1
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Olson WK, Li Y, Fenley MO. Insights into DNA solvation found in protein-DNA structures. Biophys J 2022; 121:4749-4758. [PMID: 36380591 PMCID: PMC9808563 DOI: 10.1016/j.bpj.2022.11.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
The proteins that bind double-helical DNA present various microenvironments that sense and/or induce signals in the genetic material. The high-resolution structures of protein-DNA complexes reveal the nature of both the microenvironments and the conformational responses in DNA and protein. Complex networks of interactions within the structures somehow tie the protein and DNA together and induce the observed spatial forms. Here we show how the cumulative buildup of amino acid atoms around the sugars, phosphates, and bases in different protein-DNA complexes produces a binding cloud around the double helix and how different types of atoms fill that cloud. Rather than focusing on the principles of molecular binding and recognition suggested by the arrangements of amino acids and nucleotides in the macromolecular complexes, we consider the proteins in contact with DNA as organized solvents. We describe differences in the mix of atoms that come in closest contact with DNA, subtle sequence-dependent features in the microenvironment of the sugar-phosphate backbone, a direct link between the localized buildup of ionic species and the electrostatic potential surfaces of the DNA bases, and sites of atomic buildup above and below the basepair planes that transmit the unique features of the base environments along the chain backbone. The inferences about solvation that can be drawn from the survey provide new stimuli for improvement of nucleic acid force fields and fresh ideas for exploration of the properties of DNA in solution.
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Affiliation(s)
- Wilma K Olson
- Department of Chemistry and Chemical Biology and Center for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey.
| | - Yun Li
- Department of Chemistry and Chemical Biology and Center for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey
| | - Marcia O Fenley
- Department of Chemistry and Chemical Biology and Center for Quantitative Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida
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2
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Jakubec M, Pšenáková K, Svehlova K, Curtis EA. Optimizing the Chemiluminescence of a Light-Producing Deoxyribozyme. Chembiochem 2022; 23:e202200026. [PMID: 35286749 DOI: 10.1002/cbic.202200026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/14/2022] [Indexed: 01/05/2023]
Abstract
Supernova is a chemiluminescent deoxyribozyme recently discovered in our group. It transfers the phosphate group from the 1,2-dioxetane substrate CDP-Star to its 5' hydroxyl group, which triggers a decomposition reaction and the production of light. Here we investigated the effects of reaction conditions on the ability of Supernova to generate a chemiluminescent signal (using a plate reader assay) and to phosphorylate itself (using a ligation assay). Our experiments indicate that multiple zinc ions are required for catalytic function, suggesting links between Supernova and protein enzymes that catalyze similar reactions. They also show how factors such as pH, potassium concentration, CDP-Star concentration, and DNA concentration affect the reaction. By combining information from different experiments, the rate enhancement of light production was increased by more than 1000-fold. These results should be useful for applications in which Supernova is used as a sensor.
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Affiliation(s)
- Martin Jakubec
- Institute of Organic Chemistry and Biochemistry, 160 00, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, 128 43, Prague, Czech Republic
| | - Karolína Pšenáková
- Institute of Organic Chemistry and Biochemistry, 160 00, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, 128 43, Prague, Czech Republic
| | - Katerina Svehlova
- Institute of Organic Chemistry and Biochemistry, 160 00, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, 128 43, Prague, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry, 160 00, Prague, Czech Republic
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3
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Svehlova K, Lukšan O, Jakubec M, Curtis EA. Supernova: A Deoxyribozyme that Catalyzes a Chemiluminescent Reaction. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202109347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Katerina Svehlova
- Institute of Organic Chemistry and Biochemistry ASCR Prague Czech Republic
- Faculty of Science Charles University in Prague Prague Czech Republic
| | - Ondřej Lukšan
- Institute of Organic Chemistry and Biochemistry ASCR Prague Czech Republic
| | - Martin Jakubec
- Institute of Organic Chemistry and Biochemistry ASCR Prague Czech Republic
- Faculty of Science Charles University in Prague Prague Czech Republic
| | - Edward A. Curtis
- Institute of Organic Chemistry and Biochemistry ASCR Prague Czech Republic
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4
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Svehlova K, Lukšan O, Jakubec M, Curtis EA. Supernova: A Deoxyribozyme that Catalyzes a Chemiluminescent Reaction. Angew Chem Int Ed Engl 2021; 61:e202109347. [PMID: 34559935 PMCID: PMC9298802 DOI: 10.1002/anie.202109347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/17/2021] [Indexed: 11/10/2022]
Abstract
Functional DNA molecules are useful components in nanotechnology and synthetic biology. To expand the toolkit of functional DNA parts, in this study we used artificial evolution to identify a glowing deoxyribozyme called Supernova. This deoxyribozyme transfers a phosphate from a 1,2-dioxetane substrate to its 5' hydroxyl group, which triggers a chemiluminescent reaction and a flash of blue light. An engineered version of Supernova is only catalytically active in the presence of an oligonucleotide complementary to its 3' end, demonstrating that light production can be coupled to ligand binding. We anticipate that Supernova will be useful in a wide variety of applications, including as a signaling component in allosterically regulated sensors and in logic gates of molecular computers.
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Affiliation(s)
- Katerina Svehlova
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Ondřej Lukšan
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic
| | - Martin Jakubec
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic
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5
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He W, Chen YL, Pollack L, Kirmizialtin S. The structural plasticity of nucleic acid duplexes revealed by WAXS and MD. SCIENCE ADVANCES 2021; 7:7/17/eabf6106. [PMID: 33893104 PMCID: PMC8064643 DOI: 10.1126/sciadv.abf6106] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA's diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.
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Affiliation(s)
- Weiwei He
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Chemistry, New York University, New York, NY, USA
| | - Yen-Lin Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA.
