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Litke JL, Li Y, Nocka LM, Mukerji I. Probing the Ion Binding Site in a DNA Holliday Junction Using Förster Resonance Energy Transfer (FRET). Int J Mol Sci 2016; 17:366. [PMID: 26978349 PMCID: PMC4813226 DOI: 10.3390/ijms17030366] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/21/2016] [Accepted: 02/26/2016] [Indexed: 11/17/2022] Open
Abstract
Holliday Junctions are critical DNA intermediates central to double strand break repair and homologous recombination. The junctions can adopt two general forms: open and stacked-X, which are induced by protein or ion binding. In this work, fluorescence spectroscopy, metal ion luminescence and thermodynamic measurements are used to elucidate the ion binding site and the mechanism of junction conformational change. Förster resonance energy transfer measurements of end-labeled junctions monitored junction conformation and ion binding affinity, and reported higher affinities for multi-valent ions. Thermodynamic measurements provided evidence for two classes of binding sites. The higher affinity ion-binding interaction is an enthalpy driven process with an apparent stoichiometry of 2.1 ± 0.2. As revealed by Eu(3+) luminescence, this binding class is homogeneous, and results in slight dehydration of the ion with one direct coordination site to the junction. Luminescence resonance energy transfer experiments confirmed the presence of two ions and indicated they are 6-7 Å apart. These findings are in good agreement with previous molecular dynamics simulations, which identified two symmetrical regions of high ion density in the center of stacked junctions. These results support a model in which site-specific binding of two ions in close proximity is required for folding of DNA Holliday junctions into the stacked-X conformation.
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Affiliation(s)
- Jacob L Litke
- Department of Molecular Biology and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA.
| | - Yan Li
- Department of Molecular Biology and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA.
| | - Laura M Nocka
- Department of Molecular Biology and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA.
| | - Ishita Mukerji
- Department of Molecular Biology and Biochemistry and Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA.
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Pd(0)-Catalyzed methyl transfer on nucleosides and oligonucleotides, envisaged as a PET tracer. Molecules 2013; 18:13654-65. [PMID: 24196412 PMCID: PMC6270090 DOI: 10.3390/molecules181113654] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/14/2013] [Accepted: 10/23/2013] [Indexed: 12/12/2022] Open
Abstract
The methyl transfer reaction from activated monomethyltin, via a modified Stille coupling reaction, was studied under “ligandless” conditions on fully deprotected 5'-modified nucleosides and one dinucleotide. The reaction was optimized to proceed in a few minutes and quantitative yield, even under dilute conditions, thus affording a rapid and efficient new method for oligonucleotide labelling with carbon-11.
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Oligonucleotide Labelling Using a Fluorogenic “Click” Reaction with a Hemicarboxonium Salt. Molecules 2013; 18:12966-76. [PMID: 24141246 PMCID: PMC6270631 DOI: 10.3390/molecules181012966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 09/30/2013] [Accepted: 10/09/2013] [Indexed: 11/17/2022] Open
Abstract
Two fluorescent streptocyanine labelled oligonucleotides have been synthesized by a simple “click” reaction between a non-fluorescent hemicarboxonium salt and aminoalkyl functionalized thymidines within the oligonucleotide and their spectrophotometric properties have been studied.
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Madsen CS, Nielsen LJ, Pedersen NS, Lauritsen A, Nielsen P. Double-headed nucleotides in DNA-zipper structures; base–base interactions and UV-induced cross-coupling in the minor groove. RSC Adv 2013. [DOI: 10.1039/c3ra40857d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Affiliation(s)
- Jean-Claude G. Bünzli
- Laboratory of Lanthanide Supramolecular Chemistry, École Polytechnique Fédérale de Lausanne (EPFL), BCH 1402, CH-1015 Lausanne, Switzerland, and Department of Advanced Materials Chemistry, WCU Center for Next Generation Photovoltaic Systems, Korea University, Sejong Campus, 208 Seochang, Jochiwon, Chung Nam 339-700, Republic of Korea
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Huang CH, Parish A, Samain F, Garo F, Häner R, Morrow JR. Binding of Europium(III) to a Non-Nucleosidic Phenanthroline Linker in DNA. Bioconjug Chem 2010; 21:476-82. [DOI: 10.1021/bc900386w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ching-Hui Huang
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Austin Parish
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Florent Samain
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Florian Garo
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Janet R. Morrow
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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