1
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Naranjo C, Doncel-Giménez A, Gómez R, Aragó J, Ortí E, Sánchez L. Solvent-dependent self-assembly of N-annulated perylene diimides. From dimers to supramolecular polymers. Chem Sci 2023; 14:9900-9909. [PMID: 37736635 PMCID: PMC10510848 DOI: 10.1039/d3sc03372d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023] Open
Abstract
The synthesis and self-assembling features of the N-annulated perylene diimide (NPBI) 1 in different solvents are reported. Compound 1 possesses two chiral linkers, derived from (S)-(+)-alaninol, that connect the central aromatic NPBI segment and the peripheral trialkoxybenzamide units. The Ala-based linker has been demonstrated to strongly favor the formation of intramolecularly H-bonded seven-membered pseudocycles. NPBI 1 shows a strong tendency to self-assemble even in a good solvent like CHCl3 and the formation of chiral dimers is detected in this good solvent. Both experimental techniques and theoretical calculations reveal that the intramolecular H-bonded pseudocycles are very robust and the formation of chiral dimers is driven by the π-stacking of two units of the NPBI core. Unexpectedly, an efficient transfer of the asymmetry of the point chirality at the linker to the aromatic moiety is observed in the molecularly dissolved state. Changing the solvent to more apolar methylcyclohexane modifies the self-assembly process and the formation of chiral supramolecular polymers is detected. The supramolecular polymerization of 1 is demonstrated to follow an isodesmic mechanism unlike previous referable systems. In the formation of the supramolecular polymers of 1, the combination of experimental and computational data indicates that the H-bonded pseudocycles are also present in the aggregated state and the rope-like, columnar aggregates formed by the self-assembly of 1 rely on the π-stacking of the NPBI backbones.
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Affiliation(s)
- Cristina Naranjo
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid 28040 Madrid Spain
| | - Azahara Doncel-Giménez
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia C/Catedrático José Beltrán, 2 46980 Paterna Spain
| | - Rafael Gómez
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid 28040 Madrid Spain
| | - Juan Aragó
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia C/Catedrático José Beltrán, 2 46980 Paterna Spain
| | - Enrique Ortí
- Instituto de Ciencia Molecular (ICMol), Universidad de Valencia C/Catedrático José Beltrán, 2 46980 Paterna Spain
| | - Luis Sánchez
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid 28040 Madrid Spain
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2
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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] [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
Database-derived water probability densities around structurally and sequentially distinct DNA dinucleotide fragments reproduce the known hydration motifs, which thus can be used as building blocks to predict DNA hydration. 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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3
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Recombination-independent recognition of DNA homology for meiotic silencing in Neurospora crassa. Proc Natl Acad Sci U S A 2021; 118:2108664118. [PMID: 34385329 DOI: 10.1073/pnas.2108664118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The pairing of homologous chromosomes represents a critical step of meiosis in nearly all sexually reproducing species. In many organisms, pairing involves chromosomes that remain apparently intact. The mechanistic nature of homology recognition at the basis of such pairing is unknown. Using "meiotic silencing by unpaired DNA" (MSUD) as a model process, we demonstrate the existence of a cardinally different approach to DNA homology recognition in meiosis. The main advantage of MSUD over other experimental systems lies in its ability to identify any relatively short DNA fragment lacking a homologous allelic partner. Here, we show that MSUD does not rely on the canonical mechanism of meiotic recombination, yet it is promoted by REC8, a conserved component of the meiotic cohesion complex. We also show that certain patterns of interspersed homology are recognized as pairable during MSUD. Such patterns need to be colinear and must contain short tracts of sequence identity spaced apart at 21 or 22 base pairs. By using these periodicity values as a guiding parameter in all-atom molecular modeling, we discover that homologous DNA molecules can pair by forming quadruplex-based contacts with an interval of 2.5 helical turns. This process requires right-handed plectonemic coiling and additional conformational changes in the intervening double-helical segments. Our results 1) reconcile genetic and biophysical evidence for the existence of direct homologous double-stranded DNA (dsDNA)-dsDNA pairing, 2) identify a role for this process in initiating RNA interference, and 3) suggest that chromosomes can be cross-matched by a precise mechanism that operates on intact dsDNA molecules.
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Harp JM, Coates L, Sullivan B, Egli M. Water structure around a left-handed Z-DNA fragment analyzed by cryo neutron crystallography. Nucleic Acids Res 2021; 49:4782-4792. [PMID: 33872377 PMCID: PMC8096259 DOI: 10.1093/nar/gkab264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/28/2021] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
Even in high-quality X-ray crystal structures of oligonucleotides determined at a resolution of 1 Å or higher, the orientations of first-shell water molecules remain unclear. We used cryo neutron crystallography to gain insight into the H-bonding patterns of water molecules around the left-handed Z-DNA duplex [d(CGCGCG)]2. The neutron density visualized at 1.5 Å resolution for the first time allows us to pinpoint the orientations of most of the water molecules directly contacting the DNA and of many second-shell waters. In particular, H-bond acceptor and donor patterns for water participating in prominent hydration motifs inside the minor groove, on the convex surface or bridging nucleobase and phosphate oxygen atoms are finally revealed. Several water molecules display entirely unexpected orientations. For example, a water molecule located at H-bonding distance from O6 keto oxygen atoms of two adjacent guanines directs both its deuterium atoms away from the keto groups. Exocyclic amino groups of guanine (N2) and cytosine (N4) unexpectedly stabilize waters H-bonded to O2 keto oxygens from adjacent cytosines and O6 keto oxygens from adjacent guanines, respectively. Our structure offers the most detailed view to date of DNA solvation in the solid-state undistorted by metal ions or polyamines.