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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6
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Mori Y, Kato S, Fujisawa Y, Ohnishi S, Hiraku Y, Kawanishi S, Murata M, Oikawa S. Mechanisms of DNA damage induced by morin, an inhibitor of amyloid β-peptide aggregation. Free Radic Res 2019; 53:115-123. [PMID: 30572734 DOI: 10.1080/10715762.2018.1562179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Morin is a potential inhibitor of amyloid β-peptide aggregation. This aggregation is involved in the pathogenesis of Alzheimer's disease. Meanwhile, morin has been found to be mutagenic and exhibits peroxidation of membrane lipids concurrent with DNA strand breaks in the presence of metal ions. To clarify a molecular mechanism of morin-induced DNA damage, we examined the DNA damage and its site specificity on 32P-5'-end-labeled human DNA fragments treated with morin plus Cu(II). The formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), an indicator of oxidative DNA damage, was also determined in calf thymus DNA treated with morin plus Cu(II). Morin-induced DNA strand breaks and base modification in the presence of Cu(II) were dose dependent. Morin plus Cu(II) caused piperidine-labile lesions preferentially at thymine and guanine residues. The DNA damage was inhibited by methional, catalase and Cu(I)-chelator bathocuproine. The typical •OH scavengers ethanol, mannitol and sodium formate showed no inhibitory effect on DNA damage induced by morin plus Cu(II). When superoxide dismutase was added to the solution, DNA damage was not inhibited. In addition, morin plus Cu(II) increased 8-oxodG formation in calf thymus DNA fragments. We conclude that morin undergoes autoxidation in the presence of Cu(II) via a Cu(I)/Cu(II) redox cycle and H2O2 generation to produce Cu(I)-hydroperoxide, which causes oxidative DNA damage.
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Affiliation(s)
- Yurie Mori
- a Department of Environmental and Molecular Medicine , Mie University Graduate School of Medicine , Tsu , Japan
| | - Shinya Kato
- b Radioisotope Facilities for Medical Science , Mie University , Tsu , Japan
| | - Yutaka Fujisawa
- c Faculty of Pharmaceutical Sciences , Suzuka University of Medical Science , Suzuka , Japan
| | - Shiho Ohnishi
- c Faculty of Pharmaceutical Sciences , Suzuka University of Medical Science , Suzuka , Japan
| | - Yusuke Hiraku
- a Department of Environmental and Molecular Medicine , Mie University Graduate School of Medicine , Tsu , Japan
| | - Shosuke Kawanishi
- c Faculty of Pharmaceutical Sciences , Suzuka University of Medical Science , Suzuka , Japan
| | - Mariko Murata
- a Department of Environmental and Molecular Medicine , Mie University Graduate School of Medicine , Tsu , Japan
| | - Shinji Oikawa
- a Department of Environmental and Molecular Medicine , Mie University Graduate School of Medicine , Tsu , Japan
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7
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8
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Chandraboss VL, Karthikeyan B, Senthilvelan S. Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO2 clusters of sol–gel silicate material for understanding DNA photodamage. Phys Chem Chem Phys 2015; 17:12100-14. [DOI: 10.1039/c5cp00451a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A sol–gel silicate matrix containing entrapped guanine was prepared. The SiO2 matrix provides UVA protection by reducing the light penetration to the entrapped guanine molecules.
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9
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Pan F, Roland C, Sagui C. Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study. Nucleic Acids Res 2014; 42:13981-96. [PMID: 25428372 PMCID: PMC4267617 DOI: 10.1093/nar/gku1107] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 12/30/2022] Open
Abstract
The ion atmosphere around nucleic acids is an integral part of their solvated structure. However, detailed aspects of the ionic distribution are difficult to probe experimentally, and comparative studies for different structures of the same sequence are almost non-existent. Here, we have used large-scale molecular dynamics simulations to perform a comparative study of the ion distribution around (5'-CGCGCGCGCGCG-3')2 dodecamers in solution in B-DNA, A-RNA, Z-DNA and Z-RNA forms. The CG sequence is very sensitive to ionic strength and it allows the comparison with the rare but important left-handed forms. The ions investigated include Na(+), K(+) and Mg(2 +), with various concentrations of their chloride salts. Our results quantitatively describe the characteristics of the ionic distributions for different structures at varying ionic strengths, tracing these differences to nucleic acid structure and ion type. Several binding pockets with rather long ion residence times are described, both for the monovalent ions and for the hexahydrated Mg[(H2O)6](2+) ion. The conformations of these binding pockets include direct binding through desolvated ion bridges in the GpC steps in B-DNA and A-RNA; direct binding to backbone oxygens; binding of Mg[(H2O)6](2+) to distant phosphates, resulting in acute bending of A-RNA; tight 'ion traps' in Z-RNA between C-O2 and the C-O2' atoms in GpC steps; and others.
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Affiliation(s)
- Feng Pan
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Center for High Performance Simulations (CHiPS) and Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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10
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Guéroult M, Boittin O, Mauffret O, Etchebest C, Hartmann B. Mg2+ in the major groove modulates B-DNA structure and dynamics. PLoS One 2012; 7:e41704. [PMID: 22844516 PMCID: PMC3402463 DOI: 10.1371/journal.pone.0041704] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/25/2012] [Indexed: 12/12/2022] Open
Abstract
This study investigates the effect of Mg(2+) bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5'-CpA or TpG. Based on this knowledge, molecular dynamics simulations were carried out on a DNA oligomer without or with Mg(2+) close to an ApG step. These simulations showed that the hydrated Mg(2+) forms a stable intra-strand cross-link between the two purines in solution. ApG generates an electrostatic potential in the major groove that is particularly attractive for cations; its intrinsic conformation is well-adapted to the formation of water-mediated hydrogen bonds with Mg(2+). The binding of Mg(2+) modulates the behavior of the 5'-neighboring step by increasing the BII (ε-ζ>0°) population of its phosphate group. Additional electrostatic interactions between the 5'-phosphate group and Mg(2+) strengthen both the DNA-cation binding and the BII character of the 5'-step. Cation binding in the major groove may therefore locally influence the DNA conformational landscape, suggesting a possible avenue for better understanding how strong DNA distortions can be stabilized in protein-DNA complexes.
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Affiliation(s)
- Marc Guéroult
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique, Paris, France
| | - Olivier Boittin
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
| | - Oliver Mauffret
- Laboratoire de Biologie et Pharmacologie Appliquée, UMR 8113 CNRS-ENS de Cachan, Cachan, France
| | - Catherine Etchebest
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
| | - Brigitte Hartmann
- Dynamique des Structures et Interactions des Macromolécules Biologiques, UMR 665 INSERM-Université Paris Diderot, Sorbonne Paris Cité, Institut National de la Transfusion Sanguine, Paris, France
- Laboratoire de Biologie et Pharmacologie Appliquée, UMR 8113 CNRS-ENS de Cachan, Cachan, France
- * E-mail:
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11
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Mandal PK, Venkadesh S, Gautham N. Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:393-9. [PMID: 22505405 PMCID: PMC3325805 DOI: 10.1107/s174430911200869x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 02/27/2012] [Indexed: 11/10/2022]
Abstract
The crystal structure of the tetradecanucleotide sequence d(CCCCGGTACCGGGG)(2) has been determined at 2.5 Å resolution in the tetragonal space group P4(1). This sequence was designed with the expectation of a four-way junction. However, the sequence crystallized as an A-DNA duplex and represents more than one full turn of the A-helix. The crystallographic asymmetric unit consists of one tetradecanucleotide duplex. The structural parameters of the A-type DNA duplex structure and the crystal-packing arrangement are described. One Mn(2+) ion was identified with direct coordination to the N7 position of G(13) and a water molecule at the major-groove side of the C(2)·G(13) base pair.
