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Acosta-Reyes FJ, Pagan M, Fonfría-Subirós E, Saperas N, Subirana JA, Campos JL. The influence of Ni 2+ and other ions on the trigonal structure of DNA. Biopolymers 2020; 112:e23397. [PMID: 32898299 DOI: 10.1002/bip.23397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/19/2022]
Abstract
We present a new structure of a DNA dodecamer obtained in the presence of Ni2+ ions. The DNA forms Ni-guanine cross-links between neighboring molecules. Our results show that an adequate dosage of Ni2+ may help to form well-defined DNA nanostructures. We also compare our structure with other dodecamers which present unique features and also crystallize in trigonal unit cells, strongly influenced by the counterions associated with DNA. In all cases, the DNA duplexes form parallel pseudo-helical columns in the crystal, similar to DNA-protamine and native DNA fibers.
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Affiliation(s)
| | - Mireia Pagan
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Elsa Fonfría-Subirós
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Núria Saperas
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - Juan A Subirana
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
| | - J Lourdes Campos
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain
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2
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Hardwick JS, Lane AN, Brown T. Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA. Bioessays 2018; 40. [DOI: 10.1002/bies.201700199] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/13/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Jack S. Hardwick
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew N. Lane
- Department of Toxicology and Cancer Biology; University of Kentucky; 789 S. Limestone St. Lexington KY 40536 USA
| | - Tom Brown
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
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War JA, Srivastava SK, Srivastava SD. Design, synthesis and DNA-binding study of some novel morpholine linked thiazolidinone derivatives. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:270-278. [PMID: 27673496 DOI: 10.1016/j.saa.2016.07.054] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/29/2016] [Accepted: 07/31/2016] [Indexed: 06/06/2023]
Abstract
The emergence of multiple drug resistance amongst bacterial strains resulted in many clinical drugs to be ineffective. Being vulnerable to bacterial infections any lack in the development of new antimicrobial drugs could pose a serious threat to public health. Here we report design and synthesis of a novel class of morpholine linked thiazolidinone hybrid molecules. The compounds were characterized by FT-IR, NMR and HRMS techniques. Susceptibility tests showed that most of the synthesized molecules were highly active against multiple bacterial strains. Compound 3f displayed MIC values which were better than the standard drug for most of the tested strains. DNA being a well defined target for many antimicrobial drugs was probed as possible target for these synthetic molecules. DNA-binding study of 3f with sm-DNA was probed through UV-vis absorption, fluorescence quenching, gel electrophoresis and molecular docking techniques. The studies revealed that compound 3f has strong affinity towards DNA and binds at the minor groove. The docking studies revealed that the compound 3f shows preferential binding towards A/T residues.
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Affiliation(s)
- Javeed Ahmad War
- Synthetic Organic Chemistry & Molecular Modelling Laboratory, Department of Chemistry, Dr. Hari Singh Gour Central University, Sagar, MP 470003, India
| | - Santosh Kumar Srivastava
- Synthetic Organic Chemistry & Molecular Modelling Laboratory, Department of Chemistry, Dr. Hari Singh Gour Central University, Sagar, MP 470003, India.
