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Biedermannová L, Černý J, Malý M, Nekardová M, Schneider B. Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks. Acta Crystallogr D Struct Biol 2022; 78:1032-1045. [PMID: 35916227 PMCID: PMC9344474 DOI: 10.1107/s2059798322006234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022] Open
Abstract
Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 Å) and correctly reproduced the known features of DNA hydration, for example the `spine of hydration' in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.
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Affiliation(s)
- Lada Biedermannová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Michal Malý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Michaela Nekardová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
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Schneider B, Božíková P, Nečasová I, Čech P, Svozil D, Černý J. A DNA structural alphabet provides new insight into DNA flexibility. Acta Crystallogr D Struct Biol 2018; 74:52-64. [PMID: 29372899 PMCID: PMC5786007 DOI: 10.1107/s2059798318000050] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/02/2018] [Indexed: 11/10/2022] Open
Abstract
DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson-Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2.
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Affiliation(s)
- Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
| | - Paulína Božíková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
| | - Iva Nečasová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
| | - Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czechia
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28 Prague, Czechia
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, CZ-252 50 Vestec, Czechia
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Gilski M, Drozdzal P, Kierzek R, Jaskolski M. Atomic resolution structure of a chimeric DNA-RNA Z-type duplex in complex with Ba(2+) ions: a case of complicated multi-domain twinning. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:211-23. [PMID: 26894669 DOI: 10.1107/s2059798315024365] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/17/2015] [Indexed: 11/10/2022]
Abstract
The self-complementary dCrGdCrGdCrG hexanucleotide, in which not only the pyrimidine/purine bases but also the ribo/deoxy sugars alternate along the sequence, was crystallized in the presence of barium cations in the form of a left-handed Z-type duplex. The asymmetric unit of the P21 crystal with a pseudohexagonal lattice contains four chimeric duplexes and 16 partial Ba(2+) sites. The chimeric (DNA-RNA)2 duplexes have novel patterns of hydration and exhibit a high degree of discrete conformational disorder of their sugar-phosphate backbones, which can at least partly be correlated with the fractional occupancies of the barium ions. The crystals of the DNA-RNA chimeric duplex in complex with Ba(2+) ions and also with Sr(2+) ions exhibit complicated twinning, which in combination with structural pseudosymmetry made structure determination difficult. The structure could be successfully solved by molecular replacement in space groups P1 and P21 but not in orthorhombic or higher symmetry and, after scrupulous twinning and packing analysis, was refined in space group P21 to an R and Rfree of 11.36 and 16.91%, respectively, using data extending to 1.09 Å resolution. With the crystal structure having monoclinic symmetry, the sixfold crystal twinning is a combination of threefold and twofold rotations. The paper describes the practical aspects of dealing with cases of complicated twinning and pseudosymmetry, and compares the available software tools for the refinement and analysis of such cases.
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Affiliation(s)
- Miroslaw Gilski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Pawel Drozdzal
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations. J Biol Inorg Chem 2015; 20:595-602. [PMID: 25687556 PMCID: PMC4381091 DOI: 10.1007/s00775-015-1247-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/23/2015] [Indexed: 11/25/2022]
Abstract
This work is part of our project aimed at characterizing metal-binding properties of left-handed Z-DNA helices. The three Cr3+ cations found in the asymmetric unit of the d(CGCGCG)2–Cr3+ crystal structure do not form direct coordination bonds with atoms of the Z-DNA molecule. Instead, the hydrated Cr3+ ions are engaged in outer-sphere interactions with phosphate groups and O6 and N7 guanine atoms of the DNA. The Cr3+(1) and Cr3+(2) ions have disordered coordination spheres occupied by six water molecules each. These partial-occupancy chromium cations are 2.354(15) Å apart and are bridged by three water molecules from their hydration spheres. The Cr3+(3) cation has distorted square pyramidal geometry. In addition to the high degree of disorder of the DNA backbone, alternate conformations are also observed for the deoxyribose and base moieties of the G2 nucleotide. Our work illuminates the question of conformational flexibility of Z-DNA and its interaction mode with transition-metal cations.
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Luo Z, Dauter M, Dauter Z. Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1790-800. [PMID: 25004957 PMCID: PMC4089481 DOI: 10.1107/s1399004714004684] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 02/28/2014] [Indexed: 11/11/2022]
Abstract
A large number of Z-DNA hexamer duplex structures and a few oligomers of different lengths are available, but here the first crystal structure of the d(CGCGCGCGCGCG)2 dodecameric duplex is presented. Two synchrotron data sets were collected; one was used to solve the structure by the single-wavelength anomalous dispersion (SAD) approach based on the anomalous signal of P atoms, the other set, extending to an ultrahigh resolution of 0.75 Å, served to refine the atomic model to an R factor of 12.2% and an R(free) of 13.4%. The structure consists of parallel duplexes arranged into practically infinitely long helices packed in a hexagonal fashion, analogous to all other known structures of Z-DNA oligomers. However, the dodecamer molecule shows a high level of flexibility, especially of the backbone phosphate groups, with six out of 11 phosphates modeled in double orientations corresponding to the two previously observed Z-DNA conformations: Z(I), with the phosphate groups inclined towards the inside of the helix, and Z(II), with the phosphate groups rotated towards the outside of the helix.