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Affiliation(s)
- Pradeep Kumar Mandal
- C. A. S. in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
| | - Sarkarai Venkadesh
- C. A. S. in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
| | - Namasivayam Gautham
- C. A. S. in Crystallography and Biophysics, University of Madras, Guindy, Chennai 600 025, India
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Foreman AL, Phillips L, Kanellis VG, Hammoudeh D, Naumann C, Wong H, Chisari R, Hibbert DB, Lee GSH, Patra R, Julli M, Chapman J, Cooke AR, dos Remedios CG. A DNA-based assay for toxic chemicals in wastewater. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2011; 30:1810-1818. [PMID: 21560144 DOI: 10.1002/etc.568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 01/06/2011] [Accepted: 03/14/2011] [Indexed: 05/30/2023]
Abstract
Chemical toxicants, particularly metal ions, are a major contaminant in global waterways. Live-organism bioassays used to monitor chemical toxicants commonly involve measurements of activity or survival of a freshwater cladoceran (Ceriodaphnia dubia) or light emitted by the marine bacterium Vibrio fischeri, used in the commercial Microtox® bioassay. Here we describe a novel molecule-based assay system employing DNA as the chemical biosensor. Metals bind to DNA, causing structural changes that expel a bound (intercalated) fluorescent reporter dye. Analyses of test data using 48 wastewater samples potentially contaminated by metal ions show that the DNA-dye assay results correlate with those from C. dubia and Microtox bioassays. All three assays exhibit additive, antagonistic, and synergistic responses that cannot be predicted by knowing individual metal concentrations. Analyses of metals in these samples imply the presence of chemical toxicants other than metal ions. The DNA-dye assay is robust, has a 12-month shelf life, and is only slightly affected by sample pH in the range 4 to 9. The assay is completed in a matter of minutes, and its portability makes it well suited as a screening assay for use in the field. We conclude that the DNA-dye test is a surrogate bioassay suitable for screening chemical toxicity.
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Affiliation(s)
- Amy L Foreman
- The University of Sydney, Sydney, New South Wales, Australia
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13
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Kirmizialtin S, Elber R. Computational exploration of mobile ion distributions around RNA duplex. J Phys Chem B 2010; 114:8207-20. [PMID: 20518549 DOI: 10.1021/jp911992t] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Atomically detailed distributions of ions around an A-form RNA are computed. Different mixtures of monovalent and divalent ions are considered explicitly. Studies of tightly bound and of diffusive (but bound) ions around 25 base pairs RNA are conducted in explicit solvent. Replica exchange simulations provide detailed equilibrium distributions with moderate computing resources (20 ns of simulation using 64 replicas). The simulations show distinct behavior of single and double charged cations. Binding of Mg(2+) ion includes tight binding to specific sites while Na(+) binds only diffusively. The tight binding of Mg(2+) is with a solvation shell while Na(+) can bind directly to RNA. Negative mobile ions can be found near the RNA but must be assisted by proximate and mobile cations. At distances larger than 16 A from the RNA center, a model of RNA as charged rod in a continuum of ionic solution provides quantitative description of the ion density (the same as in atomically detailed simulation). At shorter distances, the structure of RNA (and ions) has a significant impact on the pair correlation functions. Predicted binding sites of Mg(2+) at the RNA surface are in accord with structures from crystallography. Electric field relaxation is investigated. The relaxation due to solution rearrangements is completed in tens of picoseconds, while the contribution of RNA tumbling continues to a few nanoseconds.
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Affiliation(s)
- Serdal Kirmizialtin
- Department of Chemistry and Biochemistry and Institute of Computational Engineering and Sciences (ICES), 1 University Station, ICES, C0200, The University of Texas at Austin, Austin, Texas 78712, USA
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14
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Clore GM, Iwahara J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem Rev 2009; 109:4108-39. [PMID: 19522502 DOI: 10.1021/cr900033p] [Citation(s) in RCA: 588] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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15
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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 II. Electrophoresis 2008; 29:3342-8. [PMID: 18646280 DOI: 10.1002/elps.200700890] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The interactions between tetranucleotides or heptanucleotides and inorganic cations have been measured by affinity CZE. The variation in migration behavior with increasing concentrations of divalent cations (Ca(2+), Mg(2+) and Ni(2+)) in the running buffer was investigated and quantified by the calculation of binding constants for mononuclear and multinuclear interactions. In addition to these fundamental studies of binding equilibria, the effect of sequence and the position of the guanine transition metal-binding site in the oligonucleotide have been investigated.
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16
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He W, Franzini RM, Achim C. Metal-Containing Nucleic Acid Structures Based on Synergetic Hydrogen and Coordination Bonding. PROGRESS IN INORGANIC CHEMISTRY 2008. [DOI: 10.1002/9780470144428.ch8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Zhang Y, Huang K. The influence of the hydrated metal cations binding to adenine-N7 or adenine-N3 on the hydrogen bonding in adenine–thymine base pair: A comparative study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.07.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Semenov VE, Morozov VI, Chernova AV, Shagidullin RR, Mikhailov AS, Giniyatullin RK, Akamsin VD, Reznik VS. Copper(II) bromide complexes with acyclic and cyclic pyrimidine-containing phane ligands. RUSS J COORD CHEM+ 2007. [DOI: 10.1134/s1070328407090114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Vinje J, Sletten E. Internal versus terminal metalation of double-helical oligodeoxyribonucleotides. Chemistry 2007; 12:676-88. [PMID: 16208725 DOI: 10.1002/chem.200500731] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The formation of adducts between cis-[Pt(NH(3))(2)Cl(2)], Zn(II), and Mn(II) and double-stranded oligodeoxynucleotides was studied by 1D and 2D (1)H, (31)P, and (15)N NMR spectroscopy. For labile adducts involving Zn(II) and Mn(II), both (1)H chemical shifts (Zn(II)) and (1)H line-broadening effects (Mn(II)) showed that in the hexamer [d(GGCGCC)](2) I, the terminal G(1)-N7 is the exclusive binding site, while for the dodecamer [d(GGTACCGGTACC)](2) II, which contains both a terminal and internal GG pair, the preference for metal binding is the internal guanine G(7). Zn(II) binding to II was confirmed by natural-abundance 2D [(1)H,(15)N] HMBC NMR spectroscopy, which unambiguously showed that G(7)-N7 is the preferred binding site. The long duplex [d(GGTATATATACCGGTATATATACC)](2) III was expected to have a more pronounced accumulation of electrostatic potential towards the central part of the sequence (vs the terminal part) than does II. However, the Zn(II) titration of III showed no increase in coordination with the internal Gs (vs the terminal Gs), compared with what was observed for II. The reaction between the nonlabile metal complex cis-[PtCl(2)((15)NH(3))(2)] (cisplatin) and II showed a slight preference for the internal GG pair over the terminal GG pair. However, when the diaqua form of cisplatin cis-[Pt((15)NH(3))(2)(H(2)O)(2)] was reacted with II a more pronounced binding preference for the internal GG pair was observed.