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Affiliation(s)
- Joel M Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Martin Egli
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
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5
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Competition between chiral solvents and chiral monomers in the helical bias of supramolecular polymers. Nat Chem 2021; 13:200-207. [PMID: 33257888 DOI: 10.1038/s41557-020-00583-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 10/19/2020] [Indexed: 01/30/2023]
Abstract
Solute-solvent interactions are key for the assembly and proper functioning of biomacromolecules and play important roles in many fields of organic and polymer chemistry. Despite numerous reports describing the effects of (chiral) solvents on helical conformations of (supramolecular) polymers, the combination of chiral solvents and chiral monomers is unexplored. Here we report diastereomeric differences in the supramolecular polymerization of enantiomers of chiral triphenylene-2,6,10-tricarboxamides in chiral chlorinated solvents. Competition between the preferences induced by the stereocentres of the assembled monomers and those present in the solvent molecules results in unforeseen temperature-dependent solvation effects. By combining experiments and mathematical modelling, we show that the observed differences between enantiomers originate from the combined additive entropic effects of stereocentres present in the monomer and in the solvent. Remarkably, copolymerizations show that the chiral solvent can bias the copolymer helicity and thereby overrule the helical preference of the monomers. Our results highlight the importance of cumulative solvation effects in supramolecular polymerizations.
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6
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Li K, Yatsunyk L, Neidle S. Water spines and networks in G-quadruplex structures. Nucleic Acids Res 2021; 49:519-528. [PMID: 33290519 PMCID: PMC7797044 DOI: 10.1093/nar/gkaa1177] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.
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Affiliation(s)
- Kevin Li
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Liliya Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
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7
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Thomas LH, Altaner CM, Forsyth VT, Mossou E, Kennedy CJ, Martel A, Jarvis MC. Nanostructural deformation of high-stiffness spruce wood under tension. Sci Rep 2021; 11:453. [PMID: 33432070 PMCID: PMC7801420 DOI: 10.1038/s41598-020-79676-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
Conifer wood is an exceptionally stiff and strong material when its cellulose microfibrils are well aligned. However, it is not well understood how the polymer components cellulose, hemicelluloses and lignin co-operate to resist tensile stress in wood. From X-ray scattering, neutron scattering and spectroscopic data, collected under tension and processed by novel methods, the ordered, disordered and hemicellulose-coated cellulose components comprising each microfibril were shown to stretch together and demonstrated concerted, viscous stress relaxation facilitated by water. Different cellulose microfibrils did not all stretch to the same degree. Attempts were made to distinguish between microfibrils showing large and small elongation but these domains were shown to be similar with respect to orientation, crystalline disorder, hydration and the presence of bound xylan. These observations are consistent with a major stress transfer process between microfibrils being shear at interfaces in direct, hydrogen-bonded contact, as demonstrated by small-angle neutron scattering. If stress were transmitted between microfibrils by bridging hemicelluloses these might have been expected to show divergent stretching and relaxation behaviour, which was not observed. However lignin and hemicellulosic glucomannans may contribute to stress transfer on a larger length scale between microfibril bundles (macrofibrils).
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Affiliation(s)
- Lynne H Thomas
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Clemens M Altaner
- New Zealand School of Forestry, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - V Trevor Forsyth
- Institut Laue-Langevin, 38042, Grenoble Cedex 9, France.,Partnership for Structural Biology (PSB), 38042, Grenoble Cedex 9, France.,Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Estelle Mossou
- Institut Laue-Langevin, 38042, Grenoble Cedex 9, France.,Partnership for Structural Biology (PSB), 38042, Grenoble Cedex 9, France.,Faculty of Natural Sciences, Keele University, Staffordshire, ST5 5BG, UK
| | - Craig J Kennedy
- School of Energy, Geoscience, Infrastructure and Society, Heriot Watt University, Edinburgh, EH14 4AS, Scotland, UK
| | - Anne Martel
- Institut Laue-Langevin, 38042, Grenoble Cedex 9, France
| | - Michael C Jarvis
- School of Chemistry, Glasgow University, Glasgow, G12 8QQ, Scotland, UK.
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8
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Hepler NK, Bowman A, Carey RE, Cosgrove DJ. Expansin gene loss is a common occurrence during adaptation to an aquatic environment. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:666-680. [PMID: 31627246 DOI: 10.1111/tpj.14572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/24/2019] [Accepted: 10/07/2019] [Indexed: 05/15/2023]
Abstract
Expansins comprise a superfamily of plant cell wall loosening proteins that can be divided into four individual families (EXPA, EXPB, EXLA and EXLB). Aside from inferred roles in a variety of plant growth and developmental traits, little is known regarding the function of specific expansin clades, for which there are at least 16 in flowering plants (angiosperms); however, there is evidence to suggest that some expansins have cell-specific functions, in root hair and pollen tube development, for example. Recently, two duckweed genomes have been sequenced (Spirodela polyrhiza strains 7498 and 9509), revealing significantly reduced superfamily sizes. We hypothesized that there would be a correlation between expansin loss and morphological reductions seen among highly adapted aquatic species. In order to provide an answer to this question, we characterized the expansin superfamilies of the greater duckweed Spirodela, the marine eelgrass Zostera marina and the bladderwort Utricularia gibba. We discovered rampant expansin gene and clade loss among the three, including a complete absence of the EXLB family and EXPA-VII. The most convincing correlation between morphological reduction and expansin loss was seen for Utricularia and Spirodela, which both lack root hairs and the root hair expansin clade EXPA-X. Contrary to the pattern observed in other species, four Utricularia expansins failed to branch within any clade, suggesting that they may be the result of neofunctionalization. Last, an expansin clade previously discovered only in eudicots was identified in Spirodela, allowing us to conclude that the last common ancestor of monocots and eudicots contained a minimum of 17 expansins.