| | - Savitri Devi Srivastava
- Synthetic Organic Chemistry & Molecular Modelling Laboratory, Department of Chemistry, Dr. Hari Singh Gour Central University, Sagar, MP 470003, India
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Deligkaris C, Ascone AT, Sweeney KJ, Greene AJQ. Validation of a computational docking methodology to identify the non-covalent binding site of ligands to DNA. MOLECULAR BIOSYSTEMS 2015; 10:2106-25. [PMID: 24853173 DOI: 10.1039/c4mb00239c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Despite the biomedical consequences of carcinogen-DNA interactions and the potential of DNA as a drug target in medicinal chemistry, only a small number of studies have validated or used docking methods for the prediction of the physical binding of small molecules to DNA. Knowledge of the DNA-physically-bound ligand geometry can lead to the elucidation of the molecular-level mechanism of drugs as well as predicting the subsequent chemical interactions that lead to DNA damage from carcinogens. We sought to validate AutoDock 4.2, a docking method that includes a physics-based free energy function and a Lamarckian Genetic Algorithm, for the prediction of ligand geometries upon physical binding to DNA. We performed simulations by systematically changing the length of the search process for a comprehensive set of 32 ligand-DNA molecular systems with different physico-chemical properties, and we used a free-energy-based convergence criterion to terminate our simulations. For 11 out of 28 molecular systems for which convergence was achieved, the lowest binding free energy geometries were within 2 Å of the experimentally determined geometry. Considering all predicted sites with free energy changes within 20% of the lowest binding free energy site, we found a site within 2 Å of the experimentally determined geometry for 24 out of the 28 systems. However, the predicted hydrogen bonding interactions were different for most molecular systems compared to the same interactions in the experimentally determined geometry. We discuss reasons for the successes and failures, implications, and the importance of ensuring an adequate search in docking calculations. Overall, we concluded that AutoDock 4.2 can be used to predict the non-covalent binding geometry of a small molecule to DNA with some limitations.
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Wolfe KC, Hastings WA, Dutta S, Long A, Shapiro BA, Woolf TB, Guthold M, Chirikjian GS. Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups. J Phys Chem B 2012; 116:8556-72. [PMID: 22676719 PMCID: PMC4833121 DOI: 10.1021/jp2126015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Several different mechanical models of double-helical nucleic-acid structures that have been presented in the literature are reviewed here together with a new analysis method that provides a reconciliation between these disparate models. In all cases, terminology and basic results from the theory of Lie groups are used to describe rigid-body motions in a coordinate-free way, and when necessary, coordinates are introduced in a way in which simple equations result. We consider double-helical DNAs and RNAs which, in their unstressed referential state, have backbones that are either straight, slightly precurved, or bent by the action of a protein or other bound molecule. At the coarsest level, we consider worm-like chains with anisotropic bending stiffness. Then, we show how bi-rod models converge to this for sufficiently long filament lengths. At a finer level, we examine elastic networks of rigid bases and show how these relate to the coarser models. Finally, we show how results from molecular dynamics simulation at full atomic resolution (which is the finest scale considered here) and AFM experimental measurements (which is at the coarsest scale) relate to these models.
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Affiliation(s)
- Kevin C. Wolfe
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | | | - Samrat Dutta
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States
| | - Andrew Long
- Department of Mechanical Engineering, Northwestern University, Evanston, Illinois, United States
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, United States
| | - Thomas B. Woolf
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Martin Guthold
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, United States
| | - Gregory S. Chirikjian
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
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Koonammackal MV, Nellipparambil UVN, Sudarsanakumar C. Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin. J Mol Model 2011; 17:2805-16. [DOI: 10.1007/s00894-011-0954-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 01/03/2011] [Indexed: 12/27/2022]
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Moreno T, Pous J, Subirana JA, Campos JL. Coiled-coil conformation of a pentamidine–DNA complex. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:251-7. [DOI: 10.1107/s0907444909055693] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 12/29/2009] [Indexed: 01/31/2023]
Abstract
The coiled-coil structure formed by the complex of the DNA duplex d(ATATATATAT)2with pentamidine is presented. The duplex was found to have a mixed structure containing Watson–Crick and Hoogsteen base pairs. The drug stabilizes the coiled coil through the formation of cross-links between neighbouring duplexes. The central part of the drug is found in the minor groove as expected, whereas the charged terminal amidine groups protrude and interact with phosphates from neighbouring molecules. The formation of cross-links may be related to the biological effects of pentamidine, which is used as an antiprotozoal agent in trypanosomiasis, leishmaniasis and pneumonias associated with AIDS. The DNA sequence that was used is highly abundant in most eukaryotic genomes. However, very few data are available on DNA sequences which only contain A·T base pairs.