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Affiliation(s)
- Jo Vinje
- Centre of Pharmacy, Department of Chemistry, University of Bergen, Norway.
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20
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On the interactions of hydrated metal cations (Mg2+, Mn2+, Ni2+, Zn2+) with guanine–cytosine Watson–Crick and guanine–guanine reverse-Hoogsteen DNA base pairs. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.02.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Winters-Hilt S, Landry M, Akeson M, Tanase M, Amin I, Coombs A, Morales E, Millet J, Baribault C, Sendamangalam S. Cheminformatics methods for novel nanopore analysis of HIV DNA termini. BMC Bioinformatics 2006; 7 Suppl 2:S22. [PMID: 17118144 PMCID: PMC1683570 DOI: 10.1186/1471-2105-7-s2-s22] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Channel current feature extraction methods, using Hidden Markov Models (HMMs) have been designed for tracking individual-molecule conformational changes. This information is derived from observation of changes in ionic channel current blockade "signal" upon that molecule's interaction with (and occlusion of) a single nanometer-scale channel in a "nanopore detector". In effect, a nanopore detector transduces single molecule events into channel current blockades. HMM analysis tools described are used to help systematically explore DNA dinucleotide flexibility, with particular focus on HIV's highly conserved (and highly flexible/reactive) viral DNA termini. One of the most critical stages in HIV's attack is the binding between viral DNA and the retroviral integrase, which is influenced by the dynamic-coupling induced high flexibility of a CA/TG dinucleotide positioned precisely two base-pairs from the blunt terminus of the duplex viral DNA. This suggests the study of a family of such CA/TG dinucleotide molecules via nanopore measurement and cheminformatics analysis. RESULTS HMMs are used for level identification on the current blockades, HMM/EM with boosted variance emissions are used for level projection pre-processing, and time-domain FSAs are used to parse the level-projected waveform for kinetic information. The observed state kinetics of the DNA hairpins containing the CA/TG dinucleotide provides clear evidence for HIV's selection of a peculiarly flexible/interactive DNA terminus.
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Affiliation(s)
- Stephen Winters-Hilt
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - Matthew Landry
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
| | - Mark Akeson
- Department of Chemistry, University of California – Santa Cruz, Santa Cruz, CA 90560, USA
| | - Maria Tanase
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - Iftekhar Amin
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - Amy Coombs
- Department of Chemistry, University of California – Santa Cruz, Santa Cruz, CA 90560, USA
| | - Eric Morales
- The Research Institute for Children, 200 Henry Clay Ave., New Orleans, LA 70118, USA
| | - John Millet
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
| | - Carl Baribault
- Department of Computer Science, University of New Orleans, New Orleans, LA, 70148, USA
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22
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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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23
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Rai P, Wemmer DE, Linn S. Preferential binding and structural distortion by Fe2+ at RGGG-containing DNA sequences correlates with enhanced oxidative cleavage at such sequences. Nucleic Acids Res 2005; 33:497-510. [PMID: 15659581 PMCID: PMC548341 DOI: 10.1093/nar/gki192] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Certain DNA sequences are known to be unusually sensitive to nicking via the Fe2+-mediated Fenton reaction. Most notable are a purine nucleotide followed by three or more G residues, RGGG, and purine nucleotides flanking a TG combination, RTGR. Our laboratory previously demonstrated that nicking in the RGGG sequences occurs preferentially 5' to a G residue with the nicking probability decreasing from the 5' to 3'end of these sequences. Using 1H NMR to characterize Fe2+ binding within the duplex CGAGTTAGGGTAGC/GCTACCCTAACTCG and 7-deazaguanine-containing (Z) variants of it, we show that Fe2+ binds preferentially at the GGG sequence, most strongly towards its 5' end. Substitutions of individual guanines with Z indicate that the high affinity Fe2+ binding at AGGG involves two adjacent guanine N7 moieties. Binding is accompanied by large changes in specific imino, aromatic and methyl proton chemical shifts, indicating that a locally distorted structure forms at the binding site that affects the conformation of the two base pairs 3' to the GGG sequence. The binding of Fe2+ to RGGG contrasts with that previously observed for the RTGR sequence, which binds Fe2+ with negligible structural rearrangements.