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Affiliation(s)
- Nathan K Hepler
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Alexa Bowman
- Program in Biochemistry and Molecular Biology, Lebanon Valley College, 101 N. College Ave., Annville, PA, 17003, USA
| | - Robert E Carey
- Department of Biology, Lebanon Valley College, 101 N. College Ave., Annville, PA, 17003, USA
| | - Daniel J Cosgrove
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
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9
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Dans PD, Balaceanu A, Pasi M, Patelli AS, Petkevičiūtė D, Walther J, Hospital A, Bayarri G, Lavery R, Maddocks JH, Orozco M. The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules. Nucleic Acids Res 2019; 47:11090-11102. [PMID: 31624840 PMCID: PMC6868377 DOI: 10.1093/nar/gkz905] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 09/25/2019] [Accepted: 10/06/2019] [Indexed: 12/12/2022] Open
Abstract
We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distribution of its stochastic dynamics. Our analysis includes a study of first and second moments of the equilibrium distribution, which can be accurately captured by a harmonic model, but with nonlocal sequence-dependence. We characterize the sequence-dependent choreography of backbone and base movements modulating the non-Gaussian or anharmonic effects manifested in the higher moments of the dynamics of the duplex when sampling the equilibrium distribution. Contrary to prior assumptions, such anharmonic deformations are not rare in DNA and can play a significant role in determining DNA conformation within complexes. Polymorphisms in helical geometries are particularly prevalent for certain tetranucleotide sequence contexts and are always coupled to a complex network of coordinated changes in the backbone. The analysis of our simulations, which contain instances of all tetranucleotide sequences, allow us to extend Calladine-Dickerson rules used for decades to interpret the average geometry of DNA, leading to a set of rules with quantitative predictive power that encompass nonlocal sequence-dependence and anharmonic fluctuations.
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Affiliation(s)
- Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
- Department of Biological Sciences, University of the Republic (UdelaR), CENUR Gral. Rivera 1350, 50000 Salto, Uruguay
| | - Alexandra Balaceanu
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Marco Pasi
- LBPA, École normale supérieure Paris-Saclay, 61 Av. du Pdt Wilson, Cachan 94235, France
- Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - Alessandro S Patelli
- Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Daiva Petkevičiūtė
- Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
- Faculty of Mathematics and Natural Sciences, Kaunas University of Technology, Studentų g. 50, 51368 Kaunas, Lithuania
| | - Jürgen Walther
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Genís Bayarri
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
| | - Richard Lavery
- Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - John H Maddocks
- Institute of Mathematics, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain
- Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain
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10
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Wong JTY. Architectural Organization of Dinoflagellate Liquid Crystalline Chromosomes. Microorganisms 2019; 7:microorganisms7020027. [PMID: 30678153 PMCID: PMC6406473 DOI: 10.3390/microorganisms7020027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/12/2019] [Accepted: 01/17/2019] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates have some of the largest genome sizes, but lack architectural nucleosomes. Their liquid crystalline chromosomes (LCCs) are the only non-architectural protein-mediated chromosome packaging systems, having high degrees of DNA superhelicity, liquid crystalline condensation and high levels of chromosomal divalent cations. Recent observations on the reversible decompaction–recompaction of higher-order structures implicated that LCCs are composed of superhelical modules (SPMs) comprising highly supercoiled DNA. Orientated polarizing light photomicrography suggested the presence of three compartments with different packaging DNA density in LCCs. Recent and previous biophysical data suggest that LCCs are composed of: (a) the highly birefringent inner core compartment (i) with a high-density columnar-hexagonal mesophase (CH-m); (b) the lower-density core surface compartment (ii.1) consisting of a spiraling chromonema; (c) the birefringent-negative periphery compartment (ii.2) comprising peripheral chromosomal loops. C(ii.1) and C(ii.2) are in dynamic equilibrium, and can merge into a single compartment during dinomitosis, regulated through multiphasic reversible soft-matter phase transitions.
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Affiliation(s)
- Joseph Tin Yum Wong
- Division of Life Science, Hong Kong University of Life Science, Clearwater Bay, Kowloon, Hong Kong.
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11
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Vandavasi VG, Blakeley MP, Keen DA, Hu LR, Huang Z, Kovalevsky A. Temperature-Induced Replacement of Phosphate Proton with Metal Ion Captured in Neutron Structures of A-DNA. Structure 2018; 26:1645-1650.e3. [PMID: 30244969 PMCID: PMC6281803 DOI: 10.1016/j.str.2018.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/02/2018] [Accepted: 08/01/2018] [Indexed: 11/18/2022]
Abstract
Nucleic acids can fold into well-defined 3D structures that help determine their function. Knowing precise nucleic acid structures can also be used for the design of nucleic acid-based therapeutics. However, locations of hydrogen atoms, which are key players of nucleic acid function, are normally not determined with X-ray crystallography. Accurate determination of hydrogen atom positions can provide indispensable information on protonation states, hydrogen bonding, and water architecture in nucleic acids. Here, we used neutron crystallography in combination with X-ray diffraction to obtain joint X-ray/neutron structures at both room and cryo temperatures of a self-complementary A-DNA oligonucleotide d[GTGG(CSe)CAC]2 containing 2'-SeCH3 modification on Cyt5 (CSe) at pH 5.6. We directly observed protonation of a backbone phosphate oxygen of Ade7 at room temperature. The proton is replaced with hydrated Mg2+ upon cooling the crystal to 100 K, indicating that metal binding is favored at low temperature, whereas proton binding is dominant at room temperature.
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Affiliation(s)
- Venu Gopal Vandavasi
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37922, USA
| | - Matthew P Blakeley
- Large Scale Structures Group, Institut Laue-Langevin, Grenoble 38000, France
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | | | - Zhen Huang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
| | - Andrey Kovalevsky
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37922, USA.