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Fernández-Botello A, Holý A, Moreno V, Operschall BP, Sigel H. Intramolecular π–π stacking interactions in aqueous solution in mixed-ligand copper(II) complexes formed by heteroaromatic amines and the nucleotide analogue 9-[2-(phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer of the antivirally active 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA). Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.02.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Souard F, Muñoz E, Peñalver P, Badía C, del Villar-Guerra R, Asensio J, Jiménez-Barbero J, Vicent C. Sugar–Oligoamides: Bound-State Conformation and DNA Minor-Groove-Binding Description by TR-NOESY and Differential-Frequency Saturation-Transfer-Difference Experiments. Chemistry 2008; 14:2435-42. [DOI: 10.1002/chem.200701103] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Stettler AR, Chaurin V, Constable EC, Housecroft CE, Schwarz MA. Quantification of single-stranded nucleic acid and oligonucleotide interactions with metal ions by affinity capillary electrophoresis: part I. J Biol Inorg Chem 2006; 12:194-203. [PMID: 17120074 DOI: 10.1007/s00775-006-0180-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Accepted: 09/21/2006] [Indexed: 11/28/2022]
Abstract
The interactions between oligonucleotides and inorganic cations have been measured by capillary zone electrophoresis. With increasing concentrations of divalent cations (Ca(2+), Mg(2+), Mn(2+) and Ni(2+)) in the running buffer, the migration behavior was evaluated by calculation of the binding constants. Besides these fundamental studies of binding equilibria, different buffer components, tris(hydroxymethyl)aminomethane and 3-(N-morpholino)propanesulfonic acid, have been investigated and their effects on metal ion binding quantified.
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Affiliation(s)
- Alexandra R Stettler
- Department of Chemistry, University of Basel, Spitalstrasse 51, 4056, Basel, Switzerland
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Van Hecke K, Nam PC, Nguyen MT, Van Meervelt L. Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations. FEBS J 2005; 272:3531-41. [PMID: 16008554 DOI: 10.1111/j.1742-4658.2005.04773.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The structure of the complex between the minor groove binder netropsin and d(GGCCAATTGG) was determined via single-crystal X-ray techniques. The structure was refined to completion using refmac5.1.24, resulting in a residual R-factor of 20.0% (including 68 water molecules). Using crystal engineering and cryocooling techniques, the resolution could be enhanced to 1.75 A, resulting in an unambiguous determination of the drug conformation and orientation. As previously noticed, bifurcated hydrogen bonds are formed between the amide nitrogen atoms of the drug and the N3 and O2 atoms of A and T base pairs, respectively, clearly cataloging the structure to class I. As the bulky NH2 group on guanine was believed to prevent binding of the drug in the minor groove, the detailed nature of several of the amidinium and guanidinium end contacts were further investigated by ab initio quantum chemical methods.
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Affiliation(s)
- Kristof Van Hecke
- Biomolecular Architecture, Chemistry Department, K.U.Leuven, Heverlee, Belgium
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Goodwin KD, Long EC, Georgiadis MM. A host-guest approach for determining drug-DNA interactions: an example using netropsin. Nucleic Acids Res 2005; 33:4106-16. [PMID: 16049022 PMCID: PMC1181240 DOI: 10.1093/nar/gki717] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Netropsin is a well-characterized DNA minor groove binding compound that serves as a model for the study of drug-DNA interactions. Our laboratory has developed a novel host-guest approach to study drug-DNA interactions in which the host, the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) is co-crystallized with a DNA oligonucleotide guest in the presence and absence of drug. We have co-crystallized netropsin with the RT fragment bound to the symmetric 16mer d(CTTAATTCGAATTAAG)2 and determined the structure of the complex at 1.85 A. In contrast to previously reported netropsin-DNA structures, our oligonucleotide contains two AATT sites that bind netropsin with flanking 5' and 3' sequences that are not symmetric. The asymmetric unit of the RT fragment-DNA-netropsin crystals contains one protein molecule and one-half of the 16mer with one netropsin molecule bound. The guanidinium moiety of netropsin binds in a narrow part of the minor groove, while the amidinium is bound in the widest region within the site. We compare this structure to other Class I netropsin-DNA structures and find that the asymmetry of minor groove widths in the AATT site contributes to the orientation of netropsin within the groove while hydrogen bonding patterns vary in the different structures.