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Affiliation(s)
- Zhipu Luo
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Miroslawa Dauter
- Leidos Biomedical Research Inc., Basic Research Program, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA
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Drozdzal P, Gilski M, Kierzek R, Lomozik L, Jaskolski M. Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1180-90. [PMID: 23695262 DOI: 10.1107/s0907444913007798] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 03/20/2013] [Indexed: 11/10/2022]
Abstract
X-ray crystal structures of the spermine(4+) form of the Z-DNA duplex with the self-complementary d(CG)3 sequence in complexes with Mn(2+) and Zn(2+) cations have been determined at the ultrahigh resolutions of 0.75 and 0.85 Å, respectively. Stereochemical restraints were only used for the sperminium cation (in both structures) and for nucleotides with dual conformation in the Zn(2+) complex. The Mn(2+) and Zn(2+) cations at the major site, designated M(2+)(1), bind at the N7 position of G6 by direct coordination. The coordination geometry of this site was octahedral, with complete hydration shells. An additional Zn(2+)(2) cation was bis-coordinated in a tetrahedral fashion by the N7 atoms of G10 and G12 from a symmetry-related molecule. The coordination distances of Zn(2+)(1) and Zn(2+)(2) to the O6 atom of the guanine residues were 3.613 (6) and 3.258 (5) Å, respectively. Moreover, a chloride ion was also identified in the coordination sphere of Zn(2+)(2). Alternate conformations were observed in the Z-DNA-Zn(2+) structure not only at internucleotide linkages but also at the terminal C3'-OH group of G12. The conformation of the sperminium chain in the Z-DNA-Mn(2+) complex is similar to the spermine(4+) conformation in analogous Z-DNA-Mg(2+) structures. In the Z-DNA-Zn(2+) complex the sperminium cation is disordered and partially invisible in electron-density maps. In the Z-DNA-Zn(2+) complex the sperminium cation only interacts with the phosphate groups of the Z-DNA molecules, while in the Z-DNA-Mn(2+) structure it forms hydrogen bonds to both the phosphate groups and DNA bases.
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Affiliation(s)
- Pawel Drozdzal
- Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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Abstract
Metal ions play a key role in nucleic acid structure and activity. Elucidation of the rules that govern the binding of metal ions is therefore an essential step for better understanding of the nucleic acid functions. This review is as an update to a preceding one (Metal Ions Biol. Syst., 1996, 32, 91-134), in which we offered a general view of metal ion interactions with mono-, di-, tri-, and oligonucleotides in the solid state, based on their crystal structures reported before 1994. In this chapter, we survey all the crystal structures of metal ion complexes with nucleotides involving oligonucleotides reported after 1994 and we have tried to uncover new characteristic metal bonding patterns for mononucleotides and oligonucleotides with A-RNA and A/B/Z-DNA fragments that form duplexes. We do not cover quadruplexes, duplexes with metal-mediated base-pairs, tRNAs, rRNAs in ribosome, ribozymes, and nucleic acid-drug and -protein complexes. Factors that affect metal binding to mononucleotides and oligonucleotide duplexes are also dealt with.
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Peckham HE, Olson WK. Nucleic-acid structural deformability deduced from anisotropic displacement parameters. Biopolymers 2010; 95:254-69. [PMID: 21280021 DOI: 10.1002/bip.21570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 10/11/2010] [Accepted: 11/10/2010] [Indexed: 11/09/2022]
Abstract
The growing numbers of very well resolved nucleic-acid crystal structures with anisotropic displacement parameters provide an unprecedented opportunity to learn about the natural motions of DNA and RNA. Here we report a new Monte-Carlo approach that takes direct account of this information to extract the distortions of covalent structure, base pairing, and dinucleotide geometry intrinsic to regularly organized double-helical molecules. We present new methods to test the validity of the anisotropic parameters and examine the apparent deformability of a variety of structures, including several A, B, and Z DNA duplexes, an AB helical intermediate, an RNA, a ligand-DNA complex, and an enzyme-bound DNA. The rigid-body parameters characterizing the positions of the bases in the structures mirror the mean parameters found when atomic motion is taken into account. The base-pair fluctuations intrinsic to a single structure, however, differ from those extracted from collections of nucleic-acid structures, although selected base-pair steps undergo conformational excursions along routes suggested by the ensembles. The computations reveal surprising new molecular insights, such as the stiffening of DNA and concomitant separation of motions of contacted nucleotides on opposite strands by the binding of Escherichia coli endonuclease VIII, which suggest how the protein may direct enzymatic action.