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12
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Fibre diffraction studies of biological macromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:43-87. [DOI: 10.1016/j.pbiomolbio.2017.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/21/2017] [Accepted: 04/05/2017] [Indexed: 12/27/2022]
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13
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Case R, Schollmeyer H, Kohl P, Sirota EB, Pynn R, Ewert KE, Safinya CR, Li Y. Hydration forces between aligned DNA helices undergoing B to A conformational change: In-situ X-ray fiber diffraction studies in a humidity and temperature controlled environment. J Struct Biol 2017; 200:283-292. [PMID: 28734842 DOI: 10.1016/j.jsb.2017.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 07/08/2017] [Accepted: 07/18/2017] [Indexed: 10/19/2022]
Abstract
Hydration forces between DNA molecules in the A- and B-Form were studied using a newly developed technique enabling simultaneous in situ control of temperature and relative humidity. X-ray diffraction data were collected from oriented calf-thymus DNA fibers in the relative humidity range of 98%-70%, during which DNA undergoes the B- to A-form transition. Coexistence of both forms was observed over a finite humidity range at the transition. The change in DNA separation in response to variation in humidity, i.e. change of chemical potential, led to the derivation of a force-distance curve with a characteristic exponential decay constant of∼2Å for both A- and B-DNA. While previous osmotic stress measurements had yielded similar force-decay constants, they were limited to B-DNA with a surface separation (wall-to-wall distance) typically>5Å. The current investigation confirms that the hydration force remains dominant even in the dry A-DNA state and at surface separation down to∼1.5Å, within the first hydration shell. It is shown that the observed chemical potential difference between the A and B states could be attributed to the water layer inside the major and minor grooves of the A-DNA double helices, which can partially interpenetrate each other in the tightly packed A phase. The humidity-controlled X-ray diffraction method described here can be employed to perform direct force measurements on a broad range of biological structures such as membranes and filamentous protein networks.
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Affiliation(s)
- Ryan Case
- Materials, Physics and Molecular, Cellular and Developmental Biology Departments, University of California at Santa Barbara, CA 93106, United States
| | - Hauke Schollmeyer
- Materials, Physics and Molecular, Cellular and Developmental Biology Departments, University of California at Santa Barbara, CA 93106, United States
| | - Phillip Kohl
- Materials Research Laboratory, University of California at Santa Barbara, CA 93106, United States
| | - Eric B Sirota
- Corporate Strategic Research, ExxonMobil Research and Engineering Co., Annandale, NJ 08801, United States
| | - Roger Pynn
- Department of Physics and Center for the Exploration of Energy and Matter, Indiana University, Bloomington, IN 47408, United States; Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Kai E Ewert
- Materials, Physics and Molecular, Cellular and Developmental Biology Departments, University of California at Santa Barbara, CA 93106, United States
| | - Cyrus R Safinya
- Materials, Physics and Molecular, Cellular and Developmental Biology Departments, University of California at Santa Barbara, CA 93106, United States.
| | - Youli Li
- Materials Research Laboratory, University of California at Santa Barbara, CA 93106, United States.
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14
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Biological Structures. NEUTRON SCATTERING - APPLICATIONS IN BIOLOGY, CHEMISTRY, AND MATERIALS SCIENCE 2017. [DOI: 10.1016/b978-0-12-805324-9.00001-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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15
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Haertlein M, Moulin M, Devos JM, Laux V, Dunne O, Trevor Forsyth V. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. Methods Enzymol 2016; 566:113-57. [DOI: 10.1016/bs.mie.2015.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Dans PD, Faustino I, Battistini F, Zakrzewska K, Lavery R, Orozco M. Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA. Nucleic Acids Res 2014; 42:11304-20. [PMID: 25223784 PMCID: PMC4191396 DOI: 10.1093/nar/gku809] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 11/12/2022] Open
Abstract
We have made a detailed study of one of the most surprising sources of polymorphism in B-DNA: the high twist/low twist (HT/LT) conformational change in the d(CpG) base pair step. Using extensive computations, complemented with database analysis, we were able to characterize the twist polymorphism in the d(CpG) step in all the possible tetranucleotide environment. We found that twist polymorphism is coupled with BI/BII transitions, and, quite surprisingly, with slide polymorphism in the neighboring step. Unexpectedly, the penetration of cations into the minor groove of the d(CpG) step seems to be the key element in promoting twist transitions. The tetranucleotide environment also plays an important role in the sequence-dependent d(CpG) polymorphism. In this connection, we have detected a previously unexplored intramolecular C-H···O hydrogen bond interaction that stabilizes the low twist state when 3'-purines flank the d(CpG) step. This work explains a coupled mechanism involving several apparently uncorrelated conformational transitions that has only been partially inferred by earlier experimental or theoretical studies. Our results provide a complete description of twist polymorphism in d(CpG) steps and a detailed picture of the molecular choreography associated with this conformational change.
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Affiliation(s)
- Pablo Daniel Dans
- Joint BSC-CRG-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Ignacio Faustino
- Joint BSC-CRG-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Federica Battistini
- Joint BSC-CRG-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Krystyna Zakrzewska
- Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - Richard Lavery
- Bases Moléculaires et Structurales des Systèmes Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors, Lyon 69367, France
| | - Modesto Orozco
- Joint BSC-CRG-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain Departament de Bioquimica, Facultat de Biologia, Avgda Diagonal 647, Barcelona 08028, Spain
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17
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Šmarda P, Bureš P, Horová L, Leitch IJ, Mucina L, Pacini E, Tichý L, Grulich V, Rotreklová O. Ecological and evolutionary significance of genomic GC content diversity in monocots. Proc Natl Acad Sci U S A 2014; 111:E4096-102. [PMID: 25225383 PMCID: PMC4191780 DOI: 10.1073/pnas.1321152111] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Genomic DNA base composition (GC content) is predicted to significantly affect genome functioning and species ecology. Although several hypotheses have been put forward to address the biological impact of GC content variation in microbial and vertebrate organisms, the biological significance of GC content diversity in plants remains unclear because of a lack of sufficiently robust genomic data. Using flow cytometry, we report genomic GC contents for 239 species representing 70 of 78 monocot families and compare them with genomic characters, a suite of life history traits and climatic niche data using phylogeny-based statistics. GC content of monocots varied between 33.6% and 48.9%, with several groups exceeding the GC content known for any other vascular plant group, highlighting their unusual genome architecture and organization. GC content showed a quadratic relationship with genome size, with the decreases in GC content in larger genomes possibly being a consequence of the higher biochemical costs of GC base synthesis. Dramatic decreases in GC content were observed in species with holocentric chromosomes, whereas increased GC content was documented in species able to grow in seasonally cold and/or dry climates, possibly indicating an advantage of GC-rich DNA during cell freezing and desiccation. We also show that genomic adaptations associated with changing GC content might have played a significant role in the evolution of the Earth's contemporary biota, such as the rise of grass-dominated biomes during the mid-Tertiary. One of the major selective advantages of GC-rich DNA is hypothesized to be facilitating more complex gene regulation.