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Affiliation(s)
| | - Eric C. Long
- Department of Chemistry and Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI)IN 46202, USA
| | - Millie M. Georgiadis
- To whom correspondence should be addressed. Tel: +1 317 278 8486; Fax: +1 317 274 4686;
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Lah J, Vesnaver G. Energetic diversity of DNA minor-groove recognition by small molecules displayed through some model ligand-DNA systems. J Mol Biol 2004; 342:73-89. [PMID: 15313608 DOI: 10.1016/j.jmb.2004.07.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2004] [Revised: 07/05/2004] [Accepted: 07/06/2004] [Indexed: 11/22/2022]
Abstract
Energetics of interactions occurring in the model ligand-DNA systems constituted from distamycin A (DST), netropsin (NET) and the oligomeric duplexes d(GCAAGTTGCGATATACG)d(CGTATATCGCAACTTGC)=D#1 and d(GCAAGTTGCGAAAAACG)d(CGTTTTTCGCAACTTGC)=D#2 was studied by spectropolarimetry, UV-absorption spectroscopy and isothermal titration calorimetry. Model analysis of the measured signals was applied to describe individual and competitive binding in terms of populations of various species in the solution. Our results reveal several unprecedented ligand-DNA binding features. DST binds to the neighboring 5'-AAGTT-3' and 5'-ATATA-3' sites of D#1 statistically in a 2:1 binding mode. By contrast, its association to D#2 appears to be a 2:1 binding event only at the DST/D#2 molar ratios between 0 and 2 while its further binding to D#2 may be considered as a step-by-step binding to the unoccupied 5'-AAAAA-3' sites resulting first in DST3D#2 and finally in DST4D#2 complex formation. Competition between DST and NET binding shows that for the most part DST displaces NET from its complexes with D#1 and D#2. In contrast to the obligatory 1:1 binding of DST to the ligand-free 5'-AAAAA-3' sites observed at DST/5'-AAAAA-3' <1 the displacement of NET bound to the 5'-AAAAA-3' sites by added DST occurs even at the smallest additions of DST in a 2:1 manner. NET can also displace DST molecules but only those bound monomerically to the 5'-AAAAA-3' sites of DST3D#2. Actually, only half of these molecules can be displaced due to the simultaneous rebinding of the displaced DST to the unreacted 5'-AAAAA-3' sites in DST3D#2. Binding of DST and NET to D#1 and D#2 is an enthalpy driven process accompanied by large unfavorable (DST), small (NET) or large favorable (NET binding to 5'-AAAAA-3') entropy contributions and negative deltaCP degrees that are reasonably close to deltaCP degrees predicted from the calculated changes in solvent-accessible surface areas that accompany complex formation. Although various modes of DST and NET binding within D#1 and D#2 are characterized by significant energetic differences they seem to be governed by the same driving forces; the hydrophobic transfer of ligand from the solution into the duplex binding site and the accompanying specific non-covalent ligand-DNA and ligand-ligand interactions occurring within the DNA minor groove.
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Affiliation(s)
- Jurij Lah
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Askerceva 5, 1000, Slovenia
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Subirana JA, Soler-Lopez M. Cations as hydrogen bond donors: a view of electrostatic interactions in DNA. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2003; 32:27-45. [PMID: 12598364 DOI: 10.1146/annurev.biophys.32.110601.141726] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cations are bound to nucleic acids in a solvated state. High-resolution X-ray diffraction studies of oligonucleotides provide a detailed view of Mg2+, and occasionally other ions bound to DNA. In a survey of several such structures, certain general observations emerge. First, cations bind preferentially to the guanine base in the major groove or to phosphate group oxygen atoms. Second, cations interact with DNA most frequently via water molecules in their primary solvation shell, direct ion-DNA contacts being only rarely observed. Thus, the solvated ions should be viewed as hydrogen bond donors in addition to point charges. Finally, ion interaction sites are readily exchangeable: The same site may be occupied by any ion, including spermine, as well as by a water molecule.
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Affiliation(s)
- Juan A Subirana
- Departament d'Enginyeria Quimica, Universitat Politecnica de Catalunya, Barcelona, Spain.
