion of poly(quinoxaline-2,3-diyl)s containing chiral side chains in non-aqueous solvents. Chem Commun (Camb) 2015; 51:11182-5. [DOI: 10.1039/c5cc04255k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Poly(quinoxaline-2,3-diyl)s with chiral (S)-2-butoxymethyl side chains dissolved in 1,2-dichloroethane experience a reversible pressure-dependent helix inversion from P- to M-helical structures between 0.1 MPa and 200 MPa.
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Affiliation(s)
- Yuuya Nagata
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
| | - Ryohei Takeda
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
| | - Michinori Suginome
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
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13
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Liu B, Cao Y, Duan Y, Che S. Water-Dependent Optical Activity Inversion of Chiral DNA-Silica Assemblies. Chemistry 2013; 19:16382-8. [DOI: 10.1002/chem.201303073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Indexed: 11/07/2022]
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14
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Baker CM, Best RB. Matching of additive and polarizable force fields for multiscale condensed phase simulations. J Chem Theory Comput 2013; 9:2826-2837. [PMID: 23997691 PMCID: PMC3752912 DOI: 10.1021/ct400116g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Inclusion of electronic polarization effects is one of the key aspects in which the accuracy of current biomolecular force fields may be improved. The principal drawback of such approaches is the computational cost, which typically ranges from 3 - 10 times that of the equivalent additive model, and may be greater for more sophisticated treatments of polarization or other many-body effects. Here, we present a multiscale approach which may be used to enhance the sampling in simulations with polarizable models, by using the additive model as a tool to explore configuration space. We use a method based on information theory to determine the charges for an additive model that has optimal overlap with the polarizable one, and we demonstrate the feasibility of enhancing sampling via a hybrid replica exchange scheme for several model systems. An additional advantage is that, in the process, we obtain a systematic method for deriving charges for an additive model that will be the natural complement to its polarizable parent. The additive charges are found by an effective coarse-graining of the polarizable force field, rather than by ad hoc procedures.
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Affiliation(s)
- Christopher M. Baker
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert B. Best
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, U.S.A
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15
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Cagliani A, Kosaka P, Tamayo J, Davis ZJ. Monitoring the hydration of DNA self-assembled monolayers using an extensional nanomechanical resonator. LAB ON A CHIP 2012; 12:2069-2073. [PMID: 22511031 DOI: 10.1039/c2lc40047b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have fabricated an ultrasensitive nanomechanical resonator based on the extensional vibration mode to weigh the adsorbed water on self-assembled monolayers of DNA as a function of the relative humidity. The water adsorption isotherms provide the number of adsorbed water molecules per nucleotide for monolayers of single stranded (ss) DNA and after hybridization with the complementary DNA strand. Our results differ from previous data obtained with bulk samples, showing the genuine behavior of these self-assembled monolayers. The hybridization cannot be inferred from the water adsorption isotherms due to the low hybridization efficiency of these highly packed monolayers. Strikingly, we efficiently detect the hybridization by measuring the thermal desorption of water at constant relativity humidity. This finding adds a new nanomechanical tool for developing a label-free nucleic acid sensor based on the interaction between water and self-assembled monolayers of nucleic acids.
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16
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Gupta A, Jaeger HM, Compaan KR, Schaefer HF. Electron attachment to the guanine-cytosine nucleic acid base pair and the effects of monohydration and proton transfer. J Phys Chem B 2012; 116:5579-87. [PMID: 22530702 DOI: 10.1021/jp211608b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The guanine-cytosine (GC) radical anion and its interaction with a single water molecule is studied using ab initio and density functional methods. Z-averaged second-order perturbation theory (ZAPT2) was applied to GC radical anion for the first time. Predicted spin densities show that the radical character is localized on cytosine. The Watson-Crick monohydrated GC anion is compared to neutral GC·H2O, as well as to the proton-transferred analogue on the basis of structural and energetic properties. In all three systems, local minima are identified that correspond to water positioned in the major and minor grooves of macromolecular DNA. On the anionic surface, two novel structures have water positioned above or below the GC plane. On the neutral and anionic surfaces, the global minimum can be described as water interacting with the minor groove. These structures are predicted to have hydration energies of 9.7 and 11.8 kcal mol(-1), respectively. Upon interbase proton-transfer (PT), the anionic global minimum has water positioned in the major groove, and the hydration energy increases to 13.4 kcal mol(-1). PT GC·H2O(•-) has distonic character; the radical character resides on cytosine, while the negative charge is localized on guanine. The effects of proton transfer are further investigated through the computed adiabatic electron affinities (AEA) of GC and monohydrated GC, and the vertical detachment energies (VDE) of the corresponding anions. Monohydration increases the AEAs and VDEs by only 0.1 eV, while proton-transfer increases the VDEs substantially (0.8 eV). The molecular charge distribution of monohydrated guanine-cytosine radical anion depends heavily on interbase proton transfer.