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Affiliation(s)
- Petr Šmarda
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic;
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
| | - Lucie Horová
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Surrey TW93DS, United Kingdom
| | - Ladislav Mucina
- School of Plant Biology, University of Western Australia, Perth, WA 6009, Australia; Centre for Geographic Analysis, Department of Geography and Environmental Studies, Stellenbosch University, Stellenbosch 7600, South Africa; and
| | - Ettore Pacini
- Department of Life Sciences, Siena University, 53100 Siena, Italy
| | - Lubomír Tichý
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
| | - Vít Grulich
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
| | - Olga Rotreklová
- Department of Botany and Zoology, Masaryk University, CZ-61137 Brno, Czech Republic
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18
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Dupont S, Rapoport A, Gervais P, Beney L. Survival kit of Saccharomyces cerevisiae for anhydrobiosis. Appl Microbiol Biotechnol 2014; 98:8821-34. [DOI: 10.1007/s00253-014-6028-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/08/2014] [Accepted: 08/10/2014] [Indexed: 01/08/2023]
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19
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Fu K, Li S, Jiang X, Wang Y, Willis BG. DNA gold nanoparticle nanocomposite films for chemiresistive vapor sensing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14335-14343. [PMID: 24111781 DOI: 10.1021/la402626p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chemiresistive vapor sensors combining functionalized gold nanoparticles and single-stranded DNA oligomers are investigated to enhance specificity in chemical sensing. Sensors are made by depositing DNA-functionalized gold nanoparticles onto microfabricated electrodes using four distinct sequences. Sensor performance is evaluated for response to relative humidity and exposure to vapor analytes including ethanol, methanol, hexane, dimethyl methylphosphonate, and toluene under different relative humidity. It is found that sensors display a nonmonotonic resistance change toward increasing humidity due to the combined effects of hydration induced swelling and ionic conduction. Responses to vapor analytes show sequence-dependent patterns as well as a strong influence of humidity. Overall, the findings are encouraging for using DNA oligomers to enhance specificity in chemical sensing.
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Affiliation(s)
- Kan Fu
- Department of Materials Science and Engineering, University of Connecticut , Storrs, Connecticut 06269, United States
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20
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Valle-Orero J, Wildes A, Garden JL, Peyrard M. Purification of A-Form DNA Fiber Samples by the Removal of B-Form DNA Residues. J Phys Chem B 2013; 117:1849-56. [DOI: 10.1021/jp311199f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jessica Valle-Orero
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Andrew Wildes
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Jean-Luc Garden
- Institut Néel, CNRS - Université Joseph Fourier, 25 rue des Martyrs, BP
166, 38042 Grenoble cedex 9, France
| | - Michel Peyrard
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée
d’Italie, 69364 Lyon Cedex 07, France
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21
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Wei D, Wilson WD, Neidle S. Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster. J Am Chem Soc 2013; 135:1369-77. [PMID: 23276263 DOI: 10.1021/ja308952y] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported. A highly conserved cluster of 11 linked water molecules has been found in the native and all 3 ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing noncovalently binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by, hydrogen bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA.
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Affiliation(s)
- DengGuo Wei
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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22
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Sawada D, Nishiyama Y, Langan P, Forsyth VT, Kimura S, Wada M. Water in crystalline fibers of dihydrate β-chitin results in unexpected absence of intramolecular hydrogen bonding. PLoS One 2012; 7:e39376. [PMID: 22724007 PMCID: PMC3378566 DOI: 10.1371/journal.pone.0039376] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
The complete crystal structure (including hydrogen) of dihydrate β-chitin, a homopolymer of N-acetylglucosamine hydrate, was determined using high-resolution X-ray and neutron fiber diffraction data collected from bathophilous tubeworm Lamellibrachia satsuma. Two water molecules per N-acetylglucosamine residue are clearly localized in the structure and these participate in most of the hydrogen bonds. The conformation of the labile acetamide groups and hydroxymethyl groups are similar to those found in anhydrous β-chitin, but more relaxed. Unexpectedly, the intrachain O3-H…O5 hydrogen bond typically observed for crystalline β,1–4 glycans is absent, providing important insights into its relative importance and its relationship to solvation.