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Affiliation(s)
- Priyamvada Rai
- Biophysics Graduate Group, University of California BerkeleyUSA
| | - David E. Wemmer
- Biophysics Graduate Group, University of California BerkeleyUSA
- Department of Chemistry, University of California BerkeleyUSA
| | - Stuart Linn
- Department of Molecular and Cell BiologyBarker HallUniversity of California BerkeleyCA 94720-3202, USA
- Biophysics Graduate Group, University of California BerkeleyUSA
- To whom correspondence should be addressed. Tel: +1 510 642 7583; Fax: +1 510 643 3388;
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24
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Iwahara J, Anderson DE, Murphy EC, Clore GM. EDTA-derivatized deoxythymidine as a tool for rapid determination of protein binding polarity to DNA by intermolecular paramagnetic relaxation enhancement. J Am Chem Soc 2003; 125:6634-5. [PMID: 12769564 DOI: 10.1021/ja034488q] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
EDTA-derivatized deoxythymidine (dT-EDTA), incorporated into DNA and complexed to Fe2+ in the presence of dithiothreitol, is a widely used reagent for sequence-specific cleavage of duplex DNA. Using HPLC/electrospray mass spectrometry, we show that cleavage is specific to Fe2+, and no cleavage occurs when DNA-EDTA is complexed to other metal ions such as Ca2+, Mn2+, and Fe3+ even after many days. Because dT-EDTA can be incorporated at any desired position of a synthetic oligonucleotide, DNA-EDTA is ideally suited for the measurement of intermolecular paramagnetic relaxation enhancement effects between a paramagnetic ion chelated to DNA-EDTA and a bound protein. Measurements on the SRY/DNA-EDTA complex using two double-stranded oligonucleotides bearing dT-EDTA at opposite ends of the sequence indicate that intermolecular 1HN-T2 enhancement by chelated Mn2+ can be used to readily ascertain the polarity of protein binding to DNA and to derive quantitative long-range distance information for structure refinement. In the case of the SRY-DNA complex, excellent agreement between observed and calculated 1HN-T2 paramagnetic relaxation enhancement data can be achieved with insignificant shifts in the atomic coordinates ( approximately 0.25 A for all heavy atoms) while simultaneously satisfying all other experimental restraints. A unique feature of DNA-EDTA is that the relaxation enhancement effect can be tuned by judicious choice of the paramagnetic metal ion, thereby permitting a wide range of long-range intermolecular electron-proton distances, ranging from approximately 9 to 35 A, to be probed.
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Affiliation(s)
- Junji Iwahara
- Laboratories of Chemical Physics and Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases/NIH, Bethesda, MD 20892-0510, USA
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25
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Abstract
The fine structure of the DNA double helix and a number of its physical properties depend upon nucleotide sequence. This includes minor groove width, the propensity to undergo the B-form to A-form transition, sequence-directed curvature, and cation localization. Despite the multitude of studies conducted on DNA, it is still difficult to appreciate how these fundamental properties are linked to each other at the level of nucleotide sequence. We demonstrate that several sequence-dependent properties of DNA can be attributed, at least in part, to the sequence-specific localization of cations in the major and minor grooves. We also show that effects of cation localization on DNA structure are easier to understand if we divide all DNA sequences into three principal groups: A-tracts, G-tracts, and generic DNA. The A-tract group of sequences has a peculiar helical structure (i.e., B*-form) with an unusually narrow minor groove and high base-pair propeller twist. Both experimental and theoretical studies have provided evidence that the B*-form helical structure of A-tracts requires cations to be localized in the minor groove. G-tracts, on the other hand, have a propensity to undergo the B-form to A-form transition with increasing ionic strength. This property of G-tracts is directly connected to the observation that cations are preferentially localized in the major groove of G-tract sequences. Generic DNA, which represents the vast majority of DNA sequences, has a more balanced occupation of the major and minor grooves by cations than A-tracts or G-tracts and is thereby stabilized in the canonical B-form helix. Thus, DNA secondary structure can be viewed as a tug of war between the major and minor grooves for cations, with A-tracts and G-tracts each having one groove that dominates the other for cation localization. Finally, the sequence-directed curvature caused by A-tracts and G-tracts can, in both cases, be explained by the cation-dependent mismatch of A-tract and G-tract helical structures with the canonical B-form helix of generic DNA (i.e., a cation-dependent junction model).
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Affiliation(s)
- Nicholas V Hud
- School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta 30332, USA.
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26
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Liu Y, Sletten E. Interaction between macrocyclic nickel complexes and the nucleotides GMP, AMP and ApG. J Inorg Biochem 2003; 93:190-6. [PMID: 12576281 DOI: 10.1016/s0162-0134(02)00572-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactions between the nucleotides GMP, AMP and ApG and the complexes Ni(tren), Ni(cyclam) and NiCR in aqueous solution have been monitored by (1)H, (15)N NMR and UV spectroscopy. The three nickel complexes display different properties in reactions with nucleotides. Ni(tren) which has a pseudo-octahedral coordination geometry was shown to bind to all three nucleotides. Ni(cyclam) and NiCR, both with four nitrogen atoms in a square planar arrangement are not able to bind to nucleotides efficiently because of steric hindrance. Oxidation of Ni(cyclam) by KHSO(5) to produce trivalent Ni(III)(cyclam) improves the coordination capacity, while oxidation of NiCR does not produce a similar effect. The nucleotides interact with trivalent nickel complexes to different extent. Ni(III)CR is seen to oxidize GMP gradually but does not affect AMP significantly. Ni(III)(cyclam), on the other hand, does not oxidize either GMP or AMP at the 1:1 concentration of oxidant used. This result is probably due to the lower redox potential of Ni(cyclam). ApG binds less efficiently to the Ni complexes but is easier oxidized than the mononucleotides.
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Affiliation(s)
- Yangzhong Liu
- Department of Chemistry, University of Bergen, Allegt. 41, N-5007 Bergen, Norway
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27
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Zamora F, Sabat M. Simultaneous N7,O6-binding of guanine to two zinc centers and its possible biological significance. Inorg Chem 2002; 41:4976-7. [PMID: 12354023 DOI: 10.1021/ic0258532] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction of ZnCl(2) with 9-ethylguanine (9-EtGH) produced a novel dinuclear Zn(II) complex, [Zn(2)Cl(4)(H(2)O)(mu-9-EtGH-N7,O6)(9-EtGH-N7), 1. The X-ray structure analysis (monoclinic, P2(1) (No. 4), a = 11.0636(6) A, b = 6.6546(4) A, c = 15.9630(9) A, beta = 101.069(1) degrees, V = 1153.4(1) A(3), Z = 2) revealed that one of the tetrahedrally coordinated Zn(II) atoms binds to the N7 site of 9-EtGH and to the exocyclic O6 atom of another 9-EtGH molecule. The remaining Zn(II) atom binds to the N7 site of the second 9-EtGH moiety.
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Affiliation(s)
- Felix Zamora
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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28
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Davey CA, Richmond TJ. DNA-dependent divalent cation binding in the nucleosome core particle. Proc Natl Acad Sci U S A 2002; 99:11169-74. [PMID: 12169666 PMCID: PMC123228 DOI: 10.1073/pnas.172271399] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequence-specific binding of divalent cations to nucleosomal DNA can potentially influence nucleosome position and mobility, as well as modulate interactions with nuclear factors. We define the bonding and specificity of divalent cation interaction with nucleosomal DNA by characterizing Mn2+ binding in the x-ray structure of the nucleosome core particle at 1.9-A resolution. Manganese ions are found ligated with high occupancy in the major groove to 12 of 22 GG and GC base pair steps. The specific location and mode of metal binding is the consequence of unambiguous conformational differences between dinucleotide sites, owing to their sequence context and orientation in the nucleosome core.