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Affiliation(s)
- Heather E Peckham
- Wright-Riemann Laboratories, Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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Venkadesh S, Mandal PK, Gautham N. The structure of d(CACACG).d(CGTGTG). Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 65:8-13. [PMID: 19153446 DOI: 10.1107/s1744309108037706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 11/13/2008] [Indexed: 11/10/2022]
Abstract
The crystal structure of d(CACACG).d(CGTGTG) was solved to a resolution of 2.05 A in space group P2(1). The duplex assumes the left-handed Z-DNA structure. The presence of two A.T base pairs in the hexamer does not greatly affect the conformation. The most significant changes compared with the regular structure of Z-DNA are in the values of twist in the central portion of the helix. This variation, as well as others in the values of roll, inclination etc., follow the pattern observed previously in the structure of d(CGCACG).d(CGTGCG).
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Affiliation(s)
- S Venkadesh
- Centre for Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
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Bharanidharan D, Thiyagarajan S, Gautham N. Hexammineruthenium(III) ion interactions with Z-DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:1008-13. [PMID: 18084080 PMCID: PMC2344113 DOI: 10.1107/s1744309107047781] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2007] [Accepted: 09/28/2007] [Indexed: 11/11/2022]
Abstract
The hexamer duplex d(CGCGCA).d(TGCGCG) was crystallized with hexammineruthenium(III) ions in an orthorhombic space group; the crystals diffracted to 1.54 A resolution. Strong ion interactions with the adenine base induce a tautomeric shift from the amino to the imino form. Consequently, the A.T base pairing is disrupted. This structural study may be relevant to metal toxicity.
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Affiliation(s)
- D. Bharanidharan
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India
| | - S. Thiyagarajan
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India
| | - N. Gautham
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamil Nadu, India
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Liu F, Qian P, Yan S, Bu Y. Coupling characteristics and proton transfer mechanisms of guanine–Na+ monohydrate. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2005.11.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Carrasco N, Buzin Y, Tyson E, Halpert E, Huang Z. Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion. Nucleic Acids Res 2004; 32:1638-46. [PMID: 15007109 PMCID: PMC390325 DOI: 10.1093/nar/gkh325] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report here the solid phase synthesis of RNA and DNA oligonucleotides containing the 2'-selenium functionality for X-ray crystallography using multiwavelength anomalous dispersion. We have synthesized the novel 2'-methylseleno cytidine phosphoramidite and improved the accessibility of the 2'-methylseleno uridine phosphoramidite for the synthesis of many selenium-derivatized DNAs and RNAs in large scales. The yields of coupling these Se-nucleoside phosphoramidites into DNA or RNA oligonucleotides were over 99% when 5-(benzylmercapto)-1H-tetrazole was used as the coupling reagent. The UV melting study of A-form dsDNAs indicated that the 2'-selenium derivatization had no effect on the stability of the duplexes with the 3'-endo sugar pucker. Thus, the stems of functional RNA molecules with the same 3'-endo sugar pucker appear to be the ideal sites for the selenium derivatization with 2'-Se-C and 2'-Se-U. Crystallization of the selenium-derivatized oligonucleotides is also reported here. The results demonstrate that this 2'-selenium functionality is suitable for RNA and A-form DNA derivatization in X-ray crystallography.
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Affiliation(s)
- Nicolas Carrasco
- Department of Chemistry, Brooklyn College, and Program of Biochemistry and Chemistry, The Graduate School, The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
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Thorpe JH, Teixeira SCM, Gale BC, Cardin CJ. Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution. Nucleic Acids Res 2003; 31:844-9. [PMID: 12560479 PMCID: PMC149190 DOI: 10.1093/nar/gkg168] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2002] [Revised: 11/21/2002] [Accepted: 11/21/2002] [Indexed: 11/13/2022] Open
Abstract
Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 A. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)-C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson-Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7-N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.