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Affiliation(s)
- Daisuke Sawada
- Department of Biomaterials Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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23
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Valle-Orero J, Garden JL, Richard J, Wildes A, Peyrard M. Glassy Behavior of Denatured DNA Films Studied by Differential Scanning Calorimetry. J Phys Chem B 2012; 116:4394-402. [DOI: 10.1021/jp301128j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jessica Valle-Orero
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
| | - Jean-Luc Garden
- Institut Néel, CNRS - Université Joseph Fourier, 25 rue des Martyrs, BP 166, 38042 Grenoble Cedex 9, France
| | - Jacques Richard
- Institut Néel, CNRS - Université Joseph Fourier, 25 rue des Martyrs, BP 166, 38042 Grenoble Cedex 9, France
| | - Andrew Wildes
- Institut Laue Langevin, BP 156, 6, rue Jules Horowitz 38042 Grenoble Cedex 9, France
| | - Michel Peyrard
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 07, France
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24
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Cornicchi E, Sebastiani F, De Francesco A, Orecchini A, Paciaroni A, Petrillo C, Sacchetti F. Collective density fluctuations of DNA hydration water in the time-window below 1 ps. J Chem Phys 2011; 135:025101. [PMID: 21766968 DOI: 10.1063/1.3609101] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The coherent density fluctuations propagating through DNA hydration water were studied by neutron scattering spectroscopy. Two collective modes were found to be sustained by the aqueous solvent: a propagating excitation, characterised by a speed of about 3500 m/s, and another one placed at about 6 meV. These results globally agree with those previously found for the coherent excitations in bulk water, although in DNA hydration water the speed of propagating modes is definitely higher than that of the pure solvent. The short-wavelength collective excitations of DNA hydration water are reminiscent of those observed in protein hydration water and in the amorphous forms of ice.
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Affiliation(s)
- Elena Cornicchi
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy.
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25
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van Eijck L, Merzel F, Rols S, Ollivier J, Forsyth VT, Johnson MR. Direct determination of the base-pair force constant of DNA from the acoustic phonon dispersion of the double helix. PHYSICAL REVIEW LETTERS 2011; 107:088102. [PMID: 21929208 DOI: 10.1103/physrevlett.107.088102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Indexed: 05/31/2023]
Abstract
Quantifying the molecular elasticity of DNA is fundamental to our understanding of its biological functions. Recently different groups, through experiments on tailored DNA samples and numerical models, have reported a range of stretching force constants (0.3 to 3 N/m). However, the most direct, microscopic measurement of DNA stiffness is obtained from the dispersion of its vibrations. A new neutron scattering spectrometer and aligned, wet spun samples have enabled such measurements, which provide the first data of collective excitations of DNA and yield a force constant of 83 N/m. Structural and dynamic order persists unchanged to within 15 K of the melting point of the sample, precluding the formation of bubbles. These findings are supported by large scale phonon and molecular dynamics calculations, which reconcile hard and soft force constants.
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Affiliation(s)
- L van Eijck
- Reactor Institute Delft, Delft University of Technology, Mekelweg 15, 2629JB, Delft, The Netherlands.
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26
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Wildes A, Theodorakopoulos N, Valle-Orero J, Cuesta-López S, Garden JL, Peyrard M. Structural correlations and melting of B-DNA fibers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:061923. [PMID: 21797419 DOI: 10.1103/physreve.83.061923] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Indexed: 05/31/2023]
Abstract
Despite numerous attempts, understanding the thermal denaturation of DNA is still a challenge due to the lack of structural data on the transition since standard experimental approaches to DNA melting are made in solution and do not provide spatial information. We report a measurement using neutron scattering from oriented DNA fibers to determine the size of the regions that stay in the double-helix conformation as the melting temperature is approached from below. A Bragg peak from the B form of DNA is observed as a function of temperature and its width and integrated intensity are measured. These results, complemented by a differential calorimetry study of the melting of B-DNA fibers as well as electrophoresis and optical observation data, are analyzed in terms of a one-dimensional mesoscopic model of DNA.
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27
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Khesbak H, Savchuk O, Tsushima S, Fahmy K. The Role of Water H-Bond Imbalances in B-DNA Substate Transitions and Peptide Recognition Revealed by Time-Resolved FTIR Spectroscopy. J Am Chem Soc 2011; 133:5834-42. [DOI: 10.1021/ja108863v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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28
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Wildes A, Theodorakopoulos N, Valle-Orero J, Cuesta-López S, Garden JL, Peyrard M. Thermal denaturation of DNA studied with neutron scattering. PHYSICAL REVIEW LETTERS 2011; 106:048101. [PMID: 21405364 DOI: 10.1103/physrevlett.106.048101] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Indexed: 05/30/2023]
Abstract
The melting transition of DNA, whereby the strands of the double-helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fiber DNA has been measured as a function of temperature, and its widths and integrated intensities have been interpreted using the Peyrard-Bishop-Dauxois model with only one free parameter. The experiment is unique, as it gives spatial correlation along the molecule through the melting transition where other techniques cannot.
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29
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Bonnet J, Colotte M, Coudy D, Couallier V, Portier J, Morin B, Tuffet S. Chain and conformation stability of solid-state DNA: implications for room temperature storage. Nucleic Acids Res 2009; 38:1531-46. [PMID: 19969539 PMCID: PMC2836546 DOI: 10.1093/nar/gkp1060] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There is currently wide interest in room temperature storage of dehydrated DNA. However, there is insufficient knowledge about its chemical and structural stability. Here, we show that solid-state DNA degradation is greatly affected by atmospheric water and oxygen at room temperature. In these conditions DNA can even be lost by aggregation. These are major concerns since laboratory plastic ware is not airtight. Chain-breaking rates measured between 70 degrees C and 140 degrees C seemed to follow Arrhenius' law. Extrapolation to 25 degrees C gave a degradation rate of about 1-40 cuts/10(5) nucleotides/century. However, these figures are to be taken as very tentative since they depend on the validity of the extrapolation and the positive or negative effect of contaminants, buffers or additives. Regarding the secondary structure, denaturation experiments showed that DNA secondary structure could be preserved or fully restored upon rehydration, except possibly for small fragments. Indeed, below about 500 bp, DNA fragments underwent a very slow evolution (almost suppressed in the presence of trehalose) which could end in an irreversible denaturation. Thus, this work validates using room temperature for storage of DNA if completely protected from water and oxygen.
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Affiliation(s)
- Jacques Bonnet
- Université de Bordeaux-plateforme Génomique Fonctionnelle, Institut Bergonié-INSERM U916 VINCO, Bordeaux, France.