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Affiliation(s)
- Curt A Davey
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, CH-8093 Zürich, Switzerland
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29
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Hud NV, Feigon J. Characterization of divalent cation localization in the minor groove of the A(n)T(n) and T(n)A(n) DNA sequence elements by (1)H NMR spectroscopy and manganese(II). Biochemistry 2002; 41:9900-10. [PMID: 12146955 DOI: 10.1021/bi020159j] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The localization of Mn(2+) in A-tract DNA has been studied by (1)H NMR spectroscopy using a series of self-complementary dodecamer oligonucleotides that contain the sequence motifs A(n)(n) and T(n)A(n), where n = 2, 3, or 4. Mn(2+) localization in the minor groove is observed for all the sequences that have been studied, with the position and degree of localization being highly sequence-dependent. The site most favored for Mn(2+) localization in the minor groove is near the 5'-most ApA step for both the T(n)A(n) and the A(n)T(n) series. For the T(n)A(n) series, this results in two closely spaced symmetry-related Mn(2+) localization sites near the center of each duplex, while for the A(n)T(n) series, the two symmetry-related sites are separated by as much as one half-helical turn. The degree of Mn(2+) localization in the minor groove of the T(n)A(n) series decreases substantially as the AT sequence element is shortened from T(4)A(4) to T(2)A(2). The A(n)T(n) series also exhibits length-dependent Mn(2+) localization; however, the degree of minor groove occupancy by Mn(2+) is significantly less than that observed for the T(n)A(n) series. For both A(n)T(n) and T(n)A(n) sequences, the 3'-most AH2 resonance is the least broadened of the AH2 resonances. This is consistent with the observation that the minor groove of A-tract DNA narrows in the 5' to 3' direction, apparently becoming too narrow after two base pairs for the entry of a fully hydrated divalent cation. The results that are reported illustrate the delicate interplay that exists between DNA nucleotide sequence, minor groove width, and divalent cation localization. The proposed role of cation localization in helical axis bending by A-tracts is also discussed.
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Affiliation(s)
- Nicholas V Hud
- Department of Chemistry and Biochemistry, University of California, 405 Hilgard Avenue, Los Angeles, CA 90095-1569, USA.
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30
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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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31
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Rai P, Cole TD, Wemmer DE, Linn S. Localization of Fe(2+) at an RTGR sequence within a DNA duplex explains preferential cleavage by Fe(2+) and H2O2. J Mol Biol 2001; 312:1089-101. [PMID: 11580252 DOI: 10.1006/jmbi.2001.5010] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nicking of duplex DNA by the iron-mediated Fenton reaction occurs preferentially at a limited number of sequences. Of these, purine-T-G-purine (RTGR) is of particular interest because it is a required element in the upstream regulatory regions of many genes involved in iron and oxidative-stress responses. In order to study the basis of this preferential nicking, NMR studies were undertaken on the RTGR-containing duplex oligonucleotide, d(CGCGATATGACACTAG)/d(CTAGTGTCATATCGCG). One-dimensional and two-dimensional 1H NMR measurements show that Fe(2+) interacts preferentially and reversibly at the ATGA site within the duplex at a rate that is rapid relative to the chemical-shift timescale, while selective paramagnetic NMR line-broadening of the ATGA guanine H8 suggests that Fe(2+) interacts with the guanine N7 moiety. Localization at this site is supported by Fe(2+) titrations of a duplex containing a 7-deazaguanine substitution in place of the guanine in the ATGA sequence. The addition of a 100-fold excess of Mg(2+) over Fe(2+) does not affect the Fe(2+)-dependent broadening. When the ATGA site in the duplex is replaced by ATGT, an RTGR site (GTGA) is created on the opposite strand. Preferential iron localization then takes place at the 3' guanine in GTGA but no longer at the guanine in ATGT, consistent with the lack of preferential cleavage of ATGT sites relative to ATGA sites.
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Affiliation(s)
- P Rai
- Biophysics Graduate Group, University of California, Berkeley, CA 94720-3206, USA
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32
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Nakatani K, Matsuno T, Adachi K, Hagihara S, Saito I. Selective intercalation of charge neutral intercalators into GG and CG steps: implication of HOMO-LUMO interaction for sequence-selective drug intercalation into DNA. J Am Chem Soc 2001; 123:5695-702. [PMID: 11403601 DOI: 10.1021/ja003956i] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have synthesized naphthopyranone epoxide 4 from D-isoascorbic acid together with its three diastereoisomers. DNA alkylation of ODNs containing 5'XGT3' and 5'TGY3' by 4 (11R, 13R), where X and Y are any nucleotide bases, occurred at all G residues except at G of the 5'TGC3' sequence. In contrast, the three other diastereoisomers of 4 showed only weak G alkylation activity. Differential (1)H NMR NOE of the 4-G adduct confirmed the G-N7 alkylation at the epoxide carbon of 4 with concomitant S(N)2 ring opening of the epoxide. Quantitative HPLC analysis of G alkylation efficiency for 4 showed the order of G alkylation susceptibility as TGGT approximately CGT >> TGA > AGT > TGT >> TGC. The order was fully consistent with those reported for aflatoxin B(1) oxide and kapurimycin A(3), suggesting that the sequence selectivity observed for these DNA alkylating agents is not structure dependent but most likely due to the intrinsic property of DNA sequences. We found that the order of G alkylation susceptibility obtained for 4 completely matched the calculated HOMO energy level of G-containing sequences. These results underscore that 4 is a unique molecular probe for ranking the HOMO level of G-containing sequences by well-known G alkylation chemistry and suggests that the intercalation of charge neutral intercalators is a HOMO-controlled process.