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Labiuk SL, Delbaere LTJ, Lee JS. Cobalt(II), nickel(II) and zinc(II) do not bind to intra-helical N(7) guanine positions in the B-form crystal structure of d(GGCGCC). J Biol Inorg Chem 2003; 8:715-20. [PMID: 14505075 DOI: 10.1007/s00775-003-0473-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2003] [Accepted: 05/26/2003] [Indexed: 12/01/2022]
Abstract
Three novel X-ray crystal structures for the DNA hexamer d(GGCGCC) in the B-form complexed to divalent cobalt, nickel and zinc ions have been determined to a resolution of 2.9-3.0 A. The structures were isomorphous and had five DNA strands and five metal cations per asymmetric unit. In all three cases, divalent metal cations were coordinated only to the terminal guanine residue at the N(7) position, with no metal ions binding to non-terminal guanine positions. Water molecules bound to the metal cations interacted with neighboring guanine residues 3' to the ones to which the cations were coordinated, affecting the propeller twist. Even though DNA occupied only about 35% of the unit cell volume, it is interesting that the few interactions involving the metal cations were sufficient to stabilize the crystal lattice. As well as lending support to the proposal that these metals do not coordinate to B-DNA in a stable manner, the results presented here also extend the crystallographic evidence for this phenomenon to the GGC and CGC sequences for all three metal cations.
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Affiliation(s)
- Shaunivan L Labiuk
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, S7N 5E5, Saskatoon, SK, Canada
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Thomas M, Rao AR, Varshney U, Bhattacharya S. Unusual DNA binding exhibited by synthetic distamycin analogues lacking the N-terminal amide unit under high salt conditions. J Biomol Struct Dyn 2001; 18:858-71. [PMID: 11444374 DOI: 10.1080/07391102.2001.10506713] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The binding of three analogues of the minor-groove binding antiviral antibiotic distamycin (Dst) with double-stranded (ds)-DNA were monitored using ds-DNA melting temperature (Tm) measurements, ethidium bromide (EtBr) displacement assay, footprinting analysis and induced circular dichroism (ICD). These compounds contained 3-5 N-methyl-pyrrole-carboxamide units and lacked the N-terminal formamide unit present in Dst. These experiments suggested that the present analogues did not compromise their AT-specificity despite the deletion of the N-terminal formamide unit. The binding affinities, however, were significantly affected. Interestingly, the analogue with three N-methyl-pyrrole-carboxamide units exhibited an initial decrease in ICD at > 40 mM salt concentrations. This was followed by a pronounced recovery of ICD at > 1.6 M salt concentrations, a phenomenon hitherto not observed with any other DNA binding molecules. The pentapyrrole analogue exhibited the highest binding affinity with CT-DNA under normal (40 mM) salt conditions. However, it suffered maximum relative dissociation under high salt conditions and did not exhibit any recovery in ICD at higher NaCl concentrations. The analogues possessing four and five pyrrole rings exhibited intense ICD signals with poly d(GC) in the ligand absorption region in the presence of 40 mM NaCl, unlike the one with three pyrrole rings. These ICD signals were however, highly susceptible to changes in ionic strength. Thus subtle modifications in the ligand molecular structure can have dramatic effect on their DNA binding properties.
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Affiliation(s)
- M Thomas
- Department of Organic Chemistry, Indian Institute of Science, Bangalore
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17
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Abstract
We review the extra-helical guanine interactions present in many oligonucleotide crystals. Very often terminal guanines interact with other guanines in the minor groove of neighboring oligonucleotides through N2 x N3 hydrogen bonds. In other cases the interaction occurs with the help of Ni2+ ions. Guanine/netropsin stacking in the minor groove has also been found. From these studies we conclude that guanine may have multiple extra-helical interactions. In particular it may be considered a very effective minor groove binder, which could be used in the design of sequence selective binding drugs. Interactions through the major groove are seldom encountered, but might be present when DNA is stretched. Such interactions are also analyzed, since they might be important for homologous chromosome pairing during meiosis.
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Affiliation(s)
- J A Subirana
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Barcelona, Spain.
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