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Affiliation(s)
- James H Thorpe
- The University of Reading, School of Chemistry, Whiteknights, Reading, Berkshire RG6 6AD, UK
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Rulíšek L, Šponer J. Outer-Shell and Inner-Shell Coordination of Phosphate Group to Hydrated Metal Ions (Mg2+, Cu2+, Zn2+, Cd2+) in the Presence and Absence of Nucleobase. The Role of Nonelectrostatic Effects. J Phys Chem B 2003. [DOI: 10.1021/jp027058f] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lubomír Rulíšek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Dolejškova 3, 182 23 Prague, Czech Republic, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
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Muñoz J, Gelpí JL, Soler-López M, Subirana JA, Orozco M, Luque FJ. Can Divalent Metal Cations Stabilize the Triplex Motif? Theoretical Study of the Interaction of the Hydrated Mg2+ Cation with the G−G·C Triplet. J Phys Chem B 2002. [DOI: 10.1021/jp026096w] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jordi Muñoz
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - J. L. Gelpí
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - Montserrat Soler-López
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - Juan A. Subirana
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - Modesto Orozco
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - F. Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
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Muñoz J, Sponer J, Hobza P, Orozco M, Luque FJ. Interactions of Hydrated Mg2+ Cation with Bases, Base Pairs, and Nucleotides. Electron Topology, Natural Bond Orbital, Electrostatic, and Vibrational Study. J Phys Chem B 2001. [DOI: 10.1021/jp010486l] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jordi Muñoz
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jirí Sponer
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Hobza
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Modesto Orozco
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - F. Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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Šponer J, Sabat M, Gorb L, Leszczynski J, Lippert B, Hobza P. The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing. J Phys Chem B 2000. [DOI: 10.1021/jp001711m] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemistry, and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Fachbereich Chemie,
| | - Michal Sabat
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemistry, and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Fachbereich Chemie,
| | - Leonid Gorb
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemistry, and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Fachbereich Chemie,
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemistry, and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Fachbereich Chemie,
| | - Bernhard Lippert
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemistry, and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Fachbereich Chemie,
| | - Pavel Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, Department of Chemistry, and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Fachbereich Chemie,
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Robinson H, Gao YG, Sanishvili R, Joachimiak A, Wang AH. Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes. Nucleic Acids Res 2000; 28:1760-6. [PMID: 10734195 PMCID: PMC102818 DOI: 10.1093/nar/28.8.1760] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/1999] [Revised: 02/28/2000] [Accepted: 02/28/2000] [Indexed: 11/13/2022] Open
Abstract
Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H(2)O)(6)](2+)binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH(3))(6)](3+), a model ion of [Mg(H(2)O)(6)](2+), binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H(2)O)(6)](2+)ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.
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Affiliation(s)
- H Robinson
- Bl07 CLSL, Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA
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Šponer J, Šponer JE, Gorb L, Leszczynski J, Lippert B. Metal-Stabilized Rare Tautomers and Mispairs of DNA Bases: N6-Metalated Adenine and N4-Metalated Cytosine, Theoretical and Experimental Views. J Phys Chem A 1999. [DOI: 10.1021/jp992337x] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, University of Dortmund, 44221 Dortmund, Germany
| | - Judit E. Šponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, University of Dortmund, 44221 Dortmund, Germany
| | - Leonid Gorb
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, University of Dortmund, 44221 Dortmund, Germany
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, University of Dortmund, 44221 Dortmund, Germany
| | - Bernhard Lippert
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Department of Chemistry, University of Dortmund, 44221 Dortmund, Germany
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20
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Kypr J, Chládková J, Zimulová M, Vorlícková M. Aqueous trifluorethanol solutions simulate the environment of DNA in the crystalline state. Nucleic Acids Res 1999; 27:3466-73. [PMID: 10446234 PMCID: PMC148588 DOI: 10.1093/nar/27.17.3466] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We took 28 fragments of DNA whose crystal structures were known and used CD spectroscopy to search for conditions stabilising the crystal structures in solution. All 28 fragments switched into their crystal structures in 60-80% aqueous trifluorethanol (TFE) to indicate that the crystals affected the conformation of DNA like the concentrated TFE. The fragments crystallising in the B-form also underwent cooperative TFE-induced changes that took place within the wide family of B-form structures, suggesting that the aqueous and crystal B-forms differed as well. Spermine and magnesium or calcium cations, which were contained in the crystallisation buffers, promoted or suppressed the TFE-induced changes of several fragments to indicate that the crystallisation agents can decide which of the possible structures is adopted by the DNA fragment in the crystal.
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Affiliation(s)
- J Kypr
- Academy of Sciences of the Czech Republic, Institute of Biophysics, Královopolská 135, CZ-61265 Brno, Czech Republic
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21
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Abstract
Water distributions around phosphate groups in 59 B-, A-, and Z-DNA crystal structures were analyzed. It is shown that the waters are concentrated in six hydration sites per phosphate and that the positions and occupancies of these sites are dependent on the conformation and type of nucleotide. The patterns of hydration that are characteristic of the backbone of the three DNA helical types can be attributed in part to the interactions of these hydration sites.
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Affiliation(s)
- B Schneider
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, CZ-18223 Prague, Czech Republic
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