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Affiliation(s)
- K Nakatani
- Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, CREST, Japan Science and Technology Corporation (JST), Kyoto 606-8501, Japan
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33
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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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34
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Midorikawa K, Kawanishi S. Superoxide dismutases enhance H2O2-induced DNA damage and alter its site specificity. FEBS Lett 2001; 495:187-90. [PMID: 11334889 DOI: 10.1016/s0014-5793(01)02383-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Superoxide dismutases (SODs) are involved in the protection of cells from oxygen toxicity. However, several papers have reported that the overexpression of CuZn-SOD causes oxidative damage to cells. We investigated a mechanism by which an excess of SODs accelerates oxidative stress. The presence of CuZn-SOD, Mn-SOD or Mn(II) enhanced the frequency of DNA damage induced by hydrogen peroxide (H2O2) and Cu(II), and altered the site specificity of the latter: H2O2 induced Cu(II)-dependent DNA damage with high frequency at the 5'-guanine of poly G sequences; when SODs were added, the frequency of cleavages at thymine and cytosine residues increased. SODs also enhanced the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine by H2O2 and Cu(II). We conclude that SODs may increase carcinogenic risks, e.g. of tumors in Down syndrome.
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Affiliation(s)
- K Midorikawa
- Department of Hygiene, Mie University School of Medicine, 514-8507, Mie, Japan
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35
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Kawanishi S, Hiraku Y, Oikawa S. Mechanism of guanine-specific DNA damage by oxidative stress and its role in carcinogenesis and aging. Mutat Res 2001; 488:65-76. [PMID: 11223405 DOI: 10.1016/s1383-5742(00)00059-4] [Citation(s) in RCA: 329] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Reactive species generated by chemicals and UV radiation can cause sequence-specific DNA damage and play important roles in mutagenesis, carcinogenesis and aging. We have investigated sequence specificity of oxidative stress-mediated DNA damage by using 32P-labeled DNA fragments obtained from the human c-Ha-ras-1 and p53 genes. Free hydroxyl radical causes DNA damage with no marked site specificity. Reactive nitrogen species, sulfate radicals, nitrogen-centered radicals, benzoyloxyl radical and alkoxyl radical show different sequence specificity. Benzoyloxyl radical specifically causes damage to the 5'-G in GG sequence. UVA radiation also causes DNA damage at this site through electron transfer in the presence of certain photosensitizers. The 5'-G in GG sequence is easily oxidized because a large part of the highest occupied molecular orbital is distributed on this site. On the basis of these findings, the sequence specificity of DNA damage is presumably determined by (a) redox potential of reactive species; (b) ionization potential of DNA bases; and (c) site-specific binding of metal ion to DNA. Here we discuss the mechanisms of sequence-specific DNA damage in relation to carcinogenesis and aging.
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Affiliation(s)
- S Kawanishi
- Department of Hygiene, Mie University School of Medicine, 514-8507, Mie, Japan.
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36
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Khomyakova EB, Gousset H, Liquier J, Huynh-Dinh T, Gouyette C, Takahashi M, Florentiev VL, Taillandier E. Parallel intramolecular DNA triple helix with G and T bases in the third strand stabilized by Zn(2+) ions. Nucleic Acids Res 2000; 28:3511-6. [PMID: 10982870 PMCID: PMC110744 DOI: 10.1093/nar/28.18.3511] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We present evidence of formation of an intramolecular parallel triple helix with T*A.T and G*G.C base triplets (where * represents the hydrogen bonding interaction between the third strand and the duplex while. represents the Watson-Crick interactions which stabilize the duplex). The third GT strand, containing seven GpT/TpG steps, targets the polypurine sequence 5'-AGG-AGG-GAG-GAG-3'. The triple helix is obtained by the folding back twice of a 36mer, formed by three dodecamers tethered by hydroxyalkyl linkers (-L-). Due to the design of the oligonucleotide, the third strand orientation is parallel with respect to the polypurine strand. Triple helical formation has been studied in concentration conditions in which native gel electrophoresis experiments showed the absence of intermolecular structures. Circular dichroism (CD) and UV spectroscopy have been used to evidence the triplex structure. A CD spectrum characteristic of triple helical formation as well as biphasic UV and CD melting curves have been obtained in high ionic strength NaCl solutions in the presence of Zn(2+) ions. Specific interactions with Zn(2+) ions in low water activity conditions are necessary to stabilize the parallel triplex.
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Affiliation(s)
- E B Khomyakova
- Laboratoire de Spectroscopie Biomoléculaire, URA CNRS 1430, Université Paris Nord, 74 rue Marcel Cachin, F-93017 Bobigny Cedex, France
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37
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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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38
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Jonklaas M, Kane RR. The synthesis of 3′- and 5′-iminodiacetic acid derivatives of thymidine and their incorporation into synthetic oligonucleotides. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)00583-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Abrescia NG, Malinina L, Subirana JA. Stacking interaction of guanine with netropsin in the minor groove of d(CGTATATACG)2. J Mol Biol 1999; 294:657-66. [PMID: 10610787 DOI: 10.1006/jmbi.1999.3280] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We present the structure of the decanucleotide d(CGTATATACG) determined by single crystal X-ray diffraction at 1.58 A resolution. A netropsin drug is found in the minor groove with guanine stacked on a pyrrole ring of the drug, a feature described here for the first time. The stacked guanine is an extra-helical base coming from the end of a neighbour oligonucleotide. This observation may open the way to the development of minor groove binding drugs with a higher sequence selectivity. The oligonucleotide is in the B-conformation, but the terminal base-pairs are disrupted: the cytosine residues are disordered while the guanine residues penetrate into the minor groove of neighbouring duplexes. Four hydrated Ni ions with octahedral co-ordination are found associated with the N7 atoms of each guanine. The high affinity of these ions with guanine suggests that they may be used as probes for specific guanine residues.
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Affiliation(s)
- N G Abrescia
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona, E-08028, Spain
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40
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Shih HC, Kassahun H, Burrows CJ, Rokita SE. Selective association between a macrocyclic nickel complex and extrahelical guanine residues. Biochemistry 1999; 38:15034-42. [PMID: 10555986 DOI: 10.1021/bi991877h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nickel-dependent recognition and oxidation of guanine have been linked in part through the paramagnetic effects of nickel on the NMR of model oligonucleotide duplexes. Direct interaction between nickel and guanine N7 had originally been postulated from correlations between the efficiency of guanine oxidation and the environment surrounding its N7 position. (1)H and (31)P NMR spectra of DNA containing a single, isolated extrahelical guanine are consistent with selective binding of nickel to the N7 of this unique base over a background of nonspecific association to the phosphate backbone. The presence of a macrocyclic complex or simple salt of nickel did not detectably alter the structure of the duplex or extrahelical residue. Accordingly, nickel appeared to bind the extrahelical guanine N7 within the major groove as indicated by paramagnetic effects on the proton signals of nucleotides on the 5' but not 3' side of the nickel binding site. Similar (1)H NMR analysis of DNA containing a dynamic equilibrium of extrahelical guanine residues also suggested that the nickel complex did not affect the native distribution of structures. Oxidation of these sites by a nickel-mediated pathway consequently reflected their solvent accessibility in a general and metal-independent manner. The close proximity of the extrahelical guanines produced a composite of paramagnetic effects on each adjacent nucleotide resulting from both direct and proximal coordination of nickel.