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17
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Wang J, Li H, Zhang L, Bu Y. Unexpected dissociation energetics of the Na(+) counterion from GC motifs in DNA hole-migration. Phys Chem Chem Phys 2010; 12:13099-106. [PMID: 20824253 DOI: 10.1039/b927202j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We present here a theoretical investigation of the electronic and energetic properties of Na(+)GC, a DNA motif bound to a sodium ion (Na(+)) at the N(7) and O(6) sites of guanine (G), and its hole-trapped derivative [Na(+)GC](+) using density functional theory calculations. Normally, Na(+)GC has positive dissociation energies along various dissociation channels. However, hole-trapping of the Na(+)GC motif can lead to an unusual energetic phenomenon. Hole-trapping can reduce not only the dissociation barrier by destabilizing the Na(+)GC motif to a metastable state, but also the dissociation energy of the Na(+)N(7)/O(6) bond with an unexpected change from a positive to a negative value (61.51 versus-16.18 kcal mol(-1)). This unexpected negative dissociation energy phenomenon implies that this motif can store energy (∼16 kcal mol(-1)) in the Na(+)N(7)/O(6) bond zone due to hole-trapping. The topological properties of electron densities and the Laplacian values at the bond critical points indicate that this energetic phenomenon mainly originates from additional electrostatic repulsions between two moieties linked via a high-energy bond (Na(+)N(7)/O(6)). Proton transfer from G induced by hole-trapping can expand the negative dissociation energy zone to both Na(+)N(7)/O(6) and Watson-Crick (WC) H-bond zones. Similar phenomena can be observed for the Na(+) binding at the minor groove. Solvation of the hole-trapped Na(+)GC motif can change the negative dissociation energies by varying degrees, depending on the solvent-binding sites and the polarity of the solvents.
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Affiliation(s)
- Jun Wang
- The Center for Modeling & Simulation Chemistry, Institute of Theoretical Chemistry, Shandong University, Jinan 250100, PR China
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18
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Giel-Pietraszuk M, Fedoruk-Wyszomirska A, Barciszewski J. Effect of high hydrostatic pressure on hydration and activity of ribozymes. Mol Biol Rep 2010; 37:3713-9. [PMID: 20204525 DOI: 10.1007/s11033-010-0024-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 02/17/2010] [Indexed: 10/19/2022]
Abstract
Formation and stabilization of RNA structure in the cell depends on its interaction with solvent and metal ions. High hydrostatic pressure (HHP) is a convenient tool in an analysis of the role of small molecules in the structure stabilization of biological macromolecules. Analysis of HHP effect and various concentrations of ions showed that water induce formation of the active ribozyme structure. So, it is clear that water is the driving force of conformational changes of nucleic acid.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
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19
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Changes in structure and functional properties of whey proteins induced by high hydrostatic pressure: A review. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11705-009-0251-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Pressure-induced helix–coil transition of DNA copolymers is linked to water activity. Biophys Chem 2009; 144:62-6. [DOI: 10.1016/j.bpc.2009.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 06/17/2009] [Accepted: 06/17/2009] [Indexed: 11/18/2022]
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21
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Fedoruk-Wyszomirska A, Giel-Pietraszuk M, Wyszko E, Szymański M, Ciesiołka J, Barciszewska MZ, Barciszewski J. The mechanism of acidic hydrolysis of esters explains the HDV ribozyme activity. Mol Biol Rep 2008; 36:1647-50. [PMID: 18810653 DOI: 10.1007/s11033-008-9364-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Accepted: 09/11/2008] [Indexed: 10/21/2022]
Abstract
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme that catalyzes the site-specific trans-esterification reaction. Using high hydrostatic pressure (HHP) technique we showed that HDV ribozyme catalyzes the reaction of RNA cleavage in the absence of magnesium ions according to mechanism of acidic hydrolysis of esters. HHP induces changes of water structure, lowering pH and effect ribozyme catalytic site structure formation without magnesium. HHP, similarly to magnesium ion at ambient pressure stabilizes the higher order RNA structure of HDV, but Mg(2+) is not involved in the catalysis. Our results clearly support the new mechanism of HDV hydrolysis and show advantages of using HHP in analysis of macromolecules interaction.
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22
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Wilton DJ, Ghosh M, Chary KVA, Akasaka K, Williamson MP. Structural change in a B-DNA helix with hydrostatic pressure. Nucleic Acids Res 2008; 36:4032-7. [PMID: 18515837 PMCID: PMC2475645 DOI: 10.1093/nar/gkn350] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Study of the effects of pressure on macromolecular structure improves our understanding of the forces governing structure, provides details on the relevance of cavities and packing in structure, increases our understanding of hydration and provides a basis to understand the biology of high-pressure organisms. A study of DNA, in particular, helps us to understand how pressure can affect gene activity. Here we present the first high-resolution experimental study of B-DNA structure at high pressure, using NMR data acquired at pressures up to 200 MPa (2 kbar). The structure of DNA compresses very little, but is distorted so as to widen the minor groove, and to compress hydrogen bonds, with AT pairs compressing more than GC pairs. The minor groove changes are suggested to lead to a compression of the hydration water in the minor groove.