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30
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31
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Kozich V, Szyc Ł, Nibbering E, Werncke W, Elsaesser T. Ultrafast redistribution of vibrational energy after excitation of NH stretching modes in DNA oligomers. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.03.059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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Leal RMF, Teixeira SCM, Blakeley MP, Mitchell EP, Forsyth VT. A preliminary neutron crystallographic study of an A-DNA crystal. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:232-5. [PMID: 19255472 PMCID: PMC2650452 DOI: 10.1107/s1744309109002668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 01/21/2009] [Indexed: 11/10/2022]
Abstract
The LADI-III diffractometer at the Institut Laue-Langevin has been used to carry out a preliminary neutron crystallographic study of the self-complementary DNA oligonucleotide d(AGGGGCCCCT)(2) in the A conformation. The results demonstrate the viability of a full neutron crystallographic analysis with the aim of providing enhanced information on the ion-water networks that are known to be important in stabilizing A-DNA. This is the first account of a single-crystal neutron diffraction study of A-DNA. The study was carried out with the smallest crystal used to date for a neutron crystallographic study of a biological macromolecule.
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Affiliation(s)
- Ricardo M. F. Leal
- ESRF, 6 Rue Jules Horowitz, Grenoble, France
- Institut Laue–Langevin, 6 Rue Jules Horowitz, Grenoble, France
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - Susana C. M. Teixeira
- Institut Laue–Langevin, 6 Rue Jules Horowitz, Grenoble, France
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | | | - Edward P. Mitchell
- ESRF, 6 Rue Jules Horowitz, Grenoble, France
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
| | - V. Trevor Forsyth
- Institut Laue–Langevin, 6 Rue Jules Horowitz, Grenoble, France
- EPSAM and ISTM, Keele University, Staffordshire ST5 5BG, England
- Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble, France
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33
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Szyc Ł, Dwyer JR, Nibbering ET, Elsaesser T. Ultrafast dynamics of N–H and O–H stretching excitations in hydrated DNA oligomers. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Lin MM, Shorokhov D, Zewail AH. Structural ultrafast dynamics of macromolecules: diffraction of free DNA and effect of hydration. Phys Chem Chem Phys 2009; 11:10619-32. [DOI: 10.1039/b910794k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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35
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Loi P, Matsukawa K, Ptak G, Clinton M, Fulka J, Nathan Y, Arav A. Freeze-dried somatic cells direct embryonic development after nuclear transfer. PLoS One 2008; 3:e2978. [PMID: 18714340 PMCID: PMC2500158 DOI: 10.1371/journal.pone.0002978] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 07/02/2008] [Indexed: 11/19/2022] Open
Abstract
The natural capacity of simple organisms to survive in a dehydrated state has long been exploited by man, with lyophylization the method of choice for the long term storage of bacterial and yeast cells. More recently, attempts have been made to apply this procedure to the long term storage of blood cells. However, despite significant progress, practical application in a clinical setting is still some way off. Conversely, to date there are no reports of attempts to lyophilize nucleated somatic cells for possible downstream applications. Here we demonstrate that lyophilised somatic cells stored for 3 years at room temperature are able to direct embryonic development following injection into enucleated oocytes. These remarkable results demonstrate that alternative systems for the long-term storage of cell lines are now possible, and open unprecedented opportunities in the fields of biomedicine and for conservation strategies.
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Affiliation(s)
- Pasqualino Loi
- Department of Comparative Biomedical Sciences, Teramo University, Teramo, Italy.
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36
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Force-induced structural transitions in cross-linked DNA films. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:749-57. [DOI: 10.1007/s00249-008-0257-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 10/18/2007] [Accepted: 12/21/2007] [Indexed: 10/22/2022]
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37
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38
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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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Harris SA, Laughton CA. A simple physical description of DNA dynamics: quasi-harmonic analysis as a route to the configurational entropy. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2007; 19:076103. [PMID: 22251585 DOI: 10.1088/0953-8984/19/7/076103] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
It has become increasingly apparent that the dynamic as well as the structural properties of biological macromolecules are important to their function. However, information concerning molecular flexibility can be difficult to obtain experimentally at the atomic level. Computer modelling techniques such as molecular dynamics (MD) have therefore proved invaluable in advancing our understanding of biomolecular flexibility. This paper describes how a combination of atomistic MD simulations and quasi-harmonic analysis can be used to describe the dynamics of duplex DNA, with a particular emphasis on methods for calculating differences in configurational entropies. We demonstrate that DNA possesses remarkably simple mechanical properties relative to globular proteins, making it an ideal system for exploring biomolecular flexibility in general. Our results also highlight the importance of solvent viscosity in determining the dynamic behaviour of DNA in aqueous solution.
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Affiliation(s)
- S A Harris
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
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Abstract
The helix-to-coil denaturation transition in DNA has been investigated in mixed solvents at high concentration using ultraviolet light absorption spectroscopy and small-angle neutron scattering. Two solvents have been used: water and ethylene glycol. The "melting" transition temperature was found to be 94 degrees C for 4% mass fraction DNA/d-water and 38 degrees C for 4% mass fraction DNA/d-ethylene glycol. The DNA melting transition temperature was found to vary linearly with the solvent fraction in the mixed solvents case. Deuterated solvents (d-water and d-ethylene glycol) were used to enhance the small-angle neutron scattering signal and 0.1M NaCl (or 0.0058 g/g mass fraction) salt concentration was added to screen charge interactions in all cases. DNA structural information was obtained by small-angle neutron scattering, including a correlation length characteristic of the inter-distance between the hydrogen-containing (desoxyribose sugar-amine base) groups. This correlation length was found to increase from 8.5 to 12.3 A across the melting transition. Ethylene glycol and water mixed solvents were found to mix randomly in the solvation region in the helix phase, but nonideal solvent mixing was found in the melted coil phase. In the coil phase, solvent mixtures are more effective solvating agents than either of the individual solvents. Once melted, DNA coils behave like swollen water-soluble synthetic polymer chains.