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Affiliation(s)
- H C Shih
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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41
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Hud NV, Sklenár V, Feigon J. Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J Mol Biol 1999; 286:651-60. [PMID: 10024440 DOI: 10.1006/jmbi.1998.2513] [Citation(s) in RCA: 161] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Monovalent cation binding sites on nucleic acids in solution can be localized using the isotopically labeled ammonium ion (15NH4+) as a probe in high resolution NMR spectroscopy experiments. The application of this technique to a series of DNA duplexes reveals a preference for the binding of ammonium cations in the minor groove of A-tract sequences. These results are consistent with a recent report which indicates that some solvent electron densities previously identified as water molecules in DNA X-ray crystal structures are partially occupied by sodium ions. The sequence-specific nature of monovalent cation binding sites demonstrated here for A-tract DNA provides an explanation for the origin of sequence-directed bending.
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Affiliation(s)
- N V Hud
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, 405 Hilgard Ave., Los Angeles, CA, 90095-1569, USA
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42
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Montrel M, Chuprina VP, Poltev VI, Nerdal W, Sletten E. Sequence-dependent binding of metal ion to DNA oligomeres. A comparison of molecular electrostatic potentials with NMR data. J Biomol Struct Dyn 1998; 16:631-7. [PMID: 10052619 DOI: 10.1080/07391102.1998.10508275] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Experimentally observed sequence-selective binding of metal ion to DNA oligonucleotides have been compared with variations of electrostatic potential (EP) along the helix. Calculations of EP have been performed for three atomic models of the oligonucleotide duplex [d(CGCGAATTCGCG)2] using several variants of EP calculations, including a solution of non-linear Poisson-Boltzmann equation (NPBE). N7 atom of guanine adjacent to adenine base was identified as a region with the most negative electrostatic potential in the major groove. The EP value for the Me ion binding site surpasses the value for N7 of other guanines by 10-26% depending on particular duplex conformation. Qualitatively, the sequence dependent variations of EP near guanine N7 atoms are in agreement with the sequence-selective behavior of Mn(II) and Zn(II) ions as revealed by NMR experiments. But the difference in EP between the two most negative regions near guanine N7 atoms does not exceed 1.25 kT/e. Simple model suggests that metal ions are capable to form ion-hydrate complexes with G-Pu steps of DNA duplex. These complexes are formed via one Me...G and five Me...water coordination bonds with water molecules hydrogen bonded to two adjacent purine bases in the same chain. We suppose that such a stereospecific structural possibility is the main factor which control the sequence-selectivity in the metal ion binding. A combination of both mechanisms allows to explain sequence specific Mn(II) and Zn(II) binding to a set of oligonucleotides.
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Affiliation(s)
- M Montrel
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region.
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43
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Katsarou E, Kolstad A, Hadjiliadis N, Sletten E. 1H NMR study on the interaction between trans-Cl2Pd(dipeptide)2 (dipeptide is glyglyOH and gly-L-nvalOH) and the dodecanucleotide [d(CGCGAATTCGCG)]2. J Inorg Biochem 1998. [DOI: 10.1016/s0162-0134(98)10026-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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44
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Hud NV, Schultze P, Feigon J. Ammonium Ion as an NMR Probe for Monovalent Cation Coordination Sites of DNA Quadruplexes. J Am Chem Soc 1998. [DOI: 10.1021/ja9811039] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas V. Hud
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California Los Angeles, California 90095-1569
| | - Peter Schultze
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California Los Angeles, California 90095-1569
| | - Juli Feigon
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California Los Angeles, California 90095-1569
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45
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Moldrheim E, Andersen B, Frøystein NÅ, Sletten E. Interaction of manganese(II), cobalt(II) and nickel(II) with DNA oligomers studied by 1H NMR spectroscopy. Inorganica Chim Acta 1998. [DOI: 10.1016/s0020-1693(97)06010-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Fry JV, Collins JG. NMR Study of the Sequence-Specific Binding of the Delta-Tris(ethylenediamine)cobalt(III) Cation with d(TCGGGATCCCGA)(2). Inorg Chem 1997; 36:2919-2921. [PMID: 11669935 DOI: 10.1021/ic960937u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John V. Fry
- School of Chemistry, University College, University of New South Wales, Australian Defence Force Academy, Canberra 2600, Australia
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47
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Hud NV, Feigon J. Localization of Divalent Metal Ions in the Minor Groove of DNA A-Tracts. J Am Chem Soc 1997. [DOI: 10.1021/ja9704085] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas V. Hud
- Department of Chemistry and Biochemistry and the Molecular Biology Institute University of California, Los Angeles 405 Hilgard Avenue, Los Angeles, California 90095-1569
| | - Juli Feigon
- Department of Chemistry and Biochemistry and the Molecular Biology Institute University of California, Los Angeles 405 Hilgard Avenue, Los Angeles, California 90095-1569
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48
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Investigations of binding sites and stability of complexes formed in ternary Cu(II)/adenosine or cytidine/putrescine systems. J Inorg Biochem 1996. [DOI: 10.1016/0162-0134(95)00120-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Rajan MT, Kumar DC, Vishnuvardhan D, Rao KS, Viswamitra MA. Interaction of Co, Mn, Mg and Al with d(GCGTACGC): a spectroscopic study. Mol Biol Rep 1996; 22:47-52. [PMID: 8858572 DOI: 10.1007/bf00996304] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Spectroscopic study on the interactions of trace elements Co., Mn, Mg and Al with d(GCGTACGC) indicated the following: Al and Mg did not alter Tm values. Mn enhanced Tm at lower concentration and decreased it at higher concentrations. Interestingly Co at higher concentration elevated the Tm. These studies also showed lower concentrations of Mn displaced EtBr, whereas Al could displace it at higher ionic strength. Mg and Co displaced EtBr fluorescence at moderate concentrations. The binding constant values and CD spectra clearly indicated strong binding of these elements to DNA.
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Affiliation(s)
- M T Rajan
- Department of Biochemistry and Nutrition, Central Food Technological Research Institute, Mysore, India
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