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Affiliation(s)
- David J Wilton
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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23
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Kumar A, Sevilla MD, Suhai S. Microhydration of the guanine-cytosine (GC) base pair in the neutral and anionic radical states: a density functional study. J Phys Chem B 2008; 112:5189-98. [PMID: 18380501 DOI: 10.1021/jp710957p] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A density functional study of the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical is presented. Geometries of the GC base pair in the presence of 6 and 11 water molecules were fully optimized in the neutral (GC-nH2O) and anion radical [(GC-nH2O)*-] (n = 6 and 11) states using the B3LYP method and the 6-31+G** basis set. Further, vibrational frequency analysis at the same level of theory (B3LYP/6-31+G**) was also performed to ensure the existence of local minima in these hydrated structures. It was found that water molecules surrounding the GC base pair have significant effects on the geometry of the GC base pair and promote nonplanarity in the GC base pair. The calculated structures were found to be in good agreement with those observed experimentally and obtained in molecular dynamics (MD) simulation studies. The water molecules in neutral GC-nH2O complexes lie near the ring plane of the GC base pair where they undergo hydrogen bonding with both GC and each other. However, in the GC anion radical complexes (GC-nH2O, n = 6, 11), the water molecules are displaced substantially from the GC ring plane. For GC-11H2O*-, a water molecule is hydrogen-bonded with the C6 atom of the cytosine base. We found that the hydration shell initially destabilizes the GC base pair toward electron capture as a transient anion. Energetically unstable diffuse states in the hydration shell are suggested to provide an intermediate state for the excess electron before molecular reorganization of the water molecules and the base pair results in a stable anion formation. The singly occupied molecular orbital (SOMO) in the anion radical complexes clearly shows that an excess electron localizes into a pi orbital of cytosine. The zero-point-energy (ZPE-) corrected adiabatic electron affinities (AEAs) of the GC-6H2O and GC-11H2O complexes, at the B3LYP/6-31+G** level of theory, were found to be 0.74 and 0.95 eV, respectively. However, the incorporation of bulk water as a solvent using the polarized continuum model (PCM) increases the EAs of these complexes to 1.77 eV.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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24
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Amo-Ochoa P, Castillo O, Sanz Miguel PJ, Zamora F. Unusual Dimeric Zn(II)-cytosine complexes: New models of the interaction of Zn(II) with DNA and RNA. J Inorg Biochem 2008; 102:203-8. [PMID: 17870174 DOI: 10.1016/j.jinorgbio.2007.07.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 07/24/2007] [Accepted: 07/26/2007] [Indexed: 10/23/2022]
Abstract
Synthesis and crystal structure of two Zn(II) dimer complexes with 1-methylcytosine (1-MeC) are reported. In complex [Zn(2)Cl(4)(mu-1-MeC-O2,N3)(2)] (1), two 1-MeC ligands are bridging two ZnCl(2) moieties. In [Zn(2)(1-MeC-N3)(4)(mu-SO(4))(2)].2H(2)O (2), the sulfates act as bridging ligands and 1-MeC are linked via N3 to Zn(II) as terminal ligands. Both complexes represent the first examples of Zn(II)-pyrimidine dimers. The potential biological significance of 1 and 2 is discussed.
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Affiliation(s)
- Pilar Amo-Ochoa
- Departamento de Tecnología Industrial, Universidad Alfonso X El Sabio, 28691 Villanueva de la Cañada, Madrid, Spain
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25
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Bowman JP, Bittencourt CR, Ross T. Differential gene expression of Listeria monocytogenes during high hydrostatic pressure processing. Microbiology (Reading) 2008; 154:462-475. [DOI: 10.1099/mic.0.2007/010314-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- John P. Bowman
- Australian Food Safety Centre of Excellence, Tasmanian Institute of Agricultural Research, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart, Tasmania, 7001, Australia
| | - Claudio R. Bittencourt
- Australian Food Safety Centre of Excellence, Tasmanian Institute of Agricultural Research, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart, Tasmania, 7001, Australia
| | - Tom Ross
- Australian Food Safety Centre of Excellence, Tasmanian Institute of Agricultural Research, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart, Tasmania, 7001, Australia
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26
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Katrusiak A. High-pressure crystallography. Acta Crystallogr A 2007; 64:135-48. [PMID: 18156679 DOI: 10.1107/s0108767307061181] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Accepted: 11/20/2007] [Indexed: 11/10/2022] Open
Abstract
Since the late 1950's, high-pressure structural studies have become increasingly frequent, following the inception of opposed-anvil cells, development of efficient diffractometric equipment (brighter radiation sources both in laboratories and in synchrotron facilities, highly efficient area detectors) and procedures (for crystal mounting, centring, pressure calibration, collecting and correcting data). Consequently, during the last decades, high-pressure crystallography has evolved into a powerful technique which can be routinely applied in laboratories and dedicated synchrotron and neutron facilities. The variation of pressure adds a new thermodynamic dimension to crystal-structure analyses, and extends the understanding of the solid state and materials in general. New areas of thermodynamic exploration of phase diagrams, polymorphism, transformations between different phases and cohesion forces, structure-property relations, and a deeper understanding of matter at the atomic scale in general are accessible with the high-pressure techniques in hand. A brief history, guidelines and requirements for performing high-pressure structural studies are outlined.
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Affiliation(s)
- Andrzej Katrusiak
- Faculty of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland.
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27
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Kovalev NA, Medvedeva DA, Zenkova MA, Vlassov VV. Cleavage of RNA by an amphiphilic compound lacking traditional catalytic groups. Bioorg Chem 2007; 36:33-45. [PMID: 18061645 DOI: 10.1016/j.bioorg.2007.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 10/02/2007] [Accepted: 10/05/2007] [Indexed: 12/23/2022]
Abstract
Recently, in experiments with combinatorial libraries of amphiphilic compounds lacking groups, known as catalysts of transesterification reaction, we discovered novel RNA-cleaving compounds [N. Kovalev, E. Burakova, V. Silnikov, M. Zenkova, V. Vlassov, Bioorg. Chem. 34 (2006) 274-286]. In the present study, we investigate cleavage of RNA by the most active representative of these libraries, compound named Dp12. Sequence-specificity of RNA cleavage and influence of reaction conditions on cleavage rate suggested that Dp12 enormously accelerates spontaneous RNA cleavage. Light scattering experiments revealed that the RNA cleavage proceeds within multiplexes formed by assembles of RNA and Dp12 molecules, at Dp12 concentration far below critical concentration of micelle formation. Under these conditions, Dp12 is presented in the solution as individual molecules, but addition of RNA to this solution triggers formation of the multiplexes. The obtained data suggest a possible mechanism of RNA cleavage, which includes interaction of the compound with RNA sugar-phosphate backbone resulting in changing of ribose conformation. This leads to juxtaposition of the 2'-hydroxyl group and internucleotide phosphorus atom at a distance needed for the transesterification to occur.
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Affiliation(s)
- N A Kovalev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russian Federation
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28
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Ahmadibeni Y, Parang K. Synthesis and evaluation of modified oligodeoxynucleotides containing diphosphodiester internucleotide linkages. Angew Chem Int Ed Engl 2007; 46:4739-43. [PMID: 17497623 DOI: 10.1002/anie.200605029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yousef Ahmadibeni
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, 41 Lower College Road, Kingston, RI 02881, USA
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29
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Fuertes MA, Cepeda V, Alonso C, Pérez JM. Molecular mechanisms for the B-Z transition in the example of poly[d(G-C) x d(G-C)] polymers. A critical review. Chem Rev 2007; 106:2045-64. [PMID: 16771442 DOI: 10.1021/cr050243f] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miguel A Fuertes
- Centro de Biologia Molecular Severo Ochoa Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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30
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Girard E, Prangé T, Dhaussy AC, Migianu-Griffoni E, Lecouvey M, Chervin JC, Mezouar M, Kahn R, Fourme R. Adaptation of the base-paired double-helix molecular architecture to extreme pressure. Nucleic Acids Res 2007; 35:4800-8. [PMID: 17617642 PMCID: PMC1950552 DOI: 10.1093/nar/gkm511] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Revised: 06/13/2007] [Accepted: 06/13/2007] [Indexed: 11/14/2022] Open
Abstract
The behaviour of the d(GGTATACC) oligonucleotide has been investigated by X-ray crystallography at 295 K in the range from ambient pressure to 2 GPa (approximately 20,000 atm). Four 3D-structures of the A-DNA form (at ambient pressure, 0.55, 1.09 and 1.39 GPa) were refined at 1.60 or 1.65 A resolution. In addition to the diffraction pattern of the A-form, the broad meridional streaks previously explained by occluded B-DNA octamers within the channels of the crystalline A-form matrix were observed up to at least 2 GPa. This work highlights an important property of nucleic acids, their capability to withstand very high pressures, while keeping in such conditions a nearly invariant geometry of base pairs that store and carry genetic information. The double-helix base-paired architecture behaves as a molecular spring, which makes it especially adapted to very harsh conditions. These features may have contributed to the emergence of a RNA World at prebiotic stage.
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Affiliation(s)
- Eric Girard
- Synchrotron-SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192 Gif-sur-Yvette Cedex, France.
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31
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Ahmadibeni Y, Parang K. Synthesis and Evaluation of Modified Oligodeoxynucleotides Containing Diphosphodiester Internucleotide Linkages. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200605029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Fedoruk-Wyszomirska A, Wyszko E, Giel-Pietraszuk M, Barciszewska MZ, Barciszewski J. High hydrostatic pressure approach proves RNA catalytic activity without magnesium. Int J Biol Macromol 2007; 41:30-5. [PMID: 17222901 DOI: 10.1016/j.ijbiomac.2006.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Accepted: 12/08/2006] [Indexed: 10/23/2022]
Abstract
High hydrostatic pressure (HHP) technique was used to evaluate a mechanism of RNA hydrolysis with RNA. We showed that hammerhead ribozyme specifically cleaves RNA substrate at HHP in the absence of Mg(2+). A deoxyribozyme "10-23" was active in the same conditions. These results pointed out that the hydrolytic activity of nucleic acid depends on proper tertiary structure of a complex with a substrate. They prove that magnesium ion is not directly involved in catalysis process. On that basis we show the mechanism of RNA hydrolysis catalyzed with nucleic acids at HHP.
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33
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34
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Fedotova MV. The influence of pressure on the structure of aqueous solutions of NaCl over the pressure range 0.1–1000 MPa according to the integral equation method. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2007. [DOI: 10.1134/s0036024407050111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Senear DF, Tretyachenko-Ladokhina V, Opel ML, Aeling KA, Wesley Hatfield G, Franklin LM, Darlington RC, Alexander Ross J. Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interface. Nucleic Acids Res 2007; 35:1761-72. [PMID: 17324943 PMCID: PMC1874591 DOI: 10.1093/nar/gkl1122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
E. coli Integration host factor (IHF) condenses the bacterial nucleoid by wrapping DNA. Previously, we showed that DNA flexibility compensates for structural characteristics of the four consensus recognition elements associated with specific binding (Aeling et al., J. Biol. Chem. 281, 39236-39248, 2006). If elements are missing, high-affinity binding occurs only if DNA deformation energy is low. In contrast, if all elements are present, net binding energy is unaffected by deformation energy. We tested two hypotheses for this observation: in complexes containing all elements, (1) stiff DNA sequences are less bent upon binding IHF than flexible ones; or (2) DNA sequences with differing flexibility have interactions with IHF that compensate for unfavorable deformation energy. Time-resolved Förster resonance energy transfer (FRET) shows that global topologies are indistinguishable for three complexes with oligonucleotides of different flexibility. However, pressure perturbation shows that the volume change upon binding is smaller with increasing flexibility. We interpret these results in the context of Record and coworker's model for IHF binding (J. Mol. Biol. 310, 379-401, 2001). We propose that the volume changes reflect differences in hydration that arise from structural variation at IHF-DNA interfaces while the resulting energetic compensation maintains the same net binding energy.
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Affiliation(s)
- Donald F. Senear
- Department of Molecular Biology and Biochemistry, Department of Microbiology and Molecular Genetics, College of Medicine, Institute of Genomics and Bioinformatics, University of California, Irvine CA 92697 and Department of Chemistry, The University of Montana, Missoula, MT 59812, USA
- *To whom correspondence should be addressed: (949) 824-8014(949) 824-8551
| | - Vira Tretyachenko-Ladokhina
- Department of Molecular Biology and Biochemistry, Department of Microbiology and Molecular Genetics, College of Medicine, Institute of Genomics and Bioinformatics, University of California, Irvine CA 92697 and Department of Chemistry, The University of Montana, Missoula, MT 59812, USA
| | - Michael L. Opel
- Department of Molecular Biology and Biochemistry, Department of Microbiology and Molecular Genetics, College of Medicine, Institute of Genomics and Bioinformatics, University of California, Irvine CA 92697 and Department of Chemistry, The University of Montana, Missoula, MT 59812, USA
| | - Kimberly A. Aeling
- Department of Molecular Biology and Biochemistry, Department of Microbiology and Molecular Genetics, College of Medicine, Institute of Genomics and Bioinformatics, University of California, Irvine CA 92697 and Department of Chemistry, The University of Montana, Missoula, MT 59812, USA
| | - G. Wesley Hatfield
- Department of Molecular Biology and Biochemistry, Department of Microbiology and Molecular Genetics, College of Medicine, Institute of Genomics and Bioinformatics, University of California, Irvine CA 92697 and Department of Chemistry, The University of Montana, Missoula, MT 59812, USA
| | - Laurie M. Franklin
- Department of Molecular Biology and Biochemistry, Department of Microbiology and Molecular Genetics, College of Medicine, Institute of Genomics and Bioinformatics, University of California, Irvine CA 92697 and Department of Chemistry, The University of Montana, Missoula, MT 59812, USA
| | - Reuben C. Darlington
- Department of Molecular Biology and Biochemistry, Department of Microbiology and Molecular Genetics, College of Medicine, Institute of Genomics and Bioinformatics, University of California, Irvine CA 92697 and Department of Chemistry, The University of Montana, Missoula, MT 59812, USA
| | - J.B. Alexander Ross
- Department of Molecular Biology and Biochemistry, Department of Microbiology and Molecular Genetics, College of Medicine, Institute of Genomics and Bioinformatics, University of California, Irvine CA 92697 and Department of Chemistry, The University of Montana, Missoula, MT 59812, USA
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36
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37
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Kastenholz MA, Schwartz TU, Hünenberger PH. The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation. Biophys J 2006; 91:2976-90. [PMID: 16998239 PMCID: PMC1578494 DOI: 10.1529/biophysj.106.083667] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The transition between the B and Z conformations of double-helical deoxyribonucleic acid (DNA) belongs to the most complex and elusive conformational changes occurring in biomolecules. Since the accidental discovery of the left-handed Z-DNA form in the late 1970s, research on this DNA morphology has been engaged in resolving questions relative to its stability, occurrence, and function in biological processes. While the occurrence of Z-DNA in vivo is now widely recognized and the major factors influencing its thermodynamical stability are largely understood, the intricate conformational changes that take place during the B-to-Z transition are still unknown at the atomic level. In this article, we report simulations of this transition for the 3'-(CGCGCG)-5' hexamer duplex using targeted molecular dynamics with the GROMOS96 force field in explicit water under different ionic-strength conditions. The results suggest that for this oligomer length and sequence, the transition mechanism involves: 1), a stretched intermediate conformation, which provides a simple solution to the important sterical constraints involved in this transition; 2), the transient disruption of Watson-Crick hydrogen-bond pairing, partly compensated energetically by an increase in the number of solute-solvent hydrogen bonds; and 3), an asynchronous flipping of the bases compatible with a zipperlike progression mechanism.
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Affiliation(s)
- Mika A Kastenholz
- Laboratorium für Physikalische Chemie, ETH Hönggerberg, HCI, Zürich, Switzerland
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38
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Gu C, Lustig S, Trout BL. Solvation Model Based on Order Parameters and a Fast Sampling Method for the Calculation of the Solvation Free Energies of Peptides. J Phys Chem B 2006; 110:1476-84. [PMID: 16471699 DOI: 10.1021/jp054602m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An analytical solvation model is proposed as a function of an order parameter, which represents the local arrangement of water molecules in the first solvation shell of peptide atoms. The model is combined with a fast sampling method, rotational isomeric state Monte Carlo, to sample efficiently the torsional degrees of freedom on a peptide backbone. This order parameter solvation model is shown to reproduce without ad hoc fitting parameters the solvation free energies of single amino acids and tripeptides with slightly better accuracy than the generalized Born model but with several orders of magnitude improvement in efficiency. This method is a potential candidate for efficiently and accurately tackling some important issues in biophysical chemistry that are related to solvation, for example, protein folding, ligand binding, etc. Our results also present fundamental new insights into solvation. Specifically, the local water geometry, represented in this work by a properly defined order parameter, carries the majority, if not all, of the energetic information of solvation, including solute-solvent interactions and solvent reorganization in the presence of the solute.
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Affiliation(s)
- Chong Gu
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue E19-502B, Cambridge Massachusetts 02139, USA
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39
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Giel-Pietraszuk M, Barciszewski J. A nature of conformational changes of yeast tRNAPhe. Int J Biol Macromol 2005; 37:109-14. [PMID: 16236354 DOI: 10.1016/j.ijbiomac.2005.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 09/08/2005] [Accepted: 09/08/2005] [Indexed: 10/25/2022]
Abstract
We analysed conformational changes of yeast tRNA(Phe) induced by high hydrostatic pressure (HHP) measured by Fourier-transform infrared (FTIR) and fluorescence spectroscopies. High pressure influences RNA conformation without other cofactors, such as metal ions and salts. FTIR spectra of yeast tRNA(Phe) recorded at high hydrostatic pressure up to 13 kbar with and without magnesium ions showed a shift of the bands towards higher frequencies. That blue shift is due to an increase a higher energy of bonds as a result of shortening of hydrogen bonds followed by dehydration of tRNA. The fluorescence spectra of Y-base tRNA(Phe) at high pressure up to 3 kbar showed a decrease of the intensity band at 430 nm as a consequence of conformational rearrangement of the anticodon loop leading to exposure of Y-base side chain to the solution. We suggest that structural transition of nucleic acids is driven by the changes of water structure from tetrahedral to a cubic-like geometry induced by high pressure and, in consequence, due to economy of hydration.
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Affiliation(s)
- Małgorzata Giel-Pietraszuk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań 61-704, Poland.
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40
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Dohm JA, Hsu MH, Hwu JR, Huang RCC, Moudrianakis EN, Lattman EE, Gittis AG. Influence of Ions, Hydration, and the Transcriptional Inhibitor P4N on the Conformations of the Sp1 Binding Site. J Mol Biol 2005; 349:731-44. [PMID: 15896803 DOI: 10.1016/j.jmb.2005.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 03/30/2005] [Accepted: 04/01/2005] [Indexed: 11/19/2022]
Abstract
Three crystal structures containing the entire Sp1 consensus sequence d(GGGGCGGGG) with two or three additional base-pairs on either the 5' or 3' ends and overhangs have been determined. Despite the different lengths of DNA in the pseudo-dodecamers and pseudo-tridecamer, all three structures form A-DNA duplexes that share a common set of crystal contacts, including a T*(G.C) base triplet and a 5'-overhang that flips out and away from the helical axes to form a Hoogsteen base-pair with the 3'-overhang of a symmetry mate. The global conformations of the three structures differ, however, in the widths of their respective major grooves, the lengths of the molecules, and the extent of crystal packing. The structures were determined from crystals grown in an unusual precipitant for A-DNA, polyethylene glycol (PEG) 400, in combination with polyamines or ions; cobalt hexamine for the pseudo-tridecamer, and spermidine for the pseudo-dodecamers. As the Sp1 binding site is a target for antiviral and anticancer drugs, pseudo-dodecamer crystals were soaked with one such antiviral and anticancer compound, P4N. Although P4N was not visualized unambiguously in the electron density maps, the effect of the drug is evident from significant differences in the lattice constants, crystal packing, and overall conformation of the structure.
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Affiliation(s)
- Julie A Dohm
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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41
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Tobé S, Heams T, Vergne J, Hervé G, Maurel MC. The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure. Nucleic Acids Res 2005; 33:2557-64. [PMID: 15870387 PMCID: PMC1088306 DOI: 10.1093/nar/gki552] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 04/16/2005] [Accepted: 04/16/2005] [Indexed: 01/07/2023] Open
Abstract
The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 +/- 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 +/- 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms.
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Affiliation(s)
- Sylvia Tobé
- Institut Jacques-Monod, Laboratoire de Biochimie de l'Evolution et Adaptabilité MoléculaireUniversité Paris VI, Tour 43, 2 place Jussieu, 75251 Paris Cedex 05, France
- Laboratoire de Biochimie des Signaux Régulateurs Cellulaires et Moléculaires, FRE 2621 CNRS and Université Pierre et Marie Curie96 Boulevard Raspail 75006 Paris, France
| | - Thomas Heams
- Institut Jacques-Monod, Laboratoire de Biochimie de l'Evolution et Adaptabilité MoléculaireUniversité Paris VI, Tour 43, 2 place Jussieu, 75251 Paris Cedex 05, France
- Laboratoire de Biochimie des Signaux Régulateurs Cellulaires et Moléculaires, FRE 2621 CNRS and Université Pierre et Marie Curie96 Boulevard Raspail 75006 Paris, France
| | - Jacques Vergne
- Institut Jacques-Monod, Laboratoire de Biochimie de l'Evolution et Adaptabilité MoléculaireUniversité Paris VI, Tour 43, 2 place Jussieu, 75251 Paris Cedex 05, France
- Laboratoire de Biochimie des Signaux Régulateurs Cellulaires et Moléculaires, FRE 2621 CNRS and Université Pierre et Marie Curie96 Boulevard Raspail 75006 Paris, France
| | - Guy Hervé
- Laboratoire de Biochimie des Signaux Régulateurs Cellulaires et Moléculaires, FRE 2621 CNRS and Université Pierre et Marie Curie96 Boulevard Raspail 75006 Paris, France
| | - Marie-Christine Maurel
- To whom correspondence should be addressed. Tel: +33 1 44 27 40 21; Fax: +33 1 44 27 99 16;
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42
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Kumar A, Mishra PC, Suhai S. Adiabatic Electron Affinities of the Polyhydrated Adenine−Thymine Base Pair: A Density Functional Study. J Phys Chem A 2005; 109:3971-9. [PMID: 16833718 DOI: 10.1021/jp0456178] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adiabatic electron affinities (AEAs) of the adenine-thymine (AT) base pair surrounded by 5 and 13 water molecules have been studied by density functional theory (DFT). Geometries of neutral AT x nH2O and anionic (AT x nH2O)- complexes (n = 5 and 13) were fully optimized, and vibrational frequency analysis was performed at the B3LYP/6-31+G** level of theory. The optimized structures of the neutral (AT x nH2O) and (AT x nH2O)- complexes were found to be somewhat nonplanar. Some of the water molecules are displaced away from the AT ring plane and linked with one another by hydrogen bonds. The optimized structures of the complexes are found to be in a satisfactory agreement with the observed experimental and molecular dynamics simulation results. In the optimized anionic complexes, the thymine (T) moiety was found to be puckered, whereas the adenine (A) moiety remained almost planar. Natural population analysis (NPA) performed using the B3LYP/6-31+G** method shows that the thymine moiety in the anionic (AT x nH2O)- complexes (n = 5 and 13) has most of the excess electronic charge, i.e., approximately -0.87 and approximately -0.81 (in the unit of magnitude of the electronic charge), respectively. The zero-point energy corrected adiabatic electron affinities of the hydrated AT base pair were found to be positive both for n = 5 and 13 and have the values of 0.97 and 0.92 eV, respectively, which are almost three times the AEA of the AT base pair. The results show that the presence of water molecules appreciably enhances the EA of the base pair.
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Affiliation(s)
- Anil Kumar
- Department of Physics, Banaras Hindu University, Varanasi-221 005, India
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Aertsen A, Van Houdt R, Vanoirbeek K, Michiels CW. An SOS response induced by high pressure in Escherichia coli. J Bacteriol 2004; 186:6133-41. [PMID: 15342583 PMCID: PMC515162 DOI: 10.1128/jb.186.18.6133-6141.2004] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although pressure is an important environmental parameter in microbial niches such as the deep sea and is furthermore used in food preservation to inactivate microorganisms, the fundamental understanding of its effects on bacteria remains fragmentary. Our group recently initiated differential fluorescence induction screening to search for pressure-induced Escherichia coli promoters and has already reported induction of the heat shock regulon. Here the screening was continued, and we report for the first time that pressure induces a bona fide SOS response in E. coli, characterized by the RecA and LexA-dependent expression of uvrA, recA, and sulA. Moreover, it was shown that pressure is capable of triggering lambda prophage induction in E. coli lysogens. The remnant lambdoid e14 element, however, could not be induced by pressure, as opposed to UV irradiation, indicating subtle differences between the pressure-induced and the classical SOS response. Furthermore, the pressure-induced SOS response seems not to be initiated by DNA damage, since DeltarecA and lexA1 (Ind-) mutants, which are intrinsically hypersensitive to DNA damage, were not sensitized or were only very slightly sensitized for pressure-mediated killing and since pressure treatment was not found to be mutagenic. In light of these findings, the current knowledge of pressure-mediated effects on bacteria is discussed.
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Affiliation(s)
- Abram Aertsen
- Laboratory of Food Microbiology, K.U.Leuven, Kasteelpark Arenberg 22, B-3001 Heverlee, Belgium
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44
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Popenda M, Milecki J, Adamiak RW. High salt solution structure of a left-handed RNA double helix. Nucleic Acids Res 2004; 32:4044-54. [PMID: 15292450 PMCID: PMC506817 DOI: 10.1093/nar/gkh736] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in 6 M NaClO4. This is the first nucleic acid motif determined at such high salt. Sequential assignments of non-exchangeable proton resonances of the Z-form were based on the hitherto unreported NOE connectivity path [H6(n)-H5'/H5''(n)-H8(n+1)-H1'(n+1)-H6(n+2)] found for left-handed helices. Z-RNA structure shows several conformational features significantly different from Z-DNA. Intra-strand but no inter-strand base stacking was observed for both CpG and GpC steps. Helical twist angles for CpG steps have small positive values (4-7 degrees), whereas GpC steps have large negative values (-61 degrees). In the full-turn model of Z-RNA (12.4 bp per turn), base pairs are much closer to the helix axis than in Z-DNA, thus both the very deep, narrow minor groove with buried cytidine 2'-OH groups, and the major groove are well defined. The 2'-OH group of cytidines plays a crucial role in the Z-RNA structure and its formation; 2'-O-methylation of cytidine, but not of guanosine residues prohibits A to Z helicity reversal.
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Affiliation(s)
- Mariusz Popenda
- Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznań, Poland and Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
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45
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Filipponi A, De Panfilis S, Oliva C, Ricci MA, D'Angelo P, Bowron DT. Ion hydration under pressure. PHYSICAL REVIEW LETTERS 2003; 91:165505. [PMID: 14611414 DOI: 10.1103/physrevlett.91.165505] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2003] [Indexed: 05/24/2023]
Abstract
The pressure dependence of the radial distribution of water oxygen atoms around Rb+ and Br- ions in a diluted RbBr aqueous solution has been investigated by means of x-ray absorption spectroscopy at the Br and Rb K edges up to 2.8 GPa, using a large-volume high-pressure setup developed at a third generation synchrotron radiation facility. Dramatic effects in the anion hydration structure, in particular, are observed, indicating that upon increasing pressure water undergoes a structural transformation which involves considerable molecular reorientation.
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Affiliation(s)
- Adriano Filipponi
- Dipartimento di Fisica, Università degli Studi dell'Aquila, and Istituto Nazionale per la Fisica della Materia, Unità di Ricerca L'Aquila, Italy
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46
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Monleón D, Esteve V, Celda B. NMR study of hexanucleotide d(CCGCGG)2 containing two triplet repeats of fragile X syndrome. Biochem Biophys Res Commun 2003; 303:81-90. [PMID: 12646170 DOI: 10.1016/s0006-291x(03)00304-8] [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: 11/24/2022]
Abstract
Long repeated stretches of d(CCG) and tri-nucleotide are crucial mutations that cause hereditary forms of mental retardation (fragile X-syndrome). Moreover, the alternating (CG) di-nucleotide is one of the candidates for Z-DNA conformation. Solution NMR structure of d(CCGCGG)(2) has been solved and is discussed. The determined NMR solution structure is a distorted highly bent B-DNA conformation with increased flexibility in both terminal residues. This conformation differs significantly from the Z-DNA tetramer structure reported for the same hexamer in the crystal state at similar ionic strength by Malinina and co-workers. Crystal structure of d(CCGCGG)(2) at high salt concentration includes a central alternating tetramer in Z-DNA conformation, while the initial cytosine swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. In solution, NMR data for sugar ring puckering combined with restrained molecular dynamics simulations starting from a Z-DNA form show that terminal furanose residues could adopt the conformation required for aromatic bases swinging out. Therefore, tetramer formation could be considered possible once the hexanucleotide had previously adopted the Z-DNA form. This work gives some insight into correlations between anomalous crystal structures and their accessibility in the solution state.
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Affiliation(s)
- Daniel Monleón
- Departamento de Química Física, Universitat de València, Edifici d'Investigació, Lab 3-054, C/ Dr. Moliner, 50, Burjassot, 46100 Valencia, Spain
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Mielcarek M, Barciszewska MZ, Sałanski P, Stobiecki M, Jurczak J, Barciszewski J. Native transfer RNA catalyzes Diels-Alder reaction. Biochem Biophys Res Commun 2002; 294:145-8. [PMID: 12054754 DOI: 10.1016/s0006-291x(02)00452-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this paper we show that transfer ribonucleic acids (tRNAs) catalyze the Diels-Alder cycloaddition reaction. A new DNA oxidative damage product, 6-furfuryladenine (kinetin) or its riboside (diene), was transformed with dimethyl acetylenedicarboxylate or maleic anhydride (dienophile). The reaction proceeds in the presence of tRNA at high pressure but not at ambient condition. If so tRNA in prebiotic conditions (RNA world) had at least two functions: catalytic and a carrier of genetic information. It means that tRNA at high pressure shows catalytic properties and is a true Diels-Alderase.
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Affiliation(s)
- Michal Mielcarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61704 Poznan, Poland
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Macgregor RB. The interactions of nucleic acids at elevated hydrostatic pressure. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:266-76. [PMID: 11983401 DOI: 10.1016/s0167-4838(01)00349-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The application of elevated hydrostatic pressure on the order of a few thousand bar provides insight into the molecular forces responsible for stabilizing the conformations and non-covalent interactions of biological molecules in aqueous solution. In particular, the parameters derived from these studies have enabled researchers to glean information regarding the importance of hydration in the energetics and kinetics of these systems. This review presents data concerned with the application of hydrostatic pressure to study the thermodynamics, kinetics, and structure of nucleic acids and the interactions between nucleic acids and proteins, enzymes, and drugs. These complexes often form extremely stable non-covalent complexes in which electrostatic interactions play an important role. The sensitivity of these interactions to pressure offers a valuable experimental tool for investigating the energetics of the complexes.
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Affiliation(s)
- Robert B Macgregor
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
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Abstract
The pressure-temperature phase diagram of various biomolecules is reviewed. Special attention is focused on the elliptic phase diagram of proteins. The phenomenological thermodynamic theory describing this diagram explains the heat, cold and pressure denaturations in a unified picture. The limitations and possible developments of this theory are discussed as well. It is pointed out that a more complex diagram can be obtained when the intermolecular interactions are also taken into account. In this case metastable states appear on the pressure-temperature (p-T) diagram due to intermolecular interactions. Pressure-temperature phase diagrams of other biopolymers are also discussed. While the p-T diagrams of helix-coil transition of nucleic acids and of gel-liquid crystal transition of lipid bilayers are non-elliptical, those of gelatinization of starch and of phase separation of some synthetic polymers show an elliptic profile, similar to that of proteins. Finally, the p-T diagram of bacterial inactivation is shown to be elliptic. From the point of view of basic science, this fact shows that the key factor of inactivation should be the protein type, and from the viewpoint of practical applications, it serves as the theoretical basis of pressure treatment of biosystems.
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Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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Boonyaratanakornkit BB, Park CB, Clark DS. Pressure effects on intra- and intermolecular interactions within proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:235-49. [PMID: 11983399 DOI: 10.1016/s0167-4838(01)00347-8] [Citation(s) in RCA: 275] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The effects of pressure on protein structure and function can vary dramatically depending on the magnitude of the pressure, the reaction mechanism (in the case of enzymes), and the overall balance of forces responsible for maintaining the protein's structure. Interactions between the protein and solvent are also critical in determining the response of a protein to pressure. Pressure has long been recognized as a potential denaturant of proteins, often promoting the disruption of multimeric proteins, but recently examples of pressure-induced stabilization have also been reported. These global effects can be explained in terms of pressure effects on individual molecular interactions within proteins, including hydrophobic, electrostatic, and van der Waals interactions, which can now be studied in greater detail than ever before. However, many uncertainties remain, and thorough descriptions of how proteins respond to pressure remain elusive. This review summarizes basic concepts and new findings related to pressure effects on intra- and intermolecular interactions within proteins and protein complexes, and discusses their implications for protein structure-function relationships under pressure.
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