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Affiliation(s)
- Boualem Hammouda
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD, USA.
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Krisch M, Mermet A, Grimm H, Forsyth VT, Rupprecht A. Phonon dispersion of oriented DNA by inelastic x-ray scattering. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:061909. [PMID: 16906866 DOI: 10.1103/physreve.73.061909] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Indexed: 05/11/2023]
Abstract
Films of oriented deoxyribonucleic acid (DNA), prepared by the wet spinning method, have been studied using inelastic x-ray scattering. Spectra were recorded within the range of energy transfers -30< homega <30 meV at momentum transfers homegaQ ranging from 2.5 to 30 nm(-1) whereby the direction of Q essentially coincided with the helical axis. Measurements at ambient temperature cover samples in the A, B, C, and D conformations of DNA. Within the limits of the instrumental resolution, the spectra were analyzed by the response of a damped harmonic oscillator delivering dispersion and damping of modes having displacements with nonzero projections onto Q, i.e., essentially the compression waves traveling along the helical axis. The longitudinal speed of sound resulting from the sinusoidal dispersion varies only weakly with conformation. Our sound speed values are compared to results from Brillouin spectroscopy. The dispersion curves exhibit a minimum at about the inverse rise per residue, which -- together with strong elastic scattering -- reflect the large degree of disorder. Overdamping of the modes is observed for Q>5 nm(-1). The possibility that the observed large damping parameters are due to several contributing modes is discussed in terms of a simple model calculation for an idealized double helix. Whereas the quasicrystalline approximation for an effective disordered chain could well describe the sinusoidal dispersion, it fails to reproduce the observed damping by one order of magnitude. Our results indicate that the high-frequency dynamics of DNA is liquidlike and is most appropriately described by instantaneous normal modes of short correlation length.
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Affiliation(s)
- M Krisch
- European Synchrotron Radiation Facility, Boîte Postale 220, F-38043 Grenoble Cedex, France
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Langan P, Li X, Hanson BL, Coates L, Mustyakimov M. Synthesis, capillary crystallization and preliminary joint X-ray and neutron crystallographic study of Z-DNA without polyamine at low pH. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:453-6. [PMID: 16682774 PMCID: PMC2219980 DOI: 10.1107/s174430910601236x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2006] [Accepted: 04/04/2006] [Indexed: 05/09/2023]
Abstract
In order to crystallographically study the hydration of the major groove (convex surface) of Z-DNA, the oligonucleotide d(CGCGCG) has been synthesized. Single crystals were grown by vapor diffusion using the hanging-drop and sitting-drop methods for X-ray studies and by batch crystallization and evaporation within silicon tubes for neutron studies. Hexagonal crystals were obtained without the use of duplex-stabilizing polyamines and at an acid pH. X-ray data collected at room temperature (1.5 angstroms resolution; unit-cell parameters a = 17.90, b = 30.59, c = 44.61 angstroms) and at 100 K (1 angstroms resolution; a = 17.99, b = 30.98, c = 44.07 angstroms) and neutron data collected at room temperature (1.6 angstroms resolution; a = 18.00, b = 31.16, c = 44.88 angstroms) indicate that the DNA is in the Z-form packing in space group P2(1)2(1)2(1).
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Affiliation(s)
- Paul Langan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Rayan G, Macgregor RB. Comparison of the Heat- and Pressure-Induced Helix−Coil Transition of Two DNA Copolymers. J Phys Chem B 2005; 109:15558-65. [PMID: 16852973 DOI: 10.1021/jp050899c] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The helix-coil transition of poly[d(I-C)] and poly[d(A-T)] was studied as a function of hydrostatic pressure, temperature, and sodium ion concentration. These studies were undertaken in light of a recently published phase diagram for double stranded nucleic acids [Dubins et al. J. Am. Chem. Soc. 2001, 123, 9254-9259]. The sign and magnitude of the volume change for the heat-induced helix-coil transition, DeltaV(T), of poly[d(I-C)] and poly[d(A-T)] were dependent on the helix-coil transition temperature, T(M), at atmospheric pressure. The sign of DeltaV(T) changed from negative to positive as T(M) was increased by increasing the sodium ion concentration. For poly[d(I-C)], DeltaV(T) = 0 cm(3) mol(-1), when the sodium ion concentration is such that the spectroscopically monitored T(M) = 55 degrees C at atmospheric pressure. For poly[d(A-T)], the value of DeltaV(T) = 0 under conditions such that T(M) = 47 degrees C at atmospheric pressure. Negative values of DeltaV(T) imply that the helical form is destabilized at high pressure. Under experimental conditions where the DeltaV(T) for the transition is negative, the transition could be caused by increasing the pressure under isothermal conditions. At temperatures below T(M) measured at atmospheric pressure the midpoint of the pressure-induced helix-coil transition, P(M), decreases with increasing temperature. The volume change of the pressure-induced transitions helix-coil transition, DeltaV(P), was calculated assuming a two-state model. The magnitude of DeltaV(P) (per cooperative length) was much larger than the volume change (per base pair) measured for the heat-induced transition, DeltaV(T), calculated using the Clapeyron equation. The ratio of these two volume changes was used to calculate the cooperative length for the pressure-induced transition. This parameter depends strongly on temperature, becoming greater closer to T(M) measured at atmospheric pressure. At temperatures approaching T(M) the magnitude of the cooperative length of the pressure-induced transition is approximately twice that observed for the heat-induced transition (N(T)). On the basis of the temperature dependence of the DeltaV(T) for the two polymers the coefficient of thermal expansion of the two polymers was found to be 0.17 and 0.16 cm(3) K(-1) mol(-1) for poly[d(I-C)] and poly[d(A-T)], respectively.
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Affiliation(s)
- Gamal Rayan
